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Chem&BioOffice - CambridgeSoft

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Chem & Bio Office

Enterprise Solutions and Databases including E-Notebook


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User’s Guide

Chem & Bio Office Enterprise 2010

for Windows

Chem & Bio Office Enterprise is an Enterprise and Workgroup solution including:

• Knowledge Management: E-Notebook & CombiChem

• Laboratory Informatics: Workflow LIMS and Compliant SDMS

• Biological Informatics: BioAssay Enterprise, BioSAR and BioViz

• Chemical Informatics: Inventory Enterprise and Registration Enterprise

• Manufacturing Informatics: E-Notebook compliance execution and Inventory

• Scientific Databases: The Merck Index and ChemACX Database

Chem & Bio Office

®

Enterprise Solutions and Databases including E-Notebook


License Information

All resources and application files in ChemBioOffice, ChemOffice, BioOffice, ChemBioDraw,

ChemDraw, BioDraw, ChemBio3D, Chem3D, ChemFinder, BioViz, Inventory, E-Notebook, BioAssay,

ChemINDEX, ChemFinder, and ChemInfo programs, all resources in the ChemOffice,

ChemDraw, Chem3D, ChemFinder, and ChemInfo application files, and this manual are Copyright

© 1986-2009 by CambridgeSoft Corporation (“CS”) with all rights reserved worldwide. MOPAC

2002 is Copyright © 1993-2006 by Fujitsu Limited with all rights reserved.

Information in this document is subject to change without notice and does not represent a commitment

on the part of CS. Both these materials and the right to use them are owned exclusively by CS.

Use of these materials is licensed by CS under the terms of a software license agreement; they may

be used only as provided for in said agreement.

ChemBioOffice, ChemOffice BioOffice, ChemBioDraw, ChemDraw, BioDraw, ChemBio3D,

Chem3D, CS MOPAC, ChemFinder, BioViz, Inventory, E-Notebook, and BioAssay, and ChemInfo

are not supplied with copy protection. Do not duplicate any of the copyrighted materials except for

your personal backups without written permission from CS. To do so would be in violation of federal

and international law, and may result in criminal as well as civil penalties. You may use ChemBioOffice,

ChemOffice BioOffice, ChemBioDraw, ChemDraw, BioDraw, ChemBio3D, Chem3D, CS

MOPAC, ChemFinder, BioViz, Inventory, E-Notebook, and BioAssay ChemOffice, ChemDraw,

Chem3D, CS MOPAC, ChemFinder, Inventory, E-Notebook, BioAssay, and ChemInfo on any computer

owned by you; however, extra copies may not be made for that purpose. Consult the CS

License Agreement for Software and Database Products for further details.

Trademark Notices

ChemBioOffice, ChemOffice, BioOffice, ChemBioDraw. ChemDraw, BioDraw,ChemBio3D,

Chem3D, ChemINDEX, ChemFinder, ChemInfo and ChemACX are registered trademarks of

CambridgeSoft Corporation (Cambridge Scientific Computing, Inc.).

The Merck Index is a registered trademark of Merck & Co., Inc. ©2006 All rights reserved.

MOPAC 2002 is a trademark of Fujitsu Limited.

Microsoft Windows, Windows 2000, Windows XP, and Microsoft Word, Microsoft Excel, Microsoft

PowerPoint, Microsoft Access, and SQL Server 2005 are registered trademarks of Microsoft Corporation.

Apple Events, Macintosh, Laserwriter, Imagewriter, QuickDraw and AppleScript are registered

trademarks of Apple Computer, Inc. Geneva, Monaco, and TrueType are trademarks of Apple Computer,

Inc.

InChI is a trademark of the International Union of Pure and Applied Chemistry.

Jaguar is a trademark of Schrödinger, LLC.

THE MERCK INDEX ® is a trademark of Merck & Company Incorporated, Whitehouse Station,

New Jersey, USA and is registered in the United States Patent and Trademark Office.


Oracle ® is a registered trademark of Oracle Corporation and/or its affiliates. Other names may be

trademarks of their respective owners.

All other trademarks are the property of their respective holders. Any use of the marks in connection

with the sale, offering for sale, distribution or advertising of any goods and services, including any

other Web site, or in connection with labels, signs, prints, packages, wrappers, receptacles or advertisements

used for the sale, offering for sale, distribution or advertising of any goods and services,

including any other Web site, which is likely to cause confusion, to cause mistake or to deceive, is

strictly prohibited.

Copyright Notice

The materials contained in CambridgeSoft Database Products, including but not limited to, ChemACX,

ChemIndex, and The Merck Index, are protected by copyright laws and international copyright

treaties, as well as other intellectual property laws and treaties. Copyright in the materials

contained on the CD and internet subscription products, including, but not limited to, the textual

material, chemical structures representations, artwork, photographs, computer software, audio and

visual elements, is owned or controlled separately by CS.

CS is a distributor (and not a publisher) of information supplied by third parties. Accordingly, CS has

no editorial control over such information. Database Suppliers (“Supplier”) individually own all

right, title, and interest, including copyright, in their database—and retain all such rights in providing

information to Customers.

The materials contained in The Merck Index are protected by copyright laws and international copyright

treaties, as well as other intellectual property laws and treaties. Copyright in the materials contained

on the CD and internet subscription products, including, but not limited to, the textual

material, chemical structures representations, artwork, photographs, computer software, audio and

visual elements, is owned or controlled separately by Merck & Co., Inc., (“Merck”) and

CambridgeSoft Corporation (“CS”).

The ChemReact68, ChemSynth, ChemReact500, and ChemSelect Reaction Database is copyrighted

© by InfoChem GmbH 1997.

AspTear is copyrighted © by Softwing.

InChI is a trademark of the International Union of Pure and Applied Chemistry. InChI Material

in ChemDraw is © IUPAC 2005.

schrödinger ® Jaguar

GAMESS is copyrighted © by Ames Laboratory

Copyright © 1986-2009 CambridgeSoft Corporation (Cambridge Scientific Computing, Inc.) All

Rights Reserved.

Printed in the United States of America.

All other trademarks are the property of their respective holders.

CambridgeSoft End-User License Agreement for Software Products


Important: This CambridgeSoft Software License Agreement (“Agreement”) is a legal agreement

between you, the end user (either an individual or an entity), and CambridgeSoft Corporation (“CS”)

regarding the use of CS Software and Database Products, which may include computer software, the

associated media, any printed materials, and any “online” or electronic documentation. By installing,

copying, or otherwise using any CS Software Product, you signify that you have read the CS End

User License Agreement and agree to be bound by its terms. If you do not agree to the Agreement’s

terms, promptly return the package within 30 days of purchase and all its contents to the place of purchase

for a full refund.

CambridgeSoft Software and Database License

1. Grant of License. CambridgeSoft (CS) Software Products are licensed, not sold. CS grants and

you hereby accept a nonexclusive license to use one copy of the enclosed Software Product (“Software”)

in accordance with the terms of this Agreement. This licensed copy of the Software may only

be used on a single computer, except as provided below.

You may physically transfer the Software from one computer to another for your own use, provided

the Software is in use (or installed) on only one computer at a time. If the Software is permanently

installed on your computer (other than a network server), you may also use the Software on a portable

or home computer, provided that you use the software on only one computer at a time. You may

not (a) electronically transfer the Software from one computer to another, (b) distribute copies of the

Software to others, or (c) modify or translate the Software without the prior written consent of CS,

(d) place the software on a server so that it is accessible via a public network such as the Internet, (e)

sublicense, rent, lease or lend any portion of the Software or Documentation, (f) modify or adapt the

Software or merge it into another program, (g) modify or circumvent the software activation, or (h)

reverse engineer the software activation so as to circumvent it. The Software may be placed on a file

or disk server connected to a network, provided that a license has been purchased for every computer

with access to that server. You may make only those copies of the Software which are necessary to

install and use it as permitted by this agreement, or are for purposes of backup and archival records;

all copies shall bear CS’s copyright and proprietary notices. You may not make copies of any accompanying

written materials.

With a fixed license, the software cannot be installed on more than the number of computers equivalent

to the number of fixed licenses purchased. For example, a 10-user fixed license means the software

can be installed on no more than 10 different computers. A fixed license cannot be installed on

a server. With a concurrent license, the software can be installed on any number of computers at the

organization, but the number of computers using the software at any one time cannot exceed the

number of concurrent licenses purchased. For example, a 10-user concurrent license can be installed

on 20 computers, but no more than 10 users can be using it at any one time. If the number of users of

the software could potentially exceed the number of licensed copies, then Licensee must have a reasonable

mechanism or process in place to assure that the number of persons using the software does

not exceed the number of copies. CambridgeSoft reserves the right to conduct periodic audits no


more than once per year to review the implementation of this agreement at the Licensee’s site. At

CambridgeSoft’s request, Licensee will provide a knowledgeable employee to assist in said audit

2. Ownership. The Software is and at all times shall remain the sole property of CS. This ownership

is protected by the copyright laws of the United States and by international treaty provisions. Upon

expiration or termination of this agreement, you shall promptly return all copies of the Software and

accompanying written materials to CS. You may not modify, decompile, reverse engineer, or disassemble

the Software.

3. Assignment Restrictions. You may not rent, lease, or otherwise sublet the Software or any part

thereof. You may transfer on a permanent basis the rights granted under this license provided you

transfer this Agreement and all copies of the Software, including prior versions, and all accompanying

materials. The recipient must agree to the terms of this Agreement in full and register this transfer

in writing with CS.

4. Use of Included Data. All title and copyrights in and to the Software product, including but not

limited to any images, photographs, animations, video, audio, music, text, applets, Java applets, and

data files and databases (the “Included Data”), are owned by CS or its suppliers.

• You may not copy, distribute or otherwise make the Included Data publicly available.

• Licensed users of ChemOffice Enterprise and Workgroup and the accompanying Plug-in software

products may access, search, and view the Included Data and may transmit the results of any

search of the Included Data to other users of the licensed ChemOffice Enterprise and Workgroup

software products within your organization only, provided that such transmission is via an internal

corporate (or university) network and is not accessible by the public.

• You may not install the Included Data on non-licensed computers nor distribute or otherwise

make the Included Data publicly available.

• You may use the Software to organize personal data, and you may transmit such personal data

over the Internet provided that the transmission does not contain any Included Data.

• All rights not specifically granted under this Agreement are reserved by CS.

5. Limitations on Use. (a) Desktop versions of E-Notebook, Inventory, and BioAssay are licensed

for use with SQL Server Express, and are not licensed for use with SQL Server. Licenses for use with

SQL Server are available separately. (b) Workgroup versions of E-Notebook, Inventory, and BioAssay

are licensed for use with SQL Server and SQL Server Express. (c) Except as expressly provided

by copyright law, copying, redistribution, or publication, whether for commercial or non-commercial

purposes, must be with the express permission of CS, Merck, or other CS partner. In any copying,

redistribution, or publication of copyrighted material, any changes to or deletion of author attribution

or copyright notice, or any other proprietary notice of CS, Merck, or other Database producer are

prohibited.

6. Separation of Components. The Software is licensed as a single product. Its component parts may

not be separated for use on more than one computer, except in the case of ChemBioOffice Enterprise.

ChemBioOffice Enterprise includes licenses for ChemBioDraw ActiveX and licenses for


ChemBio3D ActiveX. The ActiveX software products may be installed on computers other than that

one on which ChemBioOffice Enterprise is installed. However, each copy of the ActiveX is individually

subject to the provisions of Paragraphs 1 through 4 of this Agreement.

7. Educational Use Only of Student Licenses. If you are a student enrolled at an educational institution,

the CS License Agreement grants to you personally a license to use one copy of the enclosed

Software in accordance with the terms of this Agreement. In this case the CS License Agreement

does not permit commercial use of the Software nor does it permit you to allow any other person to

use the Software.

8. Modification of Databases, Web sites, or Subscription Services. CS reserves the right to change,

modify, suspend or discontinue any or all parts of any Paid Subscription Services and databases at

any time.

9. Termination. You may terminate the license at any time by destroying all copies of the Software

and documentation in your possession. Without prejudice to any other rights, CS may terminate this

Agreement if you fail to comply with its terms and conditions. In such event, you must destroy all

copies of the Software Product and all of its component parts.

10. Revocation of Subscription Access. Any use which is commercial and/or non-personal is strictly

prohibited, and may subject the Subscriber making such uses to revocation of access to this Paid Subscription

Service, as well as any other applicable civil or criminal penalties. Similarly, sharing a Subscriber

password with a non-Subscriber or otherwise making this Paid Subscription Service available

to third parties other than the Authorized User as defined above is strictly prohibited, and may subject

the Subscriber participating in such activities to revocation of access to the Paid Subscription

Services; and, the Subscriber and any third party, to any other applicable civil or criminal penalties

under copyright or other laws. In the case of an authorized site license, a Subscriber shall cause any

employee, agent or other third party which the Subscriber allows to use the Paid Subscription Service

materials to abide by all of the terms and conditions of this Agreement. In all other cases, only the

Subscriber is permitted to access the Paid Subscription Service materials. Should CambridgeSoft

become aware of any use that might cause revocation of the license, they shall notify the Subscriber.

The Subscriber shall have 90 days from date of notice to correct such violation before any action will

be taken.

11. Confidentiality. The Software contains trade secrets and proprietary know-how that belong to CS

and are being made available to you in strict confidence. ANY USE OR DISCLOSURE OF THE SOFT-

WARE, OR USE OF ITS ALGORITHMS, PROTOCOLS OR INTERFACES, OTHER THAN IN STRICT

ACCORDANCE WITH THIS LICENSE AGREEMENT, MAY BE ACTIONABLE AS A VIOLATION OF OUR

TRADE SECRET RIGHTS.

CS Limited Warranty

Software Limited Warranty. CS’s sole warranty with respect to the Software is that it shall be free

of errors in program logic or documentation, attributable to CS, which prevent the performance of


the principal computing functions of the Software. CS warrants this for a period of thirty (30) days

from the date of receipt.

CS’s Liability. In no event shall CS be liable for any indirect, special, or consequential damages,

such as, but not limited to, loss of anticipated profits or other economic loss in connection with or

arising out of the use of the software by you or the services provided for in this agreement, even if CS

has been advised of the possibility of such damages.

CS’s entire liability and your exclusive remedy shall be, at CS’s discretion, either (A) return of any

license fee, or (B) correction or replacement of software that does not meet the terms of this limited

warranty and that is returned to CS with a copy of your purchase receipt.

Database Representations and Limited Warranty. The User shall indemnify, defend and hold CS,

Merck, and/or other Supplier harmless from any damages, expenses and costs (including reasonable

attorneys’ fees) arising out of any breach or alleged breach of these Terms and Conditions, representations

and/or warranties herein, by the User or any third party to whom User shares her/his password

or otherwise makes available this Subscription Service. The User shall cooperate in the defense of

any claim brought against CambridgeSoft, Merck, and/or other Database Suppliers. In no event shall

CS, Merck, and/or other Supplier be liable for any indirect, special, or consequential damages, such

as, but not limited to, loss of anticipated profits or other economic loss in connection with or arising

out of the use of the software by you or the services provided for in this agreement, even if CS,

Merck, and/or other Supplier has been advised of the possibility of such damages. CS and/or Merck’s

entire liability and your exclusive remedy shall be, at CS’s discretion a return of any pro-rata portion

of the subscription fee. The failure of either party to assert a right hereunder or to insist upon compliance

with any term or condition of this Agreement shall not constitute a waiver of that right or excuse

a similar subsequent failure to perform any such term or condition by the other party.

NO OTHER WARRANTIES. CS DISCLAIMS OTHER IMPLIED WARRANTIES, INCLUDING, BUT NOT LIM-

ITED TO, IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE,

AND IMPLIED WARRANTIES ARISING BY USAGE OF TRADE, COURSE OF DEALING, OR COURSE OF

PERFORMANCE. NOTWITHSTANDING THE ABOVE, WHERE APPLICABLE, IF YOU QUALIFY AS A

“CONSUMER” UNDER THE MAGNUSONMOSS WARRANTY ACT, THEN YOU MAY BE ENTITLED TO ANY

IMPLIED WARRANTIES ALLOWED BY LAW FOR THE PERIOD OF THE EXPRESS WARRANTY AS SET

FORTH ABOVE. SOME STATES DO NOT ALLOW LIMITATIONS ON IMPLIED WARRANTIES, SO THE

ABOVE LIMITATION MIGHT NOT APPLY TO YOU. THIS WARRANTY GIVES

YOU SPECIFIC LEGAL RIGHTS, AND YOU MAY ALSO HAVE OTHER RIGHTS WHICH VARY FROM

STATE TO STATE.

No Waiver. The failure of either party to assert a right hereunder or to insist upon compliance with

any term or condition of this Agreement shall not constitute a waiver of that right or excuse a similar

subsequent failure to perform any such term or condition by the other party.

Governing Law. This Agreement shall be construed according to the laws of the Commonwealth of

Massachusetts.

Export. You agree that the Software will not be shipped, transferred, or exported into any country or

used in any manner prohibited by the United States Export Administration Act or any other export

laws, restrictions, or regulations.


End-User License Agreement for CambridgeSoft Database

Products

Important: This CambridgeSoft End-User License Agreement is a legal agreement between you

(either an individual or a single entity) and CambridgeSoft Corporation for the CambridgeSoft supplied

database product(s) and may include associated media, printed materials, and “online” or electronic

documentation. By using the database product(s) you agree that you have read, understood and

will be bound by this license agreement.

Database Product License

1. Copyright Notice. The materials contained in CambridgeSoft Database Products, including but

not limited to, ChemACX, ChemIndex, and The Merck Index, are protected by copyright laws and

international copyright treaties, as well as other intellectual property laws and treaties. Copyright in

the materials contained on the CD and internet subscription products, including, but not limited to,

the textual material, chemical structures representations, artwork, photographs, computer software,

audio and visual elements, is owned or controlled separately by CambridgeSoft Corporation (“CS”).

CS is a distributor (and not a publisher) of information supplied by third parties. Accordingly, CS has

no editorial control over such information. Database Suppliers (“Supplier”) individually own all

right, title, and interest, including copyright, in their database—and retain all such rights in providing

information to Customers.

The materials contained in The Merck Index are protected by copyright laws and international copyright

treaties, as well as other intellectual property laws and treaties. Copyright in the materials contained

on the CD and internet subscription products, including, but not limited to, the textual

material, chemical structures representations, artwork, photographs, computer software, audio and

visual elements, is owned or controlled separately by the Merck & Co., Inc., (“Merck”) and

CambridgeSoft Corporation (“CS”).

2. Limitations on Use. Except as expressly provided by copyright law, copying, redistribution, or

publication, whether for commercial or non-commercial purposes, must be with the express permission

of CS and/or Merck. In any copying, redistribution, or publication of copyrighted material, any

changes to or deletion of author attribution or copyright notice, or any other proprietary notice of CS,

Merck, or other Database producer are prohibited.

3. Grant of License, CD/DVD Databases. CambridgeSoft Software Products are licensed, not sold.

CambridgeSoft grants and you hereby accept a nonexclusive license to use one copy of the enclosed

Software Product (“Software”) in accordance with the terms of this Agreement. This licensed copy

of the Software may only be used on a single computer, except as provided below. You may physically

transfer the Software from one computer to another for your own use, provided the Software is

in use (or installed) on only one computer at a time. If the Software is permanently installed on your

computer (other than a network server), you may also use the Software on a portable or home computer,

provided that you use the software on only one computer at a time. You may not (a) electronically

transfer the Software from one computer to another, (b) distribute copies of the Software to


others, or (c) modify or translate the Software without the prior written consent of CambridgeSoft,

(d) place the software on a server so that it is accessible via a public network such as the Internet, (e)

sublicense, rent, lease or lend any portion of the Software or Documentation, or (f) modify or adapt

the Software or merge it into another program. The Software may be placed on a file or disk server

connected to a network, provided that a license has been purchased for every computer with access to

that server. You may make only those copies of the Software which are necessary to install and use it

as permitted by this agreement, or are for purposes of backup and archival records; all copies shall

bear CambridgeSoft’s copyright and proprietary notices. You may not make copies of any accompanying

written materials.

4. Assignment Restrictions for CD/DVD databases. You may not rent, lease, or otherwise sublet the

Software or any part thereof. You may transfer on a permanent basis the rights granted under this

license provided you transfer this Agreement and all copies of the Software, including prior versions,

and all accompanying materials. The recipient must agree to the terms of this Agreement in full and

register this transfer in writing with CambridgeSoft.

5. Revocation of Subscription Access. Any use which is commercial and/or non-personal is strictly

prohibited, and may subject the Subscriber making such uses to revocation of access to this Paid Subscription

Service, as well as any other applicable civil or criminal penalties. Similarly, sharing a Subscriber

password with a non-Subscriber or otherwise making this Paid Subscription Service available

to third parties other than the Authorized User as defined above is strictly prohibited, and may subject

the Subscriber participating in such activities to revocation of access to the Paid Subscription

Services; and, the Subscriber and any third party, to any other applicable civil or criminal penalties

under copyright or other laws. In the case of an authorized site license, a Subscriber shall cause any

employee, agent or other third party which the Subscriber allows to use the Paid Subscription Service

materials to abide by all of the terms and conditions of this Agreement. In all other cases, only the

Subscriber is permitted to access the Paid Subscription Service materials. Should CambridgeSoft

become aware of any use that might cause revocation of the license, they shall notify the Subscriber.

The Subscriber shall have 90 days from date of notice to correct such violation before any action will

be taken.

6. Trademark Notice. THE MERCK INDEX ® is a trademark of Merck & Company Incorporated,

Whitehouse Station, New Jersey, USA and is registered in the United States Patent and Trademark

Office. CambridgeSoft ® and ChemACX are trademarks of CambridgeSoft Corporation, Cambridge,

Massachusetts, USA and are registered in the United States Patent and Trademark Office, the European

Union (CTM), Japan, and other markets.

Any use of the marks in connection with the sale, offering for sale, distribution or advertising of any

goods and services, including any other Web site, or in connection with labels, signs, prints, packages,

wrappers, receptacles or advertisements used for the sale, offering for sale, distribution or

advertising of any goods and services, including any other Web site, which is likely to cause confusion,

to cause mistake or to deceive, is strictly prohibited.


7. Modification of Databases, Web sites, or Subscription Services. CS reserves the right to change,

modify, suspend or discontinue any or all parts of any Paid Subscription Services and databases at

any time.

8. Representations and Warranties. The User shall indemnify, defend and hold CS, Merck, and/or

other Supplier harmless from any damages, expenses and costs (including reasonable attorneys’ fees)

arising out of any breach or alleged breach of these Terms and Conditions, representations and/or

warranties herein, by the User or any third party to whom User shares her/his password or otherwise

makes available this Subscription Service. The User shall cooperate in the defense of any claim

brought against CambridgeSoft, Merck, and/or other Database Suppliers.

In no event shall CS, Merck, and/or other Supplier be liable for any indirect, special, or consequential

damages, such as, but not limited to, loss of anticipated profits or other economic loss in connection

with or arising out of the use of the software by you or the services provided for in this agreement,

even if CS, Merck, and/or other Supplier has been advised of the possibility of such damages. CS

and/or Merck’s entire liability and your exclusive remedy shall be, at CS’s discretion a return of any

pro-rata portion of the subscription fee.

The failure of either party to assert a right hereunder or to insist upon compliance with any term or

condition of this

Agreement shall not constitute a waiver of that right or excuse a similar subsequent failure to perform

any such term or condition by the other party.

This Agreement shall be construed according to the laws of the Commonwealth of Massachusetts,

United States of America.


Q: IS IT OK TO COPY MY COLLEAGUE’S

SOFTWARE?

NO, it’s not okay to copy your colleague’s

software. Software is protected by federal copyright law,

which says that you can't make such additional copies

without the permission of the copyright holder. By

protecting the investment of computer software

companies in software development, the copyright law

serves the cause of promoting broad public availability of

new, creative, and innovative products. These companies

devote large portions of their earnings to the creation of

new software products and they deserve a fair return on

their investment. The creative teams who develop the

software–programmers, writers, graphic artists and

others–also deserve fair compensation for their efforts.

Without the protection given by our copyright laws, they

would be unable to produce the valuable programs that

have become so important to our daily lives: educational

software that teaches us much needed skills; business

software that allows us to save time, effort and money;

and entertainment and personal productivity software

that enhances leisure time.

Q: That makes sense, but what do I get out of

purchasing my own software?

A: When you purchase authorized copies of software

programs, you receive user guides and tutorials, quick

reference cards, the opportunity to purchase

upgrades, and technical support from the software

publishers. For most software programs, you can read

about user benefits in the registration brochure or

upgrade flyer in the product box.

Q: What exactly does the law say about copying

software?

A: The law says that anyone who purchases a copy of

software has the right to load that copy onto a single

computer and to make another copy “for archival

purposes only” or, in limited circumstances, for

“purposes only of maintenance or repair.” It is illegal

to use that software on more than one computer or to

make or distribute copies of that software for any

other purpose unless specific permission has been

obtained from the copyright owner. If you pirate

software, you may face not only a civil suit for

damages and other relief, but criminal liability as well,

including fines and jail terms of up to one year

Q: So I'm never allowed to copy software for any other

reason?

A: That’s correct. Other than copying the software you

purchase onto a single computer and making another

copy “for archival purposes only” or “purposes only of

maintenance or repair,” the copyright law prohibits

you from making additional copies of the software for

any other reason unless you obtain the permission of

the software company.

Q: At my company, we pass disks around all the time.

We all assume that this must be okay since it was

the company that purchased the software in the

first place.

A: Many employees don’t realize that corporations are

bound by the copyright laws, just like everyone else.

Such conduct exposes the company (and possibly the

persons involved) to liability for copyright

infringement. Consequently, more and more

corporations concerned about their liability have

written policies against such “softlifting”. Employees

may face disciplinary action if they make extra copies

of the company’s software for use at home or on

additional computers within the office. A good rule to

remember is that there must be one authorized copy

of a software product for every computer upon which

it is run

Q: Can I take a piece of software owned by my

company and install it on my personal computer at

home if instructed by my supervisor?

A: A good rule of thumb to follow is one software

package per computer, unless the terms of the license

agreement allow for multiple use of the program. But

some software publishers’ licenses allow for “remote”

or “home” use of their software. If you travel or

telecommute, you may be permitted to copy your

software onto a second machine for use when you are

not at your office computer. Check the license carefully

to see if you are allowed to do this.

Q: What should I do if become aware of a company

that is not compliant with the copyright law or its

software licenses?

A: Cases of retail, corporate and Internet piracy or noncompliance

with software licenses can be reported on

the Internet at http://www.siia.net/piracy/report.asp

or by calling the Anti-Piracy Hotline:

(800) 388-7478.


Q: Do the same rules apply to bulletin boards and user

groups? I always thought that the reason they got

together was to share software.

A: Yes. Bulletin boards and user groups are bound by the

copyright law just as individuals and corporations.

However, to the extent they offer shareware or public

domain software, this is a perfectly acceptable

practice. Similarly, some software companies offer

bulletin boards and user groups special demonstration

versions of their products, which in some instances

may be copied. In any event, it is the responsibility of

the bulletin board operator or user group to respect

copyright law and to ensure that it is not used as a

vehicle for unauthorized copying or distribution.

Q: I'll bet most of the people who copy software don't

even know that they're breaking the law.

A: Because the software industry is relatively new, and

because copying software is so easy, many people are

either unaware of the laws governing software use or

choose to ignore them. It is the responsibility of each

and every software user to understand and adhere to

copyright law. Ignorance of the law is no excuse. If

you are part of an organization, see what you an do to

initiate a policy statement that everyone respects.

Also, suggest that your management consider

conducting a software audit. Finally, as an individual,

help spread the word that users should be “software

legal.”

Q: What are the penalties for copyright infringement?

SIIA also offers a number of other materials designed to

help you comply with the Federal Copyright Law. These

materials include:

"It's Just Not Worth the Risk" video.

This 12–minute video, available $10, has helped over

20,000 organizations dramatize to their employees the

implications and consequences of software piracy.

“Don’t Copy that Floppy” video

This 9 minute rap video, available for $10, is designed

to educate students on the ethical use of software.

Other education materials including, “Software Use

and the Law”, a brochure detailing the copyright law

and how software should be used by educational

institutions, corporations and individuals; and several

posters to help emphasize the message that unauthorized

copying of software is illegal.

To order any of these materials, please send your request to:

“SIIA Anti-Piracy Materials”

Software & Information Industry Association

1090 Vermont Ave, Sixth Floor,

Washington, D.C. 20005

(202) 289-7442

We urge you to make as many copies as you would like

in order to help us spread the word that unauthorized

copying of software is illegal.

A: The Copyright Act allows a copyright owner to

recover monetary damages measured either by: (1) its

actual damages plus any additional profits of the

infringer attributable to the infringement, or (2)

statutory damages, of up to $150,000 for each copyrighted

work infringed. The copyright owner also has

the right to permanently enjoin an infringer from

engaging in further infringing activities and may be

awarded costs and attorneys’ fees. The law also

permits destruction or other reasonable disposition of

all infringing copies and devices by which infringing

copies have been made or used in violation of the

copyright owner’s exclusive rights. In cases of willful

infringement, criminal penalties may also be assessed

against the infringer.


A Guide to CambridgeSoft Manuals

Manuals:

Chem & Bio Draw

Chem & Bio Office

Chem & Bio Office

Includes:

Chem & Bio

Drawing Standard

Desktop Software

ChemBio 3D

Finder & BioViz

Workgroup Solutions

and Databases

Including E-Notebook

Chem & Bio Draw


Chem & Bio 3D


Databases Workgroup Solutions Desktop Applications Software

Chem & Bio Finder

BioAssay Desktop

BioViz Desktop

Inventory Desktop

E-Notebook Desktop

ChemDraw/Excel

Struct = Name

ChemNMR

CombiChem/Excel

ChemFinder/Office

MOPAC, GAMESS, MM2

CS Gaussian, Jaguar Interface

CombiChem/E-Notebook

BioAssay Workgroup

BioSAR Enterprise

Inventory Workgroup

Formulations & Mixtures

Compliant SDMS

The Merck Index

R&D Insight/Chemists

ChemINDEX Database, NCI, AIDS & Cancer

Traditional Chinese Medicines

Drugs: Synonyms & Properties

Nanogens Index; Medicinal Chemistry

























ChemACX, ChemMSDS Database


Sigma-Aldrich MSDS


ChemReact500, ChemReact68 & ChemSynth


Contents

Section I

E-Notebook

Desktop & Workgroup

Chapter 1

Getting Started .......................................3

Navigation Overview .................................4

Security Overview ......................................5

Logging into E-Notebook ...........................5

Chapter 2

E-Notebook Desktop & Workgroup ....7

About E-Notebook .....................................7

What’s New ................................................7

About this Guide ........................................8

Chapter 3

Working with E-Notebook ....................9

Notebooks .................................................10

Pages and Reaction Pages ........................10

Folders ......................................................12

Reactants Collections ...............................13

Working with a Table of Contents ...........13

Browsing the Collection Tree ..................14

Chapter 4

Managing Collections ..........................19

Organizing Collections .............................19

Viewing Collection Properties .................22

Importing and Exporting Collections .......23

Templates ................................................ 23

Form Tools .............................................. 24

Changing Collection Security Properties 24

Performing a Collection Transition ......... 25

Exporting to Word ................................... 26

Printing Collections or Sections .............. 26

Chapter 5

Working with Reactions ..................... 29

Pre-configured Sections ........................... 29

Reaction Sections .................................... 29

Batch Explorer ......................................... 42

Chapter 6

Spectra and Other Sections ................ 45

Ancillary Data Sections ........................... 45

Captured Image Sections ......................... 46

Table Sections ......................................... 48

MS Word Sections ................................... 53

MS Excel Sections ................................... 54

Chapter 7

Managing Sections ............................... 55

Creating a Section .................................... 55

Modifying a Section ................................ 55

Removing a Section ................................. 56

Moving a Section ..................................... 56

Cutting and Pasting a Section .................. 56

Renaming a Section ................................. 57

Duplicating a Section .............................. 57

Chapter 8

Saving the Collection Changes ........... 59

Working With Save Icon ......................... 59

Chem & Bio Office 2010 User Guide

i


Administrator

Saving a Collection ..................................59

Chapter 9

Working with Data ..............................61

Chemical Structure Data ..........................61

Styled Text ...............................................62

Subsections ...............................................63

Property Lists ...........................................63

Rendering .................................................66

Chapter 10

Searching ..............................................67

Searching ..................................................67

Working with Query Results ....................68

Saving a Query .........................................69

Refining a Search .....................................69

Chapter 11

Working Offline ...................................73

Creating an offline folder .........................73

Working in the Offline mode ...................73

Limitations to Offline Working ................74

Chapter 12

E-Notebook Batch Import Facility .....75

.....................................................75

...................................................75

....................................................75

.....................................75

.....................................76

...................................................76

........................................................76

......................................................77

..................................................77

Refreshing E-Notebook ........................... 79

Numerical Units ...................................... 79

Using the Session Manager ..................... 81

Appendix B

Glossary ................................................83

Terminology ............................................ 83

Section II

BioAssay

Desktop & Workgroup

BioAssay Desktop & Workgroup .......87

What’s New ............................................. 87

About this Guide ..................................... 87

Logging in to BioAssay ........................... 87

Terminology ............................................ 87

Navigation ............................................... 88

Protocols .................................................. 91

External Analysis .................................. 130

A Sample Protocol - IC50 ..................... 131

Compound Lists .................................... 145

Reporting ............................................... 145

Settings .................................................. 148

Actions Menu ........................................ 154

Prohibited Field Names ......................... 158

Security .................................................. 165

Section III

Inventory

Desktop & Workgroup

Appendix A

System Features ...................................79

Viewing User Information .......................79

Inventory Desktop & Workgroup ....169

What’s new ............................................ 169

Login and Logout .................................. 170

ii

Contents


Terminology ...........................................170

The User Interface ..................................170

Searching CS Inventory .........................184

Printing Labels and Reports ...................186

CS Inventory Tasks ................................190

Securing Structure Files .........................196

Section IV

Chem & Bio Office Enterprise

Chapter 15

Informatics Directions .......................201

Collaboration ..........................................202

Technology and Integration ...................202

Professional Services ..............................203

Summary ................................................204

Chapter 16

Supporting an Informatics Enterprise

Workflow ............................................207

Chapter 17

DocManager Enterprise ....................215

Batch Submission ...................................215

Viewing Recent Activities .....................215

Searching for Documents .......................215

Chapter 18

E-Notebook Enterprise ......................217

Working with Collections ......................220

Reaction Sections ...................................221

Spectra and Other Sections ....................223

Working with Data ................................ 224

Searching ............................................... 224

Chapter 19

CombiChem for E-Notebook ............ 229

Chapter 20

BioAssay Enterprise .......................... 231

Protocols ................................................ 231

Reporting ............................................... 232

Chapter 21

Registration ........................................ 233

Registering Records ............................... 233

Query and Reporting ............................. 233

Chapter 22

BioSAR Enterprise ............................ 235

Terminology .......................................... 235

Schema Management ............................. 236

Form Management ................................. 236

Searching ............................................... 236

Chapter 23

Inventory Enterprise ......................... 237

Overview ............................................... 237

Searching Inventory Enterprise ............. 237

Container Management ......................... 237

Grid Management .................................. 237

Managing Batching Fields ..................... 237

Plate Inventory ....................................... 238

Reports Management ............................. 238

Managing Organizations ....................... 239

Integrating with Registration Enterprise 239

Chem & Bio Office 2010 User Guide

iii


Administrator

Section V

Databases

Chapter 24

Scientific Databases ...........................243

ChemBioFinder.Com Gateway ..............243

Database Offerings .................................243

Reference Data

Chapter 25

The Merck Index ...............................245

How Is It Useful? ...................................245

About The Merck Index .........................246

Using The Merck Index Online ..............246

Compound Searching .............................247

Organic Name Reactions ........................247

Supplemental Tables ..............................248

Logging Off ............................................249

About Ashgate Drugs ............................ 255

Using Ashgate Drugs ............................. 255

Chapter 29

NCI ......................................................259

Using NCI .............................................. 259

Chapter 30

AIDS ....................................................261

Using AIDS on CD ................................ 261

Chapter 31

Traditional Chinese Medicines .........263

About TCM ........................................... 263

ChemOffice Enterprise .......................... 263

Chapter 32

Nanogens .............................................267

Chapter 33

Off-Label Database ............................269

Chapter 26

R&D Insight/Chemists ......................251

About RDIC ...........................................251

Using RDIC Online ................................251

Chapter 27

ChemINDEX ......................................253

How Is It Useful? ...................................253

About ChemIndex ..................................253

Using ChemINDEX Ultra ......................253

Chem & Bio Office Enterprise ...............254

Chapter 28

Ashgate Drugs ....................................255

Chapter 34

Martindale for Scientists ...................271

Database Contents ................................. 271

Accessibility .......................................... 271

Chapter 35

Encyclopedia of Reagents for Organic

Synthesis .............................................273

Reagents and Catalysts .......................... 273

Searchable Reactions ............................. 273

Database Contents ................................. 273

Ready Accessibility ............................... 273

iv

Contents


Sourcing & Safety Data

Chapter 36

Sourcing & Safety Databases ............275

Chapter 37

ChemACX ...........................................277

ChemACX Database ..............................277

How Is It Useful? ...................................277

Using ChemACX with ChemOffice

Enterprise ...............................................278

Chapter 38

ChemMSDX .......................................287

How is it Useful? ....................................287

Using ChemMSDX ................................287

Chapter 39

Sigma-Aldrich MSDS Collection ......289

Chapter 40

EH&S Enterprise ...............................291

How Is It Useful? ...................................291

Key Benefits ...........................................291

Reaction & Synthesis Data

Chapter 41

Reaction & Synthesis Databases ...... 293

Chapter 42

ChemReact ......................................... 295

About ChemReact ................................. 295

Searching ............................................... 296

Chapter 43

ChemRXN .......................................... 299

How Is It Useful? ................................... 299

ChemPrep .............................................. 299

ChemSelect ............................................ 300

Chapter 44

ChemSynth ......................................... 303

About ChemSynth ................................. 303

Using ChemSynth .................................. 303

Index .................................. 307

Chem & Bio Office 2010 User Guide

v


Administrator

vi

Contents


E-Notebook

Desktop & Workgroup


1

Getting Started

E-Notebook helps you manage numerous types

of data on electronic pages that are much like

the pages of a traditional, paper notebook. This

information is organized into collections —

sets of related items that appear in a tree structure

in the left frame when you are browsing E-

Notebook.

Examples of some common types of E-Notebook

collections are:

• Notebook and Page

• Therapeutic Area

• Project

• Experiment

• Reaction Scheme

• Synthesis

For example, you could create a collection that

contains all of the reaction steps for a specific

synthesis. Typically, primary research data is

stored in Reaction/Pages, which are organized

within Notebooks, just like the paper pages in

paper notebooks. In this case, the synthesis

could be a notebook, and each of the steps

could be a page. Each of the pages may come

from a different notebook and may have been

created by a different chemist, but the notebook

for this, particular synthesis could collect

all of these pages in a single place.

You can organize collections in other ways,

too. For example, you may want to create a

collection of all of the synthesis that lead to a

certain product, or all of the E-Notebook users

who are working on a specific project. E-Notebook

enables you to set up these relationships

easily.

Collections are extremely flexible, because

they are designed to allow you to organize

your information in the way that is best suited

to your workflow. E-Notebook allows you to

browse through collections and to search them

for important information. Also, you can create

references to them, duplicate them, and, to prevent

further changes, you can transition them

to a closed, read-only state.

Just as you would use pages in a paper notebook

for recording various types of data, you

can use sections in E-Notebook for recording

reactions, spectra, or any other kind of information.

For example, within pages/reactions

there may be sections for reactions, notes,

reactants, etc. — whatever you need to record

and display your information the way you

would with a paper notebook. You also have

the option to use templates, so that sections are

Chem & Bio Office 2010 User Guide 3

E-Notebook


set up automatically and uniformly with each

new page/reaction you create. Your system

configuration determines the type of collections

and sections that you can create within E-

Notebook and the rules that define their contents.

The permission to view, edit, and create

collections can be set up on a per-collection

basis.

Navigation Overview

E-Notebook is consists of two major modules:

• Browse

• Search

These modules can be accessed using the

Browse and Search buttons on the main Toolbar.

The Browse area displays the collections organized

in a tree structure. To expand a collection

and view its contents, either double-click it or

click the plus sign next to it. Clicking an individual

collection allows you to view and/or

edit it in the right frame. There are a number of

options for specifying your view of the Collec-

4 Getting Started

Chapter 1


tion Tree. See “Browsing the Collection Tree”

on page 14 for more information.

From within the Search area, you can construct

a query to search for information. For example,

you may want to search for all of the sections

that contain a certain structure, or all of the collections

created by a particular user. When you

run a query, you can see both the results list

and the query itself. Clicking any item in the

results list allows you to browse to that item.

Certain menus in E-Notebook are accessed

when a particular item or icon is right-clicked.

For example, right-clicking a collection in the

Collection Tree will display the collection

menu.

To expand the size of a field in a section:

• Double-click the title bar of the field.

The field expands to take up the entire section

area, increasing your working space.

• To shrink the field:

Double-click the title bar again.

Security Overview

Each user of E-Notebook has a unique username

and password. Thus, only valid users

may log into E-Notebook.

Once a user has logged in, security in E-Notebook

is set up on a collection basis. Security

properties may be set up for any collection in

the Collection Tree — whether it be a User, a

Notebook, a Folder, etc. The security properties

of a collection determine who has Read,

Write, or Full Control access to that collection.

These access privileges may be assigned to

individual E-Notebook users or to user groups.

• Read – permission to view the collection,

but not edit it.

• Read and Write – permission to view the

collection and edit it, if it is in a state that

permits edits.

• Full Control – Read and Write permission,

and also the ability to assign and remove

security permissions for the collection.

By default, each collection inherits the security

properties of its parent in the Collection Tree.

The inherited security option may be disabled,

however, so that the security properties of a

collection can be configured independently of

its parent.

In addition to security at the collection level,

security may also be configured for collection

transitions, specifying which users may or may

not perform certain transitions on collections.

If you have Full Control permission to a collection,

you may determine who has access to

the collection. See “Changing Collection Security

Properties” on page 24.

Logging into E-Notebook

To start E-Notebook, you must first log in.

Then, you can begin to browse or search

through E-Notebook. Follow the instructions

below to log into E-Notebook Desktop.

Instructions for E-Notebook Workgroup are

similar:

1. Go to Start>All Programs>ChemBioOffice

2010>E-Notebook>E-Notebook 12.0.

2. At the log in dialog box, enter your name

and password and click Connect.

Chem & Bio Office 2010 User Guide 5

E-Notebook


6 Getting Started

Chapter 1


2

E-Notebook Desktop & Workgroup

E-Notebook is an electronic notebook specifically

designed to help scientists maintain their

laboratory records. E-Notebook makes it possible

for you to manage diverse types of data on

electronic pages that are much like the pages of

a paper notebook. The electronic pages make it

easy to organize information and streamline

your workflow. With E-Notebook, you can set

up notebooks and pages to manage information

about organic syntheses and related information

such as stoichiometry calculations, reaction

preps, spectra, analytical methods, notes,

and spreadsheets.

About E-Notebook

E-Notebook has many advantages over traditional,

paper notebooks. Since E-Notebook has

electronic rather than paper pages, you can

conduct searches by substructure, key word,

date, and so on. You can set up templates to

avoid reentering information that you often

use. E-Notebook fully automates stoichiometric

calculations. E-Notebook also provides a

full audit trail and change tracking features for

compliance with 21 CFR Part 11.

With E-Notebook, you can create a customized

electronic notebook that matches your workflow.

You can develop new fields to manage

specialized types of data, and configure your

own forms to manage the information that is

important to you. You can also add your own

data analysis tools and customized searches to

E-Notebook.

You can use E-Notebook to organize a wide

variety of other information critical to your

work processes as well. For example, common

reactants used in reaction preparations can be

stored in the E-Notebook database and shared

among researchers.

E-Notebook supports the SQL database format.

What’s New

E-Notebook 12.0 Desktop for Chem & Bio

Office Desktop 2010 introduces a variety of

powerful new features to help you become

more productive and better manage your laboratory

data.

Microsoft ® Office 2007 Support. Chem & Bio

Office 2010 supports Microsoft Excel ® , Word,

and PowerPoint ® . Use E-Notebook and

Microsoft Office 2007 together to manage all

your laboratory data. You can now write

reports, develop spreadsheets, and create presentations

without ever leaving Chem & Bio

Office 2010.

Batch Explorer. With the Batch Explorer, you

can view a reaction tree showing successors

and predecessors of a selected batch or com-

Chem & Bio Office 2010 User Guide 7

E-Notebook


pound.For more information “Batch Explorer”

on page 42.

E-Signature. With E-Signatures, you can electronically

sign a PDF version of your completed

page/reaction page.For more

information “E-Signatures” on page 11.

Work offline. With Offline mode, you can continue

doing work when server or network is not

connected and get the data synchronized when

you work in the online mode. For more information

“Working Offline” on page 73.

Name=Struct. The Name=Struct feature in

ChemDraw 12.0 is now available in E-Notebook

Desktop 12.0. For more information, see

“Name=Struct” on page 31.

NOTE: Name=Struct is available only in the

desktop version of E-Notebook.

Full Text Search. This feature comes with

SQL Server 2005 and is used in E-Notebook

for searching. Earlier, the search was possible

for names of the collections or sections. With

Full Text Search, you can search the contents

of the collections, documents and styled text

fields for a particular word.

Appendix Rendering. Add custom a header

and footer information to your printed

pages.You must have administrator privileges

to use appendix rendering. See “Appendix

Rendering” on page 27.

NOTE: Appendix rendering is available only

in the desktop version of E-Notebook.

About this Guide

Inside this guide, you will find a full description

of E-Notebook Desktop and Workgroup,

their features, and complete instructions on

how to use them. This guide is available in

print, online, and CHM formats.

8 E-Notebook Desktop & Workgroup

Chapter 2


3

Working with E-Notebook

A collection in E-Notebook is a set of similar

or related items that you use in your work. A

collection can be a set of notebooks, reactions,

pages, folders, searches, reactants, etc. The

default collection, called your “user collection”,

is where all your other collections are

listed.

The User Collection

Each E-Notebook user has a user collection

associated with them. Your user collection is

your home collection, and appears at the top of

the Collection Tree when you first log into E-

Notebook.

When you select your user collection in the

Collection Tree, your home page appears in the

right frame. The home page displays information

about you as a user, in addition to summary

information about your open pages/

reactions.

You can add different types of collections

directly to your user collection:

• Notebooks

• Folders

• User Configurations and AutoText Definitions

• Searches - Collection Searches, Section

Searches, Text Searches, Unannotated Version

Searches, Chemical Structure

Searches.

• Pages and Reaction Pages

• References to Notebooks

• References to Folders

• References to Page or Reaction Pages Templates

Adding a New Collection

To add a new collection:

1. In the Collection Tree, right-click your user

collection. A menu appears.

2. Select New, and then a type of collection.

The new collection appears and you are

prompted to rename it.

Adding a Reference

1. In the Collection Tree, click the Notebook,

Folder, or Template to which you wish to

create the reference.

2. While holding the CONTROL and SHIFT

keys, drag the collection until the user collection

(or destination collection) is highlighted.

3. Release the mouse. The Reference appears

in the Collection Tree.

Alternatively, you may right-click the collection

you wish to reference, and select Copy

from the collection menu. Then, right-click the

Chem & Bio Office 2010 User Guide 9

E-Notebook


user collection (or destination collection) and

select Paste Reference.

Browsing up to the User Group

If you have the required security permissions,

you may browse up to the next highest level in

the Collection Tree and view the user group at

that level. To do this, right click your user collection,

and select Go Up To, and then the name

of your user group.

Alternatively, you may select View from the

menu bar, and then Go Up To.

Notebooks

Notebooks contain Page or Reaction Page collections.

Each Notebook has a table of contents

associated with it, which displays summary

information for each collection in the Notebook.

Creating a Notebook

To create a new, Notebook collection:

1. In the Collection Tree, right-click your user

collection. A menu appears.

2. Select New > Notebook.

A new Notebook collection appears and

you are prompted to rename it. The Table

of Contents section of the Notebook

appears in the right frame.

To create a new Page/Reaction Page in the

Notebook, click the New Page and then select

the page/reaction page.

Each Notebook has a Table of Contents associated

with it. The Table of Contents summarizes

all of the Pages/Reaction Pages that the notebook

contains. Clicking on any of the contained

Pages/Reaction Pages listed will allow

you to navigate to that Page/Reaction Pages.

You may also print the Table of Contents to

create a hardcopy of it; See “Printing Collections

or Sections” on page 26.

When you rename a Notebook, the names of

the Pages or Reaction Pages within it change to

match the name of the Notebook.

Pages and Reaction Pages

Pages/Reaction Pages in E-Notebook may contain

several different types of sections for

experimental data.

Creating a Page or Reaction

Page

To create a new Page or Reaction Page collection:

1. In the Collection Tree, right-click the Notebook

collection to which you would like to

add the Page or Reaction Page.

A menu appears.

2. Select New > Page (or Reaction Page).

A new Page or Reaction Page collection

appears in the Notebook. It is numbered

automatically.

You may associate several types of sections

with the Page/Reaction Page:

• Reaction Section

• MS Word Document Section

• Ancillary Data Section

• Spectrum and Spectra Sections

• Table Section

• MS Excel Spreadsheet Section

• Image Section

• MS PowerPoint Slideshow

10 Working with E-Notebook

Chapter 3


• Title Page

NOTE: On selecting a new page, a blank page

is displayed as compared to the reaction page,

reaction section is displayed.

To create a new Page or Reaction Page collection

from a template:

1. In the Collection Tree, select User Configuration>Templates.

2. Drag the template into the Notebook.

A new Page or Reaction Page is created,

based on the template.

Alternatively, you may right-click the template

and select Copy. Then, right-click the Notebook

and select Paste. (See “Templates” on

page 23 for information about creating the initial

template).

E-Signatures

With E-Signatures, you can electronically sign

a PDF version of your completed page/reaction

page. This page/reaction page rendition is then

routed to co-authors (where applicable) and

witnesses. Once all required parties have

signed the page/reaction page rendition, it is

stored in a separate database for protection of

your intellectual property.E-Signature works

on the pages/reaction pages created.

Pages/Reaction Pages have several states

which define their lifecycles. You may perform

transitions on a page or reaction page to

move it from one state to another.

• Sign and Close

• Sign and Keep Open

• View Signed Versions

Sign and Close: The Closed state may be readonly.

It may be possible to edit the collection

while it is in this state. To perform this action:

1. Right click on any page/reaction page and

select sign and close.

A confirmation dialog appears. Click Yes.

A witness selection dialog box appears

where you have to select the user and then

click Add.

Page/reaction page is rendered and displayed

in PDF. Enter the password and click Sign and

Store. The Home Page displays the submitted

document.

Once the page/reaction page is signed and

closed, an icon is displayed (Lock Sign) in the

collection tree and History shows the status as

Sign and Close

Sign and Keep Open: The Open state may have

an optional annotation, it is write only, so that

you may provide a reason for a change you

wish. To perform this action:

1. Right click on any page/reaction page and

select sign and keep open.

2. A witness selection dialog box appears

where you have to select the user and then

click Add.

Page/reaction page is rendered and displayed

in PDF. Enter the password and click Sign and

Store. The Home Page displays the submitted

document. The History shows the status as

Sign and Keep Open.

You can see two panes on the Home Page:

• Waiting Document

• Document submitted by the user (person to

whom we have assigned the document).

View Signed Versions: The signed versions

rewardable, required annotation of changes,

changes visible on the screen and in the printed

Chem & Bio Office 2010 User Guide 11

E-Notebook


copy.To view the signed versions, right click

on the submitted document and select review.

Folders

You can use folders to organize and manage

other types of collections:

• Other Folders

• Searches – Collection Searches, Section

Searches, Text Searches, Chemical Structure

Searches, Unannotated Version

Searches

• References to any type of collection

Creating a Folder

To create a new, Folder collection:

3. Release the mouse.

The Reference appears in the Collection

Tree.

Alternatively, you may right-click the collection

you wish to reference, and select Copy

from the collection menu. Then, right-click the

folder collection and select Paste Reference.

The User Configuration Folder

Within your user collection, there is a User

Configuration Folder, which can contain Reactants,

AutoText, and Templates.

To expand your User Configuration folder and

view its contents, either double-click it in the

collection tree or click the plus sign next to it.

1. In the Collection Tree, right-click your user

collection.

A menu appears.

2. Click New>Folder.

A new Folder collection appears and you

are prompted to rename it.

Or, you may right-click an existing Folder collection

and select New, then Folder, to create a

Folder within a Folder.

Adding a Reference to the

Folder

You may add references to a folder if, for

example, you would like to keep the information

from several Pages/Reaction together, but

the Pages/Reaction exist in separate notebooks.

1. In the Collection Tree, click the Collection

to which you wish to create the reference.

2. While holding the CONTROL and SHIFT

keys, drag the collection until the folder

collection is highlighted.

• Reactants Folder – contains reactants whose

structures and properties you can add to

Reaction Sections. See Reactants Collections

for information.

• AutoText Definitions – contains predefined

text fragments that you can reuse to simplify

text entry in, for example procedure

text. See “Creating New Autotext Definitions”

on page 38 for information about

configuring AutoText.

12 Working with E-Notebook

Chapter 3


• Templates folder – contains templates of

various types that you can use to avoid

unnecessary reentry of data. See “Templates”

on page 23 for more information.

Reactants Collections

Reactants are named shortcuts for a commonly

used compounds. These could be either common

reagents, or named compounds that you

use frequently, and are kept in the Reactants

Folder in the Collection Tree.

You may populate reaction sections with the

properties of reactants.See “Working with

Reactions” on page 29 for more information.

Adding Reactant Section to

Collection

To add a new reactant section to an existing

collection:

1. Browse to the Reactants collection to which

you wish to add the Reactant, clicking the

collection in the collection tree to select it.

The Reactants collection appears, with the

existing reactants displayed in the right

frame.

In the right frame, click the New Acronym.

A New Acronym dialog appears. Enter the

name of the acronym and click Create.

A new reactant section appears with name

entered for the new acronym.

2. To rename the section, right-click the section

menu icon and select Rename Section

from the menu that appears. Then type in a

name.

3. Draw or import the structure using the

Chem & Bio Draw tools.

The formula and molecular weight properties

are updated automatically. The compound

name may be updated as well. The compound

name will be displayed in the table of contents

for the Reactants Folder that contains this reactant.

Click the Reactants Folder in the Collection

Tree to view its table of contents.

Adding a new Reactant

Collection

You can add a new Reactant Collection to your

User Configuration folder in E-Notebook. To

add a new Reactant Collection:

1. Right-click the Reactants Folder and select

New>Reactants.

A Reactants collection appears, and you are

prompted to rename it.

2. Enter a name for the Reactants collection.

3. Click the New Acronym tool in the right

frame.

A New Acronym dialog appears. Enter the

name of the acronym and click Create.

A new Reactant section appears.

You may populate reaction sections with the

properties of reactants.See “Working with

Reactions” on page 29 for more information.

Working with a Table of

Contents

E-Notebook collections often have Table of

Contents sections associated with them. The

Table of Contents lists all of the collections

that fall directly within the selected collection

in the Collection Tree. For example, if a Notebook

contains Reaction Page, all of the Reaction

Pages in the Notebook will be listed. Or, if

a Folder contains templates, all of the templates

in the Folder will be listed.

Chem & Bio Office 2010 User Guide 13

E-Notebook


Double-clicking the link by any of the contained

collections listed will allow you to navigate

to that collection. You may also print the

Table of Contents to create a hardcopy of it;

See “Printing Collections or Sections” on

page 26 for more information.

You can customize a Table of Contents to display

only columns of interest or sort columns

in ascending or a descending order.

Hiding Columns

To hide columns in the Table of Contents:

1. Right-click the column to hide.

A menu appears.

2. Select Show Columns.

The Show Columns dialog appears, listing

the columns you may select for display in

the Table of Contents. The columns that are

currently displayed are denoted with

checkmarks.

3. Select and deselect columns to customize

the Table of Contents display.

The columns you selected appear with

checkmarks next to them.

4. Click OK to close the dialog.

The dialog closes, and the screen refreshes

to display the additional columns.

Sorting Items in the TOC

You may sort items in the TOC in either an

ascending or descending order. To sort items in

an ascending order:

1. Right-click the column by which you wish

to sort the Table of Contents.

A menu appears.

2. Select Sort Ascending.

2. Select Hide followed by the name of the

column.

The screen refreshes, and the column is

hidden.

Showing Columns

To show additional columns that are hidden, or

are not currently displayed in the Table of

Contents:

1. Right-click A column in the Table of Contents.

A menu appears.

The items are sorted in ascending order

according to the column you selected.

To sort items in an descending order:

1. Right-click the column by which you wish

to sort the Table of Contents.

A menu appears.

2. Select Sort Descending.

The items are sorted in descending order by

the column you selected.

Browsing the Collection

Tree

Collections and their contents are organized in

the Collection Tree on the left side of the

14 Working with E-Notebook

Chapter 3


screen. E-Notebook offers several options for

browsing and viewing collections.

To begin browsing collections:

1. Click browse at the top of the screen.

The Collection Tree appears.

2. Select a collection from either the collection

tree or the dropdown list (between the

green arrows).

3. Click the green arrows to navigate the Collection

Tree view.

NOTE: Only one user can edit an collection at

a time. A message will inform you when a collection

is locked for editing by another user.

Showing and Hiding

Collections

The Collection Tree provides you with a

means of expanding and contracting collections

so that you only see the information you

need.

To show the contents of a collection:

• Click the plus sign next to the collection

whose contents you wish to see.

The collection is expanded, and you can

view its contents.

• Click the minus sign next to the collection.

The collection is minimized, so that you

cannot see its contents.

Hiding the Collection Tree

It is possible to hide the Collection Tree if you

would to increase the screen area you have for

entering data into a section.

To hide the Collection Tree:

1. Move your cursor to the right boundary of

the tree, so that the cursor becomes a double-headed

arrow.

2. Double-click.

The Collection Tree is hidden.

To view the Collection Tree again:

1. Move your cursor to the left boundary of

the section, until the double-headed arrow

appears again.

2. Double-click.(Or, you may click the touchbar

at the left boundary of the E-Notebook

window).

The Collection Tree reappears.

Limiting Collection Browsing

You can limit your browsing by selecting a

root collection for the collection tree. The root

collection becomes the highest browsing level

in the collection tree. Limiting the collection

tree view can make it easier to find specific

information.

To set a root for the collection tree:

1. Click the browse at the top of the screen.

The collection tree appears.

2. Right-click the collection you wish to be

the root collection for browsing.

A menu appears.

3. Select Browse Here.

The collection you selected appears at the

top of the collection tree.

Browsing from Home

You can browse from your home collection,

which contains all of the collections associated

with you as a user of E-Notebook. This is the

collection that appears when you first log in.

Chem & Bio Office 2010 User Guide 15

E-Notebook


To browse to your home collection and bring

the home collection to the top of the collection

tree:

1. Click the browse.

The collection tree appears.

2. Do one of the following:

• Right-click a blank area of the collection

tree and click Go Home in the context

menu.

• Go to View>Go To>Home.

The home collection appears at the top of collection

tree.

Browsing at a Higher Level

You can browse at a higher level in the Collection

Tree, and see all the collections at that

level.

To browse at a higher level:

1. If the collection tree is not visible, click

Browse at the top of the screen. The Collection

Tree appears.

2. Do one of the following:

• Right-click a collection in the collection

tree and click Go Up To.

• Go to View>Go Up To.

The collections that either contain or reference

the item are listed.

3. Select the collection to bring to the top of

the Collection Tree.

The collection you selected appears at the

top of the tree. Its contained collections and

contained references are displayed.

Browsing the Entire Collection

Tree

Browsing the entire Collection Tree lets you

see all the E-Notebook collections at once.

To browse the entire tree:

1. If the collection tree is not visible, click

Browse at the top of the screen. The Collection

Tree appears.

2. Do one of the following:

• Right-click any blank area of the Collection

tree, and select Browse All from the context

menu that appears.

• Right-click any collection in the tree, and

select Browse All from the menu that

appears.

• In main menu, go to View>Go To>Browse

All.

NOTE: The Browse All command is available

only if you have the Read privilege for the collection

at the top of the collection hierarchy. If

not, you may need to conduct a collection

search to view some of the collections to which

you have access.

Behaviors of Collections

There are diverse behaviors associated with

Collections-such as the creating, hiding,

renaming, duplicating, and moving behaviors.

Your system configuration determines the

rules to define the traits reflected by a collection.

Therefore, depending on your system

configuration, there may be some additional

behaviors that these collections can show.

Auto-Numbered Collections

E-Notebook may be configured to automatically

number the collections contained within a

specific collection. Your system configuration

determines the parameters for auto-numbering

the collections.

16 Working with E-Notebook

Chapter 3


If E-Notebook is configured to auto-number

the collections then the newly created collections

will be automatically named by appending

a serial number to the name of the

collection that contains the newly created collection.

Collections that Cannot be Deleted

In E-Notebook, you may be prevented from

deleting the specific collections. Actually, your

system administrator may configure some specific

collections so as to prevent you from

deleting them once they have been created.

Therefore, the Delete command in the collection

menu of such collections will be grayed

out.

For example, if the Notebook collection has

been configured to avoid deleting then clicking

on it will show the menu with inactive Delete

option.

Your system configuration determines which

types of collections cannot be deleted. Also,

you cannot delete a collection if references to it

exist. E-Notebook, by default, is configured so

that you cannot delete specific collections such

as, User Collection, User Configuration

Folder, Notebook Collections and Offline

Folder.

Deleting Modified Collections

In some cases, you may delete collections only

if they have not been modified since they were

created. Once the collection is modified, the

Delete option in the collection menu is inactive

when collections of that type are selected.

Your system configuration determines which

types of collections cannot be deleted after

modification.

Renaming Collections

In E-Notebook, you may be prevented from

renaming specific collections, for example, a

collection whose name is generated by the

auto-numbering feature. If you attempt to

rename an auto-numbered collection, an error

message appears.

Your system configuration determines which

types of collections cannot be renamed.

Copying Collections that Contain

References

It is possible to copy collections that contain

references in the collection tree in the same

way as you would copy normal collections

without references. The copied collection contains

references to all of the collections that are

contained within the collection at the time the

copy is made.

In some cases, your system configuration may

prevent you from copying collections that contain

references to specific types of collections

that are in specific states. This pertains only to

references that exist in property lists and

tables. It does not pertain to references in the

collection tree. For example, an experiment/

page collection type may be configured to prevent

you from copying pages/reaction that contain

references to folders that are in a Closed

state.

Your system configuration determines which

types of collections you can copy, and into

which types of container collections you can

copy them.

For more information about copying collections,

See “Copying a Collection” on page 21

Chem & Bio Office 2010 User Guide 17

E-Notebook


18 Working with E-Notebook

Chapter 3


4

Managing Collections

All information in E-Notebook is organized

into collections. Collections may be notebooks,

folders, reaction/pages, templates, and

other content. Collections are listed in the collection

tree at the left of the screen. E-Notebook

lets you browse through collections and

to search them.

It is possible to manage collections in a number

of ways, as discussed in the following topics:

• Organizing Collections

• Templates

• Viewing Collection Properties

• Changing Collection Security Properties

• Performing a Collection Transition

• Importing and Exporting Collections

• Exporting to Word

• Printing Collections or Sections

Your system configuration determines the

types of collections that you can create within

E-Notebook and the rules that define their contents.

The permission to view, edit, and create

collections can be set up on a per-collection

basis. These rules are configurable in E-Notebook.

Organizing Collections

You can organize collections in the Collection

Tree to make their order meaningful to you and

other E-Notebook users. Collections can be

moved up and down within a container collection.

In some cases, collections can be moved

from one container collection to another. Your

system configuration determines which items

can be moved into which types of collections.

Moving a Collection

Within a Container Collection

You can organize collections within a container

collection by moving them up and down.

To move a collection within its container:

Chem & Bio Office 2010 User Guide 19

E-Notebook


1. Click Browse at the top of the screen. The

Collection Tree appears.

Between Container Collections

You can move collections from one container

collection to another.

NOTE: Your system configuration defines the

rules that determine which collections can be

moved into which types of container collections.

Figure 4.1 A sample collection tree for a workgroup

that includes two users.

2. To expand a collection and view its contents,

either double-click the collection or

click the plus sign next to it.

3. Right-click the collection you want to

move.

In the context menu, select the appropriate

option:

• Move Up: moves the collection up one position

in the Collection Tree.

• Move Down: moves the collection down one

position in the Collection Tree.

TIP: You can also move collections using your

keyboard. Hold down the CTRL key and use the

up and down arrows.

To move a collection between container collections:

1. If the collection tree is not visible, click

Browse at the top of the screen. The Collection

Tree appears.

2. In the Collection Tree, click and drag the

collection you want to move to the new

container.

If your system configuration permits the move,

the collection appears in the new location.

Depending upon the rules that define your system

configuration, a copy or a reference may

appear instead. Also, it may not be possible to

move the collection into a particular type of

container. If the new container will not accept

the collection you are attempting to move, you

will be unable to highlight the container when

you attempt to drag the collection into it.

Creating a Reference

Within the collection tree, you can create a reference

to a collection that exists elsewhere in

the tree. The reference acts as a shortcut to the

original collection, and it reflects any changes

that are made to the original. Also, if you have

editing privileges to the original, any changes

made to the reference are reflected in the original.

To create a reference in the collection tree:

20 Managing Collections

Chapter 4


1. Click Browse.

The Collection Tree appears.

2. Click the collection that you wish to reference.

The collection is highlighted.

3. Holding down the CONTROL and SHIFT

keys, drag the item into the Collection

where you would like it to be referenced.

A Reference to the item appears in the Collection

Tree, within the collection you

selected. The icon contains a small arrow,

which indicates that it is a reference.

An alternate method for creating a reference in

the collection tree is the following:

1. Right-click the collection that you wish to

reference.

The collection menu appears.

2. Select Copy.

3. Right-click the collection into which you

wish to add the reference.

The collection menu appears.

4. Select Paste Reference.

The reference appears in the Collection

Tree, within the container collection you

selected.

NOTE: Your system configuration determines

which collections can be referenced within

which container collections.

It is also possible to create references to collections

from property lists and tables.

Duplicating a Collection

You can duplicate a collection within its container

collection in the Collection Tree. The

duplicate you create contains references to all

of the collections that are contained within the

collection at the time the copy is made.

To duplicate an item within the same container

collection:

1. Click Browse.

The Collection Tree appears.

2. Right-click the collection that you wish to

duplicate.

The collection menu appears.

3. Select Duplicate.

A copy of the collection appears within the

same container collection.

NOTE: Your system configuration determines

which collections can be duplicated, and where

the duplicates can reside in the Collection Tree.

Copying a Collection

You can copy a collection in the Collection

Tree.

To do this:

1. Click the browse.

The Collection Tree appears.

2. Right-click the collection you wish to copy

and select Copy from the menu that

appears.

3. Right-click the collection that is to be the

container collection for the copy.

4. Select Paste from the menu that appears.

A copy of the collection appears in the Collection

Tree, within the container you

selected.

Alternatively, you may click the collection you

are copying to select it. Then, while holding

Chem & Bio Office 2010 User Guide 21

E-Notebook


down the CONTROL key, drag it into a container

collection to create a copy.

NOTE: Your system configuration determines

which type of collections you can copy, and into

which type of container collections you can

copy them.

Renaming a Collection

You can rename a collection to avoid a duplicate

name, or simply to make the name more

meaningful to you and other E-Notebook

users.

To rename a collection:

1. Click the browse.

The Collection Tree appears.

2. Right-click the collection you wish to

rename in the Collection Tree.

The collection menu appears.

3. Select Rename.

You are prompted to enter another name.

4. Enter a name.

The collection is renamed.

Your system configuration determines naming

conventions for various types of collections. If

you enter a name that does not adhere to the

naming conventions, an error message appears

and you are prompted to enter another name. In

some cases, a name may be assigned to a collection

automatically, and it may not be possible

to rename the collection at all.

Deleting a Collection

You can delete a collection from the Collection

Tree so that you manage only the information

that is relevant to your current needs. Your system

configuration determines which types of

collections can be deleted.

To delete a collection from the Collection

Tree:

1. Click Browse.

The Collection Tree appears.

2. Right-click the collection you wish to

delete.

The collection menu appears.

3. Select Delete.

If your system configuration permits it, the

collection is deleted.

You may also delete a collection by clicking it

in the tree to select it, and then pressing the

DELETE key.

Note that you cannot delete a collection if references

to it exist. Also, in some cases, it may

only be possible to delete collections if they

have not been modified since they were created.

Viewing Collection

Properties

You can see specific information about a collection

by viewing the Collection Properties.

To view properties of a Collection:

1. If the collection tree is not visible, click

Browse at the top of the screen. The Collection

Tree appears.

2. Right-click the item whose properties you

wish to view.

A menu appears.

3. Select Collection Properties. The properties

dialog box appears.

The General tab lists the following:

Name - the name of the collection.

22 Managing Collections

Chapter 4


Owner - the user who created the collection.

Type - the type of the Collection or Page.

Contents - the number of collections contained

in the collection.

Created - the date on which the collection was

created.

Last Modified - the date on which the Collection

or Page was last changed.

Status - the status of the collection in its life

cycle. If no states are defined for the collection,

the status is Created.

Autosave Interval the time interval after which

the collection is saved automatically.

NOTE: To view the Collection Security or

Transition Security properties, click the appropriate

tab. If the collection is a user collection,

the Region tab also appears.

Importing and Exporting

Collections

E-Notebook provides the ability to export and

import collections as XML files. Each XML

file contains all of the data and formatting

associated with the collection.

Importing a Collection

To import a collection:

1. Click Browse.

The Collection Tree appears.

2. In the Collection Tree, right-click the collection

into which you would like the collection

to be imported. For example, if you

would like to import page/reaction page

into a Notebook, you would right-click the

Notebook.

The collection menu appears.

3. Select Import.

A dialog appears and you are prompted to

select the XML file you wish to import.

4. Select the file and click Open.

The collection is imported into E-

Notebook.

Exporting a Collection

To export a collection:

1. Click Browse.

The Collection Tree appears.

2. In the Collection Tree, right-click the collection

that you wish to export as an XML

file.

The collection menu appears.

3. Select Export.

A dialog appears, and you are prompted to

select a location for the exported file.

4. Select the location for the file and click the

save.

The collection is exported to the XML file.

NOTE: When a collection is exported, the

export file does not include any of the contained

collections. Each collection must be exported

separately. For example, if you export a Notebook

that contains Pages/Reactions, only the

Notebook is exported; each page/reaction must

be exported as a separate XML file.

Templates

E-Notebook gives you the ability to use templates

so that you can avoid re-entry of the

information. For example, you may create a

Chem & Bio Office 2010 User Guide 23

E-Notebook


template for a particular type of page/reaction

page. It may contain data and notes that you

often use, or typical values for various properties.

To create a new template:

1. In the Collection Tree, right-click the container

collection to which you wish to add

the template.

The collection menu appears.

2. Select New> Page Template

The template is created within the container

collection, and its sections appear in the

right frame.

3. Edit the template to your wish.

To use the template, click and drag it into

another collection to create a new Page, Reactant,

etc., and avoid creating a collection from

scratch each time. E-Notebook is often configured

so that you can drag a template of an

Experiment or Page into a Notebook, thereby

creating a new Experiment or Page based on

the template.

You may also right-click the template in the

Collection Tree and select Copy from the menu

that appears. Then, right-click the container

collection (for example, the Notebook) and

select Paste from the menu.

Your system configuration determines which

types of templates you can create as a user of

E-Notebook, and which types of collections

can contain them.

Form Tools

A form tool is used to perform a particular

function in an E-Notebook form/field. There

are several standard form tools in E-Notebook

that may be associated with the section or collection

types, for example, the New Section

Form Tool associated with Notebook collection

type or Import/Export Form Tool, which is

present in new section types you create.

NOTE: Your system configuration determines

the collections to which this form tool can be

added.

Changing Collection

Security Properties

You can change the access that other E-Notebook

users have to a specific collections. In

order to change the security properties of a collection,

you must have Full Control privileges

to the collection. Your system configuration

determines who has Full Control privileges for

each collection in E-Notebook.

The default security for any new collection is

Inherits Security, meaning that a collection has

the same security profile as its parent collection

in the Collection Tree.

To disable inherited security:

1. Right-click the collection for which you

wish to disable inherited security.

A menu appears.

2. If Inherits Security is checked, select it to

clear the checkmark.

Inherits Security is disabled.

Collection Security

To change the Security Properties of a collection:

1. Right-click the collection whose Security

Properties you want to change.

2. In the context menu, select Collection Properties.

The Collection Properties dialog box

appears.

24 Managing Collections

Chapter 4


3. Click the Collection Security tab.

The Groups and Users who have permission to

access this item appear in one of the two lists:

• Inherited Permissions

• Assigned Permissions

Inherited Permissions are permissions inherited

from the parent collection in the collection

tree. These permissions can not be changed

from this dialog. Only the Assigned Permissions

can be changed from this dialog.

Transition Security

Transition Security is the security applied to

the collection transitions. For example, some

users may be allowed to close a collection

while others can also reopen the collection.

To change the Transition Security Properties

of a collection:

1. Right-click the collection whose Security

Properties you wish to change.

A menu appears.

2. Select Collection Properties.

The Collection Properties dialog box

appears.

3. Click the Transition Security tab.

The Security tab appears. The Groups and

Users who have permission to apply a transition

to this item appear in one of the two lists:

• Inherited Permissions

• Assigned Permissions.

Inherited Permissions are permissions inherited

from the parent collection in the Collection

Tree. These permissions can not be

changed from this dialog. Only the Assigned

Permissions can be changed from this dialog.

Performing a Collection

Transition

Collections may be configured to have states

associated with them. These states define the

life cycle of the collections. For example, a

Notebook may have Open and Closed states;

the Open state may permit editing, and the

Closed state may be a read-only state that does

not allow edits. Transitions are the actions you

perform to move a collection from one state to

another, for example, from Open to Closed.

In order to perform a transition on a collection:

1. Click Browse.

The Collection Tree appears.

2. Right-click the collection in the Collection

Tree that is to undergo the transition.

The collection menu appears.

3. Select the name of the transition from the

menu, for example Sign and Close, Sign and

Keep Open, and View Signed Versions. See

Chem & Bio Office 2010 User Guide 25

E-Notebook


“E-Signatures” on page 11 for more information.

The transition occurs and the collection

enters the new state. You may always view

the state of the collection by right-clicking

it in the Collection Tree, and then selecting

Collection Properties.

Transitions may also perform certain functions,

such as printing a copy of the collection.

Your system configuration determines which

transitions may be performed, and by whom.

Exporting to Word

You can export collections and sections to

Microsoft Word. Afterward, they are just like

any Word documents.

To export to Word:

1. In the collection tree, right-click the item

containing the section(s) to export.

A menu appears.

2. Select Export to MS Word.

You are prompted to choose a destination

folder and file name.

3. Choose a folder and file name and click the

save.

You are prompted to choose an export

range.

4. Select an export range:

• All Sections – to export all of the Sections.

• Sections from X to Y – to export a range of

Sections, where X and Y are values you

specify.

• Current Section – to export only the current

Section.

5. Select the Open Document After Export if

you would like the file to be opened after

the export is complete.

6. Click export.

If you chose to open the document after export,

the MS Word document is opened, and it displays

the Sections you selected for export. If

you choose not to open the document, the document

is saved in the folder you specified.

Printing Collections or

Sections

You can print collections from E-Notebook to

maintain your hardcopy archives.

To print a collection:

26 Managing Collections

Chapter 4


1. From the Collection Tree, right-click the

collection.

The collection menu appears.

2. Select Print.

Your printer dialog box appears, and you

are prompted to enter the information you

normally do when printing, such as page

printer and number of copies, etc.

3. Select the printer options.

4. Select the Page Range:

• All – prints all of the sections in the collection.

• Selection – prints only the selected section.

• Pages – allows you to specify a range of

sections to print. For example 1-5 would

print the first five sections in the collection.

5. Make your selections and click OK.

The collection or the selected portion is

printed.

NOTE: Your system configuration contains

templates that determine exactly how the

printed page appears.

If Visual Display of Changes is enabled, the

print will include the following:

• The collection data as is exists in the current

version of the collection.

• The version history, including the date and

the author for each version after the baseline

version. (The baseline version is the

version that existed when visual display of

changes begin).

• A list of changes grouped by field.

In some configurations, there is a Final Print

transition that automatically creates a complete

printout of the collection.

Appendix Rendering

If you have administrator privileges, you can

apply headers and footers to printed collection

pages. The header and footer appears only on

the printed pages.

NOTE: Appendix rendering is available only

in E-Notebook Desktop.

Applying appendix rendering

You first need to import the header/footer

XML file into E-Notebook.

To import the file:

1. In the collection tree, right click a collection

type or user name and select Import in

the context menu.

2. In the Import dialog box, navigate to the

folder:

[drive]:\Program

Files\CambridgeSoft

\ChemOffice2010\Utilities\AppendixRenderer\

3. In the AppendixRenderer folder, select

to open the Import.xml file.

After you import the file, the default header

and footer is applied to all printed pages.

Customizing the header/footer

1. In the collection tree, right-click a collection

type and select Collection Type Configuration.

2. In the left pane of the Collection Type Configuration

dialog box, navigate to:

Chem & Bio Office 2010 User Guide 27

E-Notebook


[name of collection type]/Commands/Export

to PDF/Command

Listeners/.

3. In the left page, click Appendix Renderer

Config.

In the right pane, the name

AppendixRenderer9.ARConfig

appears in the Implementation dropdown

list.

4. Click Custom Properties.

5. In the Command Listener dialog box, edit

the Header and footer as desired.

NOTE: The three text boxes in the Header and

Footer tabs correspond to the left, center, and

right positions of the page.

6. When you are finished editing the header

and footer content, click OK.

28 Managing Collections

Chapter 4


5

Working with Reactions

This portion of the user guide provides instructions

for working with the various sections or

forms in E-Notebook data. Just as you would

use pages in a paper notebook for recording

various types of data, you can use sections in

E-Notebook for recording reactions, spectra,

and other types of information.

For general information about deleting, moving,

and copying sections, etc., see “Managing

Collections” on page 19.

You can also use templates to set up sections

automatically and uniformly. See “Templates”

on page 23. for more information.

Your system configuration determines the

types of sections that are available in E-Notebook.

• Table Sections

• MS Word Sections

• MS Excel Sections

Reaction Sections

A reaction section shows one step in a reaction.

It contains a stoichiometry grid that analyzes

the reaction drawing automatically. The Auto-

Text feature updates the preparation text when

you change the reaction drawing and/or information

in the stoichiometry grid.

Pre-configured Sections

E-Notebook comes preconfigured with a number

of useful Sections that you can add to your

pages. Your system administrator may have

modified these Sections, eliminated them, or

added new Sections that more closely match

your workflow.

The preconfigured Sections are:

• Reaction Sections

• Reactant Sections

• Spectrum and Spectra Sections

To create a Reaction Section:

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E-Notebook


1. In the Collection Tree, click the collection

to which you would like to add the Reaction

Section.

2. Click the New Section menu icon on the

right side of the screen.

A menu appears, listing the sections you

may add.

3. Select Reaction.

A new blank Reaction Section appears in

the right frame.

Within a Reaction Section, you can record the

following:

• Chemical Structure – Draw and store chemical

structures and reactions using the Chem

& Bio Draw toolbar. You may import a

reaction drawing as well.

• Reaction Conditions – Record pressure,

temperature, and other conditions for the

reaction.

• Preparation for the Reaction — Enter the

procedure used to prepare for the reaction

in an AutoText field.

• Solvents - Records name, ratio and volume

for reaction.

Drawing and Analyzing

Reactions

You can draw a reaction using the Chem & Bio

Draw reaction field. When you draw a reaction,

the stoichiometry grid is automatically

populated with the properties of the reactants

and products. If you remove a reactant or product

from the stoichiometry grid, the corresponding

structure will be removed from the

reaction drawing.

The Chem & Bio Draw Toolbar allows you to

create a chemical structure by connecting frequently

used substructures together. For more

information about using the Chem & Bio Draw

Toolbar, please see the Chem & Bio Draw

User Guide.

Drawing a Structure or Reaction

To draw a reaction:

• Stoichiometry Table – The stoichiometry

table calculates and stores amount, formula

mass, molarity, density, volume, and many

other variables. This table is populated

automatically as you modify the reaction

drawing.

1. Click within a reaction field.

The Chem & Bio Draw toolbar appears.

2. Using the Chem & Bio Draw tools, draw a

reaction.

TIP: You can access a drawing menu by rightclicking

in the structure window. This menu

allows you to, among other things, copy and

paste structures.

Expanding the Drawing Window

To expand the drawing window:

30 Working with Reactions

Chapter 5


1. Double-click the title bar of the chemical

structure field.

The chemical structure field expands.

2. Using the Chem & Bio Draw tools, draw

the structure or reaction.

3. When you are finished editing, double-click

the frame of the chemical structure field to

return it to its original size in the form.

Analyzing a Reaction

After you draw a chemical reaction in the reaction

field of a reaction section, you can analyze

the reaction. When you analyze a reaction, the

Stoichiometry Grid of the reaction section is

automatically populated with information

about the reactants and products.

NOTE: You can automatically populate Stoichiometry

Grid only if information has not

already been added into it manually. For more

information about entering stoichiometric data

manually and adding reactant data automatically,

see “Adding Information” on page 35.

Based upon the chemical drawing in the reaction

field, new reactants and products are

added to the stoichiometry table. By default,

the names of the reactants and products are

determined from the molecular formulas in the

drawing.

When a value is calculated, the number of significant

digits is the minimum number of significant

digits for any cell in the table that has

been edited manually. If none of the table cells

have been edited, calculations are to four significant

digits.

The Reaction Toolbar

The reaction toolbar provides several features

for managing the reactants and products in

your reaction section.

The reaction toolbar normally appears just

below the reaction field.

See these topics for more information.

• Adding Structures with the Reaction Toolbar.

• Filtering Acronyms with the Reaction Toolbar.

• Defining a new Acronym with the Reaction

Toolbar.

• Deleting a Structure with the Reaction

Toolbar.

Name=Struct

The Name=Struct feature available in E-Notebook

Desktop 12.0 enables you to add the

names of compounds you draw in a reaction to

the stoichiometry grid automatically, using

ChemDraw’s Name=Struct feature.

NOTE: You need to have ChemDraw Ultra

installed on your computer to use this feature.

To convert a name to a structure:

1. Draw the structures in the reaction section.

Chem & Bio Office 2010 User Guide 31

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2. Save your changes. The structure names

appear in the stoichiometry grid.

If you make changes to the reaction drawing,

the names will be updated automatically.

4. At the top of the dialog box, click the Add

down arrow for a list of options for adding a

structure.

NOTE: If you manually change the name of

any structure in the grid, your change will NOT

be overwritten when you alter the corresponding

structure drawing.

Adding Structures with the Reaction

Toolbar

With the reaction toolbar, you can add reactants

and products from your Acronyms collections

in E-Notebook. There are two methods

for adding a structure with the reaction toolbar.

Adding a Structure

The Add on the reaction toolbar brings up a

dialog that allows you to select a structure and

add it to your reaction section.

To add a structure:

1. Click Add in the reaction toolbar.

The Select and Add Structure dialog

appears, displaying the acronyms in your

Reactants Folder.

2. In the Search In dropdown list, select the

structure list from which you want to

choose a structure.

3. In the right pane, select the name of a structure.

The structure itself appears in the left

pane.

The options are:

• Left of Arrow as Reactant – adds the structure

to the reaction drawing to the left of

the arrow, and adds it to the reactants table

in the grid.

• Above Arrow as Reagent – adds the structure

to the reaction drawing above the

arrow, and adds it to the reactants table in

the grid.

• Right of Arrow as Product – adds the

structure to the reaction drawing to the

right of the arrow, and adds it to the products

table in the grid.

• To Grid as Reagent – adds the structure to

the grid only, in the reactants table.

5. Select the desired option and click Add.

The structure is added to the reaction section in

the manner you selected.

There are several options for filtering the acronyms

displayed in the dialog. See Filtering

Acronyms with the Reaction Toolbar for more

information.

Quick Add

With the Quick Add, you can bypass the Add

Structure dialog and remove several steps from

the process of adding a structure to your reaction.

To add a structure with the Quick Add:

1. Select an acronym from the dropdown list

that appears in the reaction toolbar. This

32 Working with Reactions

Chapter 5


dropdown lists all of the acronyms in your

Reactants Folder.

2. Click the down arrow by the Quick Add in

the reaction toolbar.

The options for adding the structure are:

• Left of Arrow as Reactant – adds the structure

to the reaction drawing to the left of the

arrow, and adds it to the reactants table in

the grid.

• Above Arrow as Reagent – adds the structure

to the reaction drawing above the

arrow, and adds it to the reactants table in

the grid.

• Right of Arrow as Product – adds the structure

to the reaction drawing to the right of

the arrow, and adds it to the products table

in the grid.

• To Grid as Reagent – adds the structure to

the grid only, in the reactants table.

3. Select the option you desired.

4. Click Quick Add in the reaction toolbar.

The structure you selected is added to your

reaction.

Filtering Acronyms with the Reaction

Toolbar

The reaction toolbar offers several options for

filtering acronyms before selecting one to add

to your reaction section.

To jump to a particular structure:

1. Click the Add in the reaction toolbar.

The Select and Add Structure dialog

appears, displaying the acronyms in your

Reactants Folder.

2. Begin typing the name of the structure you

wish to select.

The selected structure changes to match the

text you have typed.

Applying a Filter

To filter the acronyms that are displayed in the

dialog

1. Click the Filter at the top of the dialog.

The Apply Filter window is displayed.

2. From the dropdown list, select either Names

Starting with or Names Containing.

3. Enter the text for the filter.

4. Click OK to close the Apply Filter window.

The filtered list of acronyms is displayed.

Removing a Filter

To remove a filter,

• Click the Remove Filter.

The filter is removed, and the entire list of

acronyms is displayed.

Defining a New Acronym

You can use the reaction toolbar to add new

acronyms to reactants collections in E-Notebook.

To do this:

1. In the reaction drawing, use the Chem &

Bio Draw tools to select the structure you

wish to define as an acronym.

2. Click the Define in the reaction toolbar.

A dialog appears, prompting you to select

the Acronyms collection where you wish to

add the new acronym.

3. Select the collection and click the Create

Here.

The structure you selected is added to the

collection.

4. Close the dialog.

Deleting a Structure

You can use the reaction toolbar to delete

structures from a reaction.

To do this:

Chem & Bio Office 2010 User Guide 33

E-Notebook


1. In the reaction drawing, use the Chem &

Bio Draw toolbar to select the structure you

wish to delete.

2. Click the down Delete in the reaction toolbar.

The structure is deleted.

The Stoichiometry Table

The stoichiometry table calculates and stores

stoichiometric data for a reaction. It is filled in

automatically as you modify a reaction drawing.

You may change values manually as well.

It is also possible to add reactants from the

Collection Tree to the stoichiometry table.

Depending upon your system configuration,

certain of these properties may not appear, or

additional properties may be present.

Reactant properties:

• Reactant – the text name of the reactant.

• MF (Molecular Formula) – the chemical formula

that shows the number and kinds of

atoms in a molecule of the reactant.

• Limit? – a yes or no value, indicating

whether the reactant is the limiting reactant

in the reaction.

• MW (Molecular Weight) – sum of the

atomic masses (atomic weights) of the

atoms in the molecular formula, as set forth

in the periodic table.

• Eq (Equivalents) – the proportion of the

reactant relative to the other components in

the reaction.

• Moles – the number of 6.023 * 10 23 molecules

of the reactant.

• Sample Mass- the total quantity of the reactant

sample.

• Vol (Volume) – the three-dimensional measurement

of the reactant, such as mL, L, etc.

• Molarity – the number of moles per volume

of the reactant.

• d (density) – the mass per unit volume of the

reactant.

• % Wt (% by Weight) – the percentage of

reactant in the sample.

• FM (Formula Mass) – sum of the atomic

masses (atomic weights) of the atoms in the

formula of the compound. This tends to be

a more general term than molecular weight,

and can be applied to compounds such as

ionic compounds.

• Reactant Mass – the total quantity of the

reactant.

• Loading - The number of reactant moles per

amount of the reactant sample.

Product Properties:

• Product – the text name of the product.

• MF (Molecular) Formula) – as above.

• Actual Mass – the actual mass of product

the reaction yields.

• Actual Mol – the actual number of moles of

the product that the reaction yields.

• Yield – the ratio of the actual amount to the

theoretical amount.

• Purity – the percentage of the actual amount

that is the product.

• MW (Molecular Weight) – as above.

• Eq (Equivalents) – the proportion of the

product relative to the other components in

the reaction.

• Theo Mol (Theoretical Moles) – the calculated

number of moles of the product that

the reaction yields.

• Theo Mass (Theoretical Mass) – the calculated

mass of product the reaction yields.

• FM (Formula Mass) – as above.

34 Working with Reactions

Chapter 5


• Loading - The number of product moles per

amount of the product.

See the following topics for more information:

• Adding Information

• Removing Reactants and Products

Adding Information

You can manually type stoichiometric information

into the stoichiometry table of a reaction

section, as well as add reactants from the

Collection Tree.

To manually add information to a Stoichiometry

Table:

1. In the reaction section, click a cell in the

stoichiometry table.

2. Type the information into the cell.

The information is saved, and the text is displayed

in blue. If you have entered a number

and there are default units associated with the

property, the units are displayed. (See “Numerical

Units” on page 79.

3. Repeat the process for other cells in the

table, if necessary.

To automatically enter reactant information

into the Stoichiometry Table:

1. Right-click a cell in the Reactants section

of the Stoichiometry Table.

A menu appears.

2. Select Add Reactant After to add a reactant

after the selected item, or Add Reactant

Before to add a reactant before the selected

item.

A new column (selected item) is added in

the stoichiometry table.

3. Type in the reactant information.

Removing Reactants and Products

You can remove all of the information pertaining

to a particular product or reactant from the

Stoichiometry Table automatically. If the reactant

you remove is the limiting reactant in the

reaction, the first remaining reactant becomes

the limiting reactant.

To remove a reactant or product from the stoichiometry

table:

1. Right-click the reactant or product you wish

to remove.

A menu appears.

2. Select Remove Product if it is a product, or

Remove Reactant if it is a reactant.

A message appears, asking you if you are

sure you want to delete the reactant or product.

3. Click Yes.

The reactant or product is removed from

the Stoichiometry Table as well as from the

reaction drawings, if already present.

Salts and Solvates

In a reaction section, it is easier to represent a

compound that is present in a salt or hydrated

form. You can enter a formula that accounts

for salts and hydrates.

To enter a formula:

1. In the stoichiometry grid, double-click the

molecular formula cell.

A dialog appears.

Chem & Bio Office 2010 User Guide 35

E-Notebook


Select a salt code or solvate from the dropdown

list. This list displays all of the salt codes

and solvates in your User Configuration folder.

2. Click OK to close the dialog.

The formula you entered appears in the stoichiometry

grid.

Adding New Solvates and Salts

To add a solvate or salt that does not appear in

the drop-down list:

1. Click the New Solvate. (Or, to add a new

salt code, click the New Salt Code).

A dialog appears and you can browse to

solvates or salts in your User Configuration

folder.

2. Click New Solvate (or New Salt Code) and

enter the structure and name.

Autotext

With the AutoText feature, you can add predefined

fragments of text to a field. This allows

you to create the contents of a text field

quickly. You may also add text that is pulled

from other fields, for example, reaction properties

or values in the stoichiometry grid of a

reaction section. As you update the reaction

drawing and the stoichiometry grid, your

changes are reflected in the AutoText.

The example below shows the Preparation

field of the reaction section.

See the following topics for more information:

• Inserting Reactants and Products with Auto-

Text- provides instructions for adding and

managing reactants and products in the text.

• Inserting Reactants and Products from the

Stoichiometry Grid– provides instructions

for adding and managing reactants and

products in the text.

• Adding items from the AutoText Pane - provides

instructions for adding AutoText

items (as shown in the left pane of the

image above) to the text.

36 Working with Reactions

Chapter 5


• Inserting Links with AutoText- offers instructions

for adding and managing hyperlinks

in the text.

• Inserting Custom AutoText – provides

instructions for using the Custom AutoText

dialog.

• Creating New AutoText Definitions – provides

instructions for setting up your own,

custom AutoText.

Inserting structure names with AutoText

When you modify reactants and products in the

reaction drawing or stoichiometry grid, the

AutoText is updated automatically.

Inserting structure names from the

Stoichiometry Grid

To insert a reactant or product from the stoichiometry

grid:

1. Right-click within the text field.

A menu appears.

2. Select Insert, followed by the name of the

reactant or product.

The name and properties of the reactant or

product you selected are inserted. The text

appears in purple, and is updated automatically

if you change the name or properties in the stoichiometry

grid.

You may also use the reactants/products to

populate the AutoText.

To do this:

1. With your cursor in the text field at the

point where you wish to insert the reactant

or product, click the reactants/products.

A menu appears.

2. Select one of the options:

• Insert Reactant... – allows you to browse to

a new reactant, and add it to the text and

stoichiometry grid.

• Insert Product... – allows you to browse to a

new product, and add it to the text and stoichiometry

grid.

• Insert “[Reactants]” AutoText – inserts the

text [Reactants], which you may then rightclick

to select a reactant from the stoichiometry

grid, or to browse to a new reactant.

• Insert “[Products]” AutoText – inserts the

text [Products], which you may then rightclick

to select a product from the stoichiometry

grid, or to browse to a new product.

The text is updated automatically if you

change the properties of the reactant or product.

Adding Items from the AutoText Pane

You can populate the text field by selecting

items from the AutoText pane. If you wish to

add your own custom AutoText to this pane,

set up your own AutoText definitions. See Creating

New Autotext Definitions.

To add AutoText items to the text field:

1. Click the drop down arrow next to the font

name [Arial] in the upper left corner of the

text field.

Chem & Bio Office 2010 User Guide 37

E-Notebook


The AutoText pane appears, listing the

available AutoText items.

2. Double-click any of the items in the list to

insert the corresponding AutoText.

Text that can have multiple values appears in

red.

A dialog appears, prompting you to enter

the text that will appear with the link.

3. Enter the text or accept the default text, and

click OK.

The link appears in the text field.

4. Double-click the link to browse to its target.

Alternatively, you may right-click within the

text field, and select Insert Link from the menu

that appears and follow the steps given above

(2-4).

Inserting Custom AutoText

You can insert custom AutoText in a text field.

To do this:

3. Right-click the text within brackets to view

a list of the options and select one of the

values.

In the example shown below, several possible

options are listed for the extraction solvent.

You may right-click the red text again to modify

your selection.

Certain items in the AutoText list may refer to

other data in the section. For example, doubleclicking

Conditions in the Autotext pane automatically

fills the Reaction Conditions into the

text field.

Inserting Links with AutoText

You can insert links in a text field to other sections

and collections

1. Click Link in the toolbar of the text field.

A dialog appears, prompting you to select a

collection or section you want to link to.

2. Select the collection or section and click

OK.

1. Right-click in the text field.

A menu appears.

2. Select Insert Custom AutoText.

The Insert Custom AutoText dialog

appears.

3. Select one of the AutoText items in the left

frame.

4. Click Insert.

The text appears in the text field.

5. Right-click the inserted text to see the

options associated with it.

Creating New Autotext Definitions

Depending upon your system configuration, it

may be possible for you to set up your own

AutoText definitions for use in E-Notebook

text fields. You can then use these predefined

fragments to add text to the styled text field

automatically.

1. In the collection tree, right-click the User

Configuration and select New>AutoText Definitions.

(Or, select an existing AutoText

collection to modify by clicking the collection

in the tree).

2. Enter a name for the new collection.

38 Working with Reactions

Chapter 5


3. In the new AutoText Definitions window,

click New Section.

4. Right-click the gray bar under Usage and

select New Row.

5. Right-click the new row and select Add

Property.

6. In the Add Property dialog box, select Field

and Section Type.

7. Enter the following information:

• Section Type – select a value from the dropdown

list if you would like the AutoText to

apply to a particular type of section exclusively.

For example, you may only want to

use the text in reaction sections. If you do

not select a section type, the AutoText will

be associated with all text fields, in all types

of sections.

• Field Type – if you select a Section Type,

you may select a particular field within it. If

you leave the Field blank, the AutoText will

apply to all text fields in the section type.

• Items – These are the AutoText items that

will appear in the AutoText list. Double

clicking the name of an item will fill in the

corresponding text. Click the New AutoText

Item to add a new item.

• Keywords – These are the keywords, or

choices, that you may define for a particular

item. Click the New Keywords to add new

AutoText keywords.

In the example below, AutoText has been set

up so that a user may automatically enter a sentence

for a machine type, and select from a list

of several machine types. Double-clicking

Machine Type in the AutoText list for any

styled text field would cause the corresponding

sentence to appear. Then, the user would rightclick

[MACHINE TYPES] to select from the

list of machine types.

NOTE: The title of the keywords tab must

match the field descriptor exactly. In this case,

MACHINE TYPES is the name of the keywords

tab, and [MACHINE TYPES] appears in the

AutoText item.

Autotext Based on Other Fields in the

Section

You may also set up AutoText that will fill in

the values from property lists and tables in a

section. To do this, you use a field name as a

keyword in an AutoText Item. The keywords

and the field names must match exactly in

order for the substitution to take effect.

Property Lists

For the AutoText Item to populate the styled

text field with all of the properties in a property

list, simply use the name of the property list as

the keyword in the AutoText Item. For example,

say there is a Conditions field, which is a

property list that contains reaction conditions.

The AutoText Item Conditions: [CONDI-

TIONS] (without quotes) will fill in all of the

properties in the Conditions property list - for

Chem & Bio Office 2010 User Guide 39

E-Notebook


example, Conditions: (Pressure: 200 atm,

Temperature: 100 °C).

The keyword CONDITIONS followed by a

property name, such as [CONDITIONS:Temperature],

will populate the styled text field

with that specific property, for example., Temperature:

100 °C.

Tables

As with Property Lists, the AutoText Item

referring to a Table should contain bracketed

UPPERCASE keywords. For example:

[REACTANTS1] is added dropwise to a 500

ml round-bottom flask charged with

[REACTANTS2] in [SOLVENT].

[REACTANTS1], [REACTANTS2], and

[SOLVENT] are replaced by the complete

description of a compound from one of these

tables. REACTANTS1 refers to a column in

the table REACTANTS (or, if the table is pivoted

with properties appearing as columns, it

refers to a row). REACTANTS is the name of

the table field.

In this case, the number — such as in

REACTANTS1 and REACTANTS2 — is

used to indicate that different compounds are

to be used in the AutoText. In order to determine

which reactant is to be used where more

than one is present in the reactants table, the

user right-clicks the keyword that appears

within brackets. This displays a popup menu

containing all of the possible values. Choosing

a value will substitute the data. If other keywords

refer to the same compound (for example,

REACTANTS1), they will be substituted

as well.

The description that populates the styled text

field consists of the name (or text of the form

Reactant 1 if the name is absent) followed by a

list of the properties of that compound.

To select individual properties, an AutoText

Item can contain a keyword followed by a

property name, for example, [REAC-

TANTS:Amount] is replaced by the value

from the Amount property for a reactant.

Section Names as Categories

If you add multiple sections to an AutoText

Collection, the section names will appear as

categories in the AutoText list. For example,

Reaction and Workup are two section names

that appear as categories below:

Solvents

You can populate the solvents in the reaction

section from the solvents folder in the User

Configuration Folder. These solvents are

named shortcuts for the commonly used solvents.

To enter a solvent into the Solvents Table:

1. Right-click a cell in the Solvents Table of

the reaction section.

A menu appears.

40 Working with Reactions

Chapter 5


2. Select Add Solvent After to add a solvent

after the selected item, or Add Solvent

Before to add a solvent before the selected

item.

A dialog box appears.

3. Select a solvent from the list. This list displays

all of the solvents in your User Configuration

folder.

4. Click Add to close the dialog.

The formula you entered appears in the solvents

table.

If a solvent which you wish to add in the solvents

table is not listed in the Solvents Folder

in your User Configuration Folder, then you

can manually add it in the table cell.

To do this:

1. Repeat the first two steps in the procedure

above.

The Add Solvent dialog appears.

2. Select the box Add Blank Solvent at the bottom

of the dialog box.

3. Click Add to close the dialog.

A blank row is added to the solvents table

in the reaction section where you can enter

the solvent of your choice manually.

4. Repeat the process for other cells in the

table, as necessary.

Adding a New Solvent Collection

To add a new solvent collection to your user

configuration folder:

1. Right-click your user configuration collection

in the collection tree and select

New>Solvents Folder.

A new Solvents Folder appears in the Collection

Tree and you are prompted to

rename it.

2. Enter a name for the folder.

3. Right-click the new solvents folder and

select New>Solvents.

A Solvents collection appears, and you are

prompted to rename it.

4. Enter a name for the solvents collection.

5. In the right pane, click New Solvent Table.

The solvents section containing the three

columns, Solvents, R Values, and Density

appears.

6. Right click the table header and select Add

Row.

7. Enter a value for the Solvent property, the R

values, and the Density property.

8. Click Save.

9. Repeat steps 6-8 to add more solvents.

Reactants

Reactants are named shortcuts for a commonly

used compounds. These could be either common

reagents, or named compounds that you

use frequently.

Adding a New Reactant to an Existing

Reactant Collection

To add a new reactant section to an existing

collection.

1. Browse to the Reactants collection to which

you wish to add the Reactant, clicking the

collection in the Collection Tree to select it.

The Reactants collection appears, with the

existing reactants displayed in the right

frame.

2. Click the New Acronym in the right frame.

A new acronym section appears.

3. To rename the section from the default

name (Acronym), right-click its section tab

and select Rename Section from the menu

that appears. Type a name in the text box

that appears.

Chem & Bio Office 2010 User Guide 41

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4. Draw or import the structure using the

Chem & Bio Draw tools.

The formula and molecular weight properties

are updated automatically.

5. Enter text for the compound name.

This text will be displayed in the table of

contents for the Reactants Folder that contains

this reactant. (Click the Reactants

Folder in the Collection Tree to view its

table of contents).

Adding a new Reactant Collection

You can add a new Reactant Collection to your

User Configuration folder in E-Notebook.

To add a new Reactant Collection:

1. Right-click your User Configuration collection

in the Collection Tree and select

New>Reactants Folder.

A new Reactants Folder appears in the Collection

Tree and you are prompted to

rename it.

2. Enter a name for the folder.

3. Right-click the Reactants Folder and select

New>Reactants.

A Reactants collection appears, and you are

prompted to rename it.

4. Enter a name for the Reactants collection.

5. Click the New Acronym in the right frame.

A new Reactant section appears.

You may populate reaction sections with the

properties of reactants. See “Adding Information”

on page 35 for more information.

Batch Explorer

Before performing the Batch Explorer, two

requirements are there:

• Creating a Task

• Creating a Template

To create a task:

1. Right click the User Configuration folder.

2. Select New>Tasks.

3. Right click on the Tasks folder and select

Batch Explorer.

For creating Template see “Templates” on

page 23. Add a reaction section to the templates

and draw reaction in this template.

There are different options in the Batch

Explorer to view the successor or predecessor

of the batch or compound created:

• View Batch Explorer

• View Synthetic Path

• Create Page As Next Step In same 'Untitled

Templates'

• Create Page As Next Step In Another 'Untitled

Templates'

• Create step Link To Existing 'Untitled Templates'

View Batch Explorer

View Batch Explorer option allows you to

view the reactants and products of the current

page template in the form of reaction tree.

To view the Batch Explorer in the current

Notebook:

1. Click the Batch Explorer tool icon in the

Reaction Section.

With the Batch Explorer, you can view a reaction

tree showing successors and predecessors

of a selected batch or compound.

42 Working with Reactions

Chapter 5


A menu appears.

2. Select View Batch Explorer. The Batch

Explorer section appears showing the reactants

and products of the current page template

in the form of reaction tree.

View Synthetic Path

View Synthetic Path option allows you to view

all the successors and predecessors of the current

page template.

To view synthetic path:

1. Click Batch Explorer tool icon in the reaction

section.

A menu appears.

2. Select View Synthetic Path option from

the Batch Explorer menu. The Batch

Explorer section appears showing the successors

and predecessors of the current

chemistry experiment.

Create Page/Reaction Page As

Next Step In same Notebook

This allows you to create a new page/reaction

page within the same notebook.

To do this:

1. Select the product of the reaction.

2. Click the Batch Explorer and select the

option from the menu “Create Page/Reaction

Page As Next Step In same Notebook”.

A dialog box appears.

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E-Notebook


3. Select the template and click Select.

A dialog box for successful link setting

message and asking you to whether to navigation

from reaction section of the selected

notebook collection.

4. Click Yes for navigation.

Create Page/Reaction Page As

Next Step In Another Notebook

This allows you to create a new page/reaction

page in another notebook.

To do this:

1. Select the product of the reaction.

2. Click the Batch Explorer and select the

option from the menu “Create Page/Reaction

Page As Next Step In another Notebook”.

A dialog box appears.

3. Select the notebook in which you want to

create page/ reaction page.Click Select.

4. A dialog box appears.

5. Select the Template the reaction page.

A dialog box for successful link setting

message and asking you to whether to navigation

from reaction section of the selected

notebook collection.

6. Click Yes for navigation.

Create Step Link to Existing

Notebook

This allows you to create a between two existing

reactions same/existing notebook as a

result one product of a reaction is reactant in

the other.

To do this:

1. Select the product of the reaction.

2. Click the Batch Explorer and select the

option from the menu “Create Step Link to

Existing Notebook”.

A dialog box ‘Select a Section That Contains

a Reaction’ appears.

3. Select the page/reaction page that contains

a Reaction section with a molecule that will

be reactant in the other.

A dialog box for successful link setting

message and asking you to whether to navigation

from reaction section of the selected

notebook collection.

4. Click Yes for navigation.

44 Working with Reactions

Chapter 5


6

Spectra and Other Sections

This chapter continues the description of sections

begun in the previous chapter. For a list

of the preconfigured sections covered in this

chapter, see “Pre-configured Sections” on page

29.

Ancillary Data Sections

You can use an ancillary data section to associate

a file, such as a PDF or PowerPoint file,

with a page/reaction page. When you import

the file, the checksum, source path, and source

file name are populated automatically.

Although the file cannot be viewed from

within E-Notebook, it can be exported to a

selected location, and then opened and viewed

or edited from there.

1. In the Collection Tree, click the Page or

reaction page to which you would like to

add the Ancillary Data Section.

2. Click the New Section in the right frame.

A list of the section types that can be added

appears.

3. Select Ancillary Data.

A new Ancillary Data section appears in

the right frame.

4. To save the section, go to File>Save.

5. Click the Import to import a file.

A menu appears.

6. Select Import Ancillary Data.

A dialog box appears, and you are

prompted to select the file.

7. Select the file and click Open.

The type of file and its size are displayed in

E-Notebook.

To edit a stored document file, you must first

export it to another location.

1. Click the import tool.

A menu appears.

To create a new Ancillary Data section:

2. Select Export....

A dialog appears prompting you to select a

location for the exported file.

3. Enter a destination for the file and a file

name, and click the Save.

Chem & Bio Office 2010 User Guide 45

E-Notebook


4. Open the appropriate application, and open

the file you created.

5. Edit the file as you normally would.

6. Save the file.

7. From the section, click the import tool

again.

A menu appears.

3. Select Image.The new section appears

within the page.

4. To add an image or document, go to Import/

Export>Import Image and browse to the file

to import. The image appears in the image

pane.

8. Select Import....

A dialog appears and you are prompted to

select the file to import.

9. Select the file and click Open.

The edited document with your changes is

stored in E-Notebook.

To clear a stored document file from a section

in E-Notebook:

1. Click the import tool.

A menu appears.

2. Select Clear Ancillary Data.

You are prompted to confirm whether you

wish to clear the document file.

3. Click OK.

The file is cleared.

Captured Image Sections

Captured Image Sections let you import,

export, view, and annotate images and documents,

using the same tools as Adobe Reader

software. The section supports a wide variety

of file types, such as JPG, GIF, PNG, TIFF and

BMP.

To create a new Captured Image Section:

1. In the Collection Tree, click the page or

experiment to which you would like to add

the section.

2. Click New Section. A list of the section

types that can be added appears.

Managing Spectral data

You can manage your spectral data easily and

effectively using Spectrum and Spectra sections.

There are two types of sections for spectra.

Each type contains properties, and notes for

each spectrum.

• Spectrum Section – this section can contain

a single spectrum.

• Spectra Section – this section can contain

multiple spectra, organized in subsections.

To create a new Spectrum section:

1. In the Collection tree, click the page or

experiment to which you wish to add the

Spectrum section.

2. Click the New Section button.

A menu appears, listing the types of sections

that you may add.

3. Select Spectrum.

46 Spectra and Other Sections

Chapter 6


The new section appears in the page.

To create a new Spectra section for multiple

spectra:

1. In the Collection Tree, click the page/reaction

page to which you wish to add the

Spectra section.

2. Click the New Section button. A list of the

section types that can be added appears.

3. Select Spectra.

The new section appears within the page.

You may add as many spectrum subsections

as you wish by clicking the New Spectrum

button.

Adding a Spectrum

To add a spectrum:

1. From within a section with a spectrum

field, click the import/export button.

A menu appears.

2. Select Import Spectrum.

The Import Spectrum dialog box appears

and you are prompted to select a spectrum

image file.

spectrum section, you can replace the image.

To do this, you may import a new image, See

“Captured Image Sections” on page 46. The

new image will replace the old. Or, you may

copy an image from another section.

To replace a spectrum image:

1. From within the section containing the

image you wish to copy, click the import/

export button.

A menu is displayed.

2. Select Copy Spectrum.

3. Browse to the section containing the spectrum

image you wish to replace.

4. Click the import/export button.

5. Select Paste Spectrum. The new spectrum

image replaces the image in the section.

Zooming in on a Spectrum

Peak

To zoom in on a spectrum peak:

1. Click the spectrum image and drag your

mouse to draw a box around the area you

wish to zoom.

2. Click within the box. The zoomed view

appears.

3. To zoom out again, simply right-click in the

spectrum image.

Other Fields in a Spectra Data

After you add a spectrum, you can include

information about it.

Spectrum Properties – use this list to store Analyst,

Type, and Date.

Replacing a Spectrum

If you would like another spectrum image to

take the place of an image within a spectra or

Chem & Bio Office 2010 User Guide 47

E-Notebook


Notes – Record any notes that pertain to a

Spectrum in the text field.

See “Adding Properties” on page 63. for more

information.

Property After, to add a property after the

current property.

Table Sections

You can use table sections to organize the

chemical properties of compounds that interest

you. You can add properties to a table, pivot a

table, resize columns and rows, and organize

columns and rows. You can also insert links to

other sections or collections into a table.

4. In the Add Property dialog box, highlight

the properties to add and click Add.

The property appears as a column in the

table, immediately in front of the location

you selected.

To add a row to:

Adding Columns and Rows

You can add columns and rows to a table in E-

Notebook.

To add a column:

1. Browse to the section that contains the

table.

2. Right-click the table at the location where

you would like to add the column.

A menu appears.

3. Select Add Property Before, to add a property

before the current property, or Add

1. Right-click the table where you would like

to add the row.

A menu appears.

2. Select Add Row Before, to add a row before

the current row, or Add Row After, to add a

row after the current row.

NOTE: If the Table has been pivoted, you

would select Add Property to add a row, and

Add Row to add a column. (Pivoting transposes

the rows and columns in the table).

Removing Columns and Rows

You can remove columns and rows from a

table.

To remove a column:

48 Spectra and Other Sections

Chapter 6


1. Right-click the column or property you

wish to remove from the table.

A menu appears.

2. Select Remove Property.

A dialog box appears, asking you if you are

sure you want to delete the property from

the table.

3. Click Yes. The column is removed.

NOTE: If the table has been pivoted, rightclick

a row to remove a property.

To remove a row:

1. Right-click the row to remove from the

table.

A menu appears.

2. Select Remove Row.

A dialog box appears, asking you if you are

sure you want to delete the row from the

Table.

3. Click Yes. The row is removed.

Organizing Columns and Rows

You can easily rearrange rows and columns in

a table, organizing them so that the information

is displayed more effectively. You can move

columns left or right, move rows up or down,

and sort data in the table in ascending or

descending order.

To move a column left or right:

1. In the table, right-click the column you

wish to move.

A menu appears.

2. Select Move Property Left or Move Property

Right.

The column is moved either one place to

the left or one place to the right, depending

upon your selection.

To move a row up or down:

1. In the table, right-click the row to move. A

menu appears.

2. Select Move Row Up or Move Row Down.

The row is moved either up one place or

down one place in the table, depending

upon your selection.

Sort Data by a Property

To sort the table by a particular property:

1. Right-click the row or column corresponding

to the property by which you wish to

sort the table.

A menu appears.

2. Select either Sort Ascending or Sort

Descending.

The data is sorted according to the values of

the property you selected.

Resizing Columns and Rows

To resize a row or column:

1. Move the cursor to the border of the row or

column in a table.

A double-headed arrow appears.

2. Drag the border in the direction you desire

until the column or row is the correct size.

The resized column or row appears in the

table.

To autofit a column or row to the size of its

contents, move your cursor to the name of the

row or column and double-click. The column

or row resizes.

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E-Notebook


Pivoting a Table

When you pivot a table, its rows become columns

and its columns become rows. Pivoting a

table does not alter the data.

To pivot a table:

1. Right-click the table.

A menu appears.

2. Select Pivot Table.

The rows and columns of the table are

transposed.

Figure 6.1 A table before and after pivoting.

Adding Information

There are a number of ways to add information

to a table cell. Data may be text, numbers,

dates, or structures. Your system configuration

determines what type of data it is possible to

add to any particular cell.

There are three ways to add information to a

cell:

• Choose a value from the drop-down menu

that appears in the cell. You will use this

option when the cell has a list of possible

values associated with it.

• Enter a value using the keyboard.

• Draw a Chemical Structure — See Structures

and Images for more information.

In some cases, your system administrator may

have configured E-Notebook such that a particular

property in the table has one or several

of the following qualities:

• Read-Only – certain properties in the table

may be for display only, and it may not be

possible to edit them.

• Required – it may not be possible to delete a

particular property from a table. If a property

is required, you will be presented with

an error message when you attempt to

delete it.

• Not Blank – it may be necessary to enter a

value for a particular property before you

can perform a transition on the collection.

For example, an experiment collection may

be set up such that it is necessary to enter an

equipment id before you can close the

experiment. If this is the case, you will be

prompted to add the values to the table

when you attempt to perform the transition.

See “Performing a Collection Transition”

on page 25. for more information about

transitions.

• Validated - Values you enter into a table

may be checked against an external database,

to ensure that they are valid values. In

50 Spectra and Other Sections

Chapter 6


this case, if you enter an invalid value, you

will receive an error message, and E-Notebook

will not accept the value.

• Enumerated from a database – values displayed

in a drop-down list for any particular

cell may be pulled from an external database.

Certain numerical properties in a table may

have units associated with them. See “Numerical

Units” on page 79. for more information.

The Edit Structure dialog box appears.

You can use the Chem & Bio Draw tools to

edit the structure or copy an image file into

the field.

Structures and Images

Tables may contain chemical structure fields,

which you can use to manage data about the

structures of compounds that interest you. You

can also add standard image files to the chemical

structure fields.

To add a structure or image to a table:

1. Double-click a table cell corresponding to a

structure or image.

The Edit Structure dialog box appears,

and you can use the Chem & Bio Draw

tools to draw the structure. Or, you may

copy a standard image file into the field.

2. Draw the structure or paste in the image and

click OK. Copy in an image by right-clicking

within the field and selecting Edit, then

Paste.

The structure or image appears in the table.

Editing a Structure or Image

To edit a structure or image in a table:

1. Double-click the table cell containing the

structure or image.

2. Edit the structure or change the image and

click OK.

The modified structure or image appears in

the table.

Delete a Structure

To delete a structure or image from a table:

1. Double-click the cell of the structure or

image you wish to delete.

The Edit Structure dialog box appears.

2. Using the Chem & Bio Draw tools, select

the entire structure or image and delete it.

3. Click OK.

The dialog box closes and the structure or

image is deleted from the table.

Changing Information in a

Table Cell

The data type of a cell determines what type of

information you add to a cell. For example,

Chem & Bio Office 2010 User Guide 51

E-Notebook


you can only draw a chemical structure in a

cell with a data type of structure.

Depending upon the data type, you can edit the

information in a cell one of the following

ways:

• Choose another value from the menu that

appears in the cell – use this option when

the cell has enumerated values associated

with it.

• Enter a value with the keyboard.

• Edit a Chemical Structure or change and

image – See Structures and Images for

more information.

Certain numerical properties in a table may

have units associated with them. See “Numerical

Units” on page 79. for more information.

Creating a Reference within a

Table Cell

Within a table cell, you can add a link to

another collection/section in E-Notebook or a

link to an external URL. This makes it easy to

browse back and forth between related data.

Adding a Link from a Table to a Collection

To add a link from a table cell to a collection in

E-Notebook:

1. In the Collection Tree, click the collection

containing the table, then select the section

containing the table.

2. Click the table cell to which you wish to

add the reference.

3. In the Collection Tree, click the collection

you would like to reference and, holding

the mouse down, drag the collection into

the upper-left corner of the table cell.

4. Release the mouse.

The reference is created, and the text in

table cell is converted into blue colored

hyperlink.

You can navigate to the collection you have

referenced by clicking the hyperlink text, and

click the Back arrow to return to the table.

Alternatively, you may right-click the collection

you wish to reference and select Copy.

Then, right-click within the table cell to which

you are adding the reference, and select Paste

Reference.

Adding a Link from a Table to a Section

To add a link from a table cell to a section in E-

Notebook:

1. In the Collection Tree, click the collection

containing section that you would like to

reference, then select the section.

The section to which you would like to

make a reference appears.

2. Right-click the Section menu icon, and

select Copy Section.

3. In the Collection Tree, click the collection

containing the table to which you are adding

the reference, and then click the section

that contains the table.

4. Right-click within a table cell and select

Paste Reference from the menu that

appears.

The reference is added to the table cell.

Clicking the hyperlink will display the section

you have referenced.

52 Spectra and Other Sections

Chapter 6


Adding a Link from a Property List to an

External URL

To add a link from a table cell to an external

URL or an intranet URL:

1. Right-click within the table cell to which

you wish to add the reference.

A menu appears.

2. Select Edit Reference.

The Edit Reference dialog appears.

3. Enter the URL and click OK.

The reference is added to the table cell. Clicking

the hyperlink will display the URL you

have referenced.

MS Word Sections

Use MS Word sections to manage information

that you record in Microsoft ® Word.

To create an MS Word Section:

1. In the Collection Tree, click the page or

experiment to which you would like to add

the MS Word Section.

2. Click New Section in the right frame and

select MS Word Document.

A new Word document appears in the right

frame.

Importing an existing Word Document:

1. Click the import/Export icon in the right

frame.

A menu appears.

2. Select Insert MS Word Document.

A file system dialog box appears.

3. Browse to the file and click Open.

The file appears in the MS Word field.

Exporting a Word Document:

1. Click the import/Export icon in the right

frame.

A menu appears.

2. Select Export MS Word Document.

A dialog box appears.

3. Enter a name for the file and click Save.

Editing Word document:

4. Open Microsoft Word, and open a file you

created.

5. Edit the file.

6. Save the file in MS Word.

7. From the E-Notebook section that contains

the MS Word field, click the import icon

again.

A menu appears.

8. Select Insert MS Word Document.

9. Select the file you edited.

The document with your changes appears

in E-Notebook.

Displaying MS Word Toolbars

The toolbars displayed with an MS Word field

in E-Notebook are the toolbars that appear

when you open MS Word. If you would like

Chem & Bio Office 2010 User Guide 53

E-Notebook


additional toolbars to appear with your MS

Word fields, close E-Notebook and open MS

Word. Then, change your settings for display

or hiding of tool bars in MS Word. When you

restart E-Notebook, it will use the settings

established by MS Word.

If you would like access to additional toolbars

within an MS Word field when you are editing,

right-click the toolbar at the top of the field to

select other toolbars to display. The toolbars

you add will persist until you navigate away

from the section.

Spelling Check

To conduct a spelling check on an MS Word

field, click within the field to select it, then hit

F7 on the keyboard.

MS Excel Sections

Use Microsoft Excel sections to manage Excel

spreadsheets in E-Notebook.

3. Select MS Excel Spreadsheet. A new MS

Excel Spreadsheet appears.

4. Edit the spreadsheet as desired.

To import an MS Excel document:

1. Click the import tool icon for the MS Excel

field.

A menu appears.

2. Select Import MS Excel Spreadsheet.

A dialog box appears, and you are

prompted to select the file.

3. Browse to the file, then click open.

The spreadsheet appears in E-Notebook.

The section of the spreadsheet that was

most recently active is displayed.

To export the file:

1. Click the import tool icon.

A menu appears.

2. Select Export MS Excel Spreadsheet.

A dialog appears prompting you to select a

location for the exported file.

3. Enter a destination for the file and a file

name, and click Save.

The file is exported to the location you

selected.

To clear an MS Excel file from a section in E-

Notebook:

To create a new, MS Excel Section:

1. In the Collection Tree, click the page or

experiment to which you would like to add

the section.

2. Click New Section.

A list of the section types that can be added

appears.

1. Click the import tool icon.

A menu appears.

2. Select Clear MS Excel Spreadsheet.

You are prompted to confirm whether you

wish to clear the document file.

3. Click OK.

The file is cleared.

54 Spectra and Other Sections

Chapter 6


7

Managing Sections

A section is a form for E-Notebook data. Just

as you would use pages in a paper notebook for

recording various types of data, you can use

sections in E-Notebook for recording reactions,

spectra, and other types of information.

You can also use templates to set up sections

automatically and uniformly. See “Templates”

on page 23. for more information.

Your system configuration determines the

types of sections that are available in E-Notebook.

A menu appears, listing the types of sections

that you may add.

Creating a Section

You can create a new section within a collection.

To create a section:

1. In the Collection Tree, click the collection

in which you wish to add the section.

If the collection already contains sections,

they appear in the right frame.

2. Click the New Section icon in the right

frame.

3. Select the type of section you wish to create.

A new section of that type appears.

Your system configuration determines which

types of sections can be added to which types

of collections. These rules are flexible, allowing

you to customize E-Notebook to your

workflow.

Modifying a Section

To modify a section within a collection:

Chem & Bio Office 2010 User Guide 55

E-Notebook


1. Go to the section you wish to change.

2. Edit the data in the section.

It is only possible for one E-Notebook user to

edit the sections in an individual collection at

any given time. If another user is editing a particular

collection and you attempt to edit it, you

will be presented with a message informing

you that the collection is locked for editing by

the other user.

In some cases, you will only have Read permission

for a collection, meaning that you may

view the collection but not edit it.

See Changes and Audit Trail in the E-Notebook

Administrator Guide for more information

about saving your changes.

Removing a Section

To remove a section from a collection:

1. Right-click the tab for the section to

remove.

2. In the context menu that appears, click

Delete Section.

A message appears, prompting you to confirm

that you wish to remove the section.

3. Click Yes.

NOTE: Your system configuration may prevent

you from deleting some sections. For example,

if you are working with a collection that has

Visual Display of Changes enabled, you cannot

delete a section.

In some cases, you may delete sections only if

no data has been added to them.

Moving a Section

You can organize sections within a collection.

To move a section:

1. Go to the section to move.

2. Right-click the section menu icon.

A menu appears.

3. Select Move Up to move the section the left

a single position, or select Move Down to

move the section to the right a single position.

The section is moved in the way you

selected.

4. Repeat the process until the section is in the

desired location.

Cutting and Pasting a

Section

To cut a section and paste it into another collection:

1. Go to the section you wish to cut.

2. Right-click the section menu icon.

The section menu appears.

56 Managing Sections

Chapter 7


3. Select Cut Section.

4. In the Collection Tree, click the collection

in which you would like the copied section

to appear.

5. Right-click the section menu icon.

The section menu appears.

6. Select Paste Section.

The section appears in the right frame.

NOTE: Your system configuration determines

where you may paste sections of various types.

Renaming a Section

To rename a section:

1. Go to the section you wish to rename.

2. Right-click the section menu icon.

The section menu appears.

3. Select Rename Section.

A dialog box appears, and you are

prompted to type in a new name for the section.

4. Type in a new name and click the Rename.

The dialog box closes and the new name of

the section appears.

NOTE: Your system configuration may prevent

you from renaming certain sections.

Duplicating a Section

1. Go to the section you wish to duplicate.

2. Right-click the section menu icon.

The section menu appears.

3. Select Duplicate Section.

A copy of the section appears.

In some cases, your system configuration may

prevent you from duplicating a particular section

within a collection.

To duplicate a section from one collection to

another:

1. Go to the section you wish to duplicate.

2. Right-click the section menu icon.

The section menu appears.

3. Select Copy Section.

4. In the Collection Tree, click the collection

in which you would like the copied section

to appear.

5. Right-click the section menu icon.

The section menu appears.

6. Select Paste Section.

A copy of the section appears in the right

frame.

NOTE: In some cases, your system configuration

may prevent you from copying the section

into a collection.

For Exporting Sections to MS Word and Printing

Section see chapter “Managing Collections”

on page 19.

To duplicate a section within a collection:

Chem & Bio Office 2010 User Guide 57

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58 Managing Sections

Chapter 7


8

Saving the Collection Changes

E-Notebook provides auditing and change control

features that you can use to save the

changes in a collection.

For every change made to E-Notebook data, an

audit trail records the logged in identity of the

user, the date, and the time. This is done automatically

when you add, delete, or update data.

The audit trail information is stored in the E-

Notebook database.

You can also view prior versions of collections

and, if Visual Display of Changes is enabled,

you can view and print the changes that were

made to the data in a collection.

Working With Save Icon

The Save icon appears in the main menu toolbar.

The appearance of the icon changes to

indicate various conditions:

• When you first select a collection in the collection

tree, the Save icon is disabled. This

indicates that you have not made unsaved

changes to the collection, and that you have

not opened the collection for editing.

• If you perform any modifications in any of

the section of a collection, the Save icon

gets enabled. This indicates that you have

locked the collection for editing and other

E-Notebook users may not edit it at this

time.

• The enabled Save icon also indicates that

you have made some unsaved changes to

the collection.

In addition, E-Notebook may be configured so

that you can annotate the changes you make to

collections by providing reasons for them.

Saving a Collection

There are several ways save changes to a collection:

• Click the Save icon.

• Select the collection in the collection tree

and go to File>Save or Save and Annotate.

• Browsing to another collection.

• Use the autosave function to periodically

save your work (see your system administrator

to set this up).

• Close E-Notebook.

Annotate and Save:

You can annotate a file with information that

you may not want appearing in the file. For

example, you can record changes you plan to

make or errors that you have fixed without

your comments appearing in the file itself.

To annotate a file:

1. Select the file in the collection tree.

2. Go to File>Save and Annotate.

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You are prompted to enter an annotation.

3. Click Save. The version is saved and is

listed in the History Pane.

NOTE: Your system configuration may require

you to enter an annotation every time you save.

See you system administrator for more information.

• The version is displayed in the section

frame, to the right.

• The Save icon is disables when you are

viewing older versions of a collection.

To view the properties of a version of a collection:

1. Right-click the version in the history pane.

2. Select Properties from the menu that

appears.

History Pane

The History Pane indicates whether prior versions

of a collection exist, and lets you view

them. A version of the collection is created

each time the collection is saved. For each version,

the history pane shows the date, time, and

the action name - which may be save,

autosave, or a transition name.

To view the History Pane of a collection:

1. Select Show History icon on the toolbar.

2. Select the collection in the Collection Tree.

The History Pane appears below the Collection

Tree. It displays all versions and

transitions for the collection, in reverse

chronological order. A save operation is

denoted with a paper and pencil icon. A

collection transition is denoted with a rubber

stamp icon.

3. To view a version, click the version in the

History Pane.

The Version Properties dialog appears.

• The dialog displays the following information

about the version you selected:

• Name – the action that created the version

(save, autosave, transition name).

• Operator – the person who performed the

action.

• Date – the date and time when the version

was created.

• If there is an annotation associated with

the change, the following information

appears as well:

a. Person who entered the annotation.

b. Date and time the annotation occurred.

c. Text of the annotation.

3. Click the Previous to view information

about the previous version of the collection,

or the Next to view information about the

next version of this collection.

4. Click OK to dismiss the Version Properties

dialog.

60 Saving the Collection Changes

Chapter 8


9

Working with Data

E-Notebook enables you to work with many,

diverse types of data, and then keep related

data together in collections such as reaction

and pages.

Your system configuration determines what

types of data you can add to the sections in E-

Notebook To model your workflow and ensure

that E-Notebook accommodates the data types

you frequently use, your system configuration

may include modified versions of these data

types. Also, certain data types may not appear

in your configuration, and additional, custom

data types may have been added.

Chemical Structure Data

Chemical structures can be drawn with the use

of the Chem & Bio Draw Toolbar. The Chem

& Bio Draw Toolbar allows users to create a

chemical structure by connecting frequently

used substructures together. For more information

about using the Chem & Bio Draw Toolbar,

please see the Chem & Bio Draw User

Guide.

It is also possible to paste standard image files

into chemical structure fields (see Images in

Chemical Structure Fields), and then use the

Chem & Bio Draw toolbar for annotation, such

as text and arrows. Text in the chemical structure

fields is searchable.

Drawing a Structure

To draw a chemical structure:

1. Click within a chemical structure field.

The Chem & Bio Draw toolbar appears.

2. Using the Chem & Bio Draw tools, draw a

structure or reaction.

TIP: Users can access a drawing menu by

right-clicking in the structure window. This

menu allows you to, among other things, copy

and paste structures.

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Expanding the Drawing

Window

The image appears in the chemical structure

field.

To expand the drawing window:

1. Double-click the frame of the chemical

structure field.

The chemical structure field expands.

2. Using the Chem & Bio Draw tools, draw

the structure or reaction.

3. When you are finished editing, double-click

the frame of the chemical structure field to

return it to its original size in the form.

Images in Chemical Structure

Fields

Chemical Structure Fields can also be used to

display and annotate standard image files.

You can paste standard image files into chemical

structure fields, and then use the Chem &

Bio Draw toolbar for annotation, such as text

and arrows. Text in the chemical structure

fields is searchable.

Inserting an Image in a Structure

To insert an image into a chemical structure

field:

1. Copy the image onto the clipboard. You

may do this by, for example, selecting the

Select All and Copy commands when the

image file is open in Microsoft Photo Editor.

2. Right-click within the structure field in E-

Notebook.

A menu appears.

3. Select Edit>Paste.

4. Use F7 to zoom in, and F8 to zoom out.

You can access the drawing menu by rightclicking

in the structure window. This

menu allows you to, among other things,

annotate the image.

Annotating the Image

To annotate the image:

1. Click the A in the Chem & Bio Draw toolbar.

2. Click in the chemical structure field, and

type any text you would like to enter.

The text appears in the field.

3. Click the arrow tool in the toolbar to select

it if you would like to draw arrows to annotate

the image.

Styled Text

You can use styled text boxes to record notes,

preparation information, and other content that

you may want to include with your experiment

data. Besides formatting text, you can also use

the autotext feature to quickly add long or

62 Working with Data

Chapter 9


complicated phrases (such as structure names)

without having to type them. See “Autotext”

on page 36. for more information.

To format the text:

• From within a section, click in the styled

text box.

• A cursor appears in the box, and you can

begin typing.

• Immediately above the box, there may be a

toolbar for formatting the text.

You can change these formats:

• Font type

• Font size

• Bolded Text

• Italicized Text

• Superscript

• Subscript

• Left-alignment

• Center-alignment

• Right-alignment

You can also type the text, highlight it, and

select the text options to apply. You can also

use the standard Windows editing keys such as

Control-C (for copy) and Control-V (for

paste).

NOTE: In your system configuration, the

styled text box may not include the formatting

toolbar or it may be read-only.

A styled text box may also be required. You

may need to enter text into the box before you

can perform a transition on a particular collection.

For example, you may need to enter text

into a text field before you can close a Page or

Experiment.

Subsections

In E-Notebook, certain sections may be set up

to contain other sections, known as subsections.

The subsections appear as tabs within a

section. For example, in a Spectra section each

spectrum is in a separate subsection.

Property Lists

Property Lists are used in forms to record various

types of data properties such as temperature

or pressure.

Adding Properties

To add a property to a property list:

1. Right-click the within the property list in a

section.

A menu appears.

2. Select Add Property....

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The Add Property dialog box appears, listing

the properties you may add.

The property is removed from the Property

List.

Setting and Editing Values

You can set and edit values for the properties

in a property list, such as the list shown below.

To set or edit the value of a property:

3. Click the property you wish to add. You

may use CTRL+click to select multiple

properties, or SHIFT+click to select a

range.

4. Click Add.

The property or properties appear in the

list.

You system configuration determines which

properties may be added to the list, and which

properties appear by default.

Removing Properties

To remove a property from a property list:

1. Right-click the property you wish to

remove from the Property List.

A menu appears.

2. Select Remove Property.

A message appears, asking you if you are

sure you want to remove the property.

3. Click Yes.

1. Click a cell in the property list. The values

you can enter will depend upon the data

type of the specific property.

2. Enter an appropriate value.

3. Click elsewhere in the section.

The value is displayed in the cell.

Depending upon your system configuration,

certain properties may have one or several of

the following attributes:

• Read-Only – certain properties may be for

display only, and it may not be possible to

edit them.

• Required – it may not be possible to delete a

particular property from a property list. If a

property is required, you will be presented

with an error message when you attempt to

delete it.

• Not Blank – it may be necessary to enter a

value for a particular property before you

can perform a transition on the collection.

For example, an experiment collection may

be set up such that it is necessary to enter an

equipment id before you can close the

64 Working with Data

Chapter 9


experiment. If this is the case, you will be

prompted to add the values to the table

when you attempt to perform the transition.

See “Performing a Collection Transition”

on page 25. for more information about

transitions.

• Validated – Values you enter into a property

list may be checked against an external

database, to ensure that they are valid values.

In this case, if you enter an invalid

value, you will receive an error message,

and E-Notebook will not accept the value.

• Enumerated from a database – values displayed

in a drop-down list for any particular

property may be pulled from an external

database.

When searching with the Property Query Field,

numeric values for properties are interpreted

by evaluating the longest possible set of characters

that are converted into a number, starting

with the first character. For example, a

search for 37.5 will find 37.5g. A search for 2

will find 2 ATM/50. Also, conversion is performed

to find equivalent values. For example,

when searching over a volume property for

which mL are the default units, a search for 50

mL (without quotes) will return both 0.05 L

and 50 mL.

Creating a Reference

Within a property list, you can add a link to

another collection/section in E-Notebook or a

link to an external URL. This makes it easy to

browse back and forth between related data.

Adding a Link from a Property List to a

Collection

To add a link from a property list cell to a collection

in E-Notebook:

1. In the Collection Tree, click the collection

containing the property list, then select the

section containing the property list.

The section containing the property list

appears.

2. Click the cell of the property list to which

you wish to add the reference.

3. In the Collection Tree, click the collection

you would like to reference and, holding

the mouse down, drag the collection into

the upper-left corner of the property list

cell.

4. Release the mouse.

The reference is created.

Alternatively, you may right-click the collection

you wish to reference and select Copy.

Then, right-click within the property list to

which you are adding the reference, and select

Paste Reference.

Adding a Link from a Property List to

Section

To add a link from a property list cell to a section

in E-Notebook:

1. In the Collection Tree, click the collection

containing section that you would like to

reference, and then select the section.

The section to which you would like to

make a reference appears.

2. Right-click the Section menu icon, and

select Copy Section.

3. In the Collection Tree, click the collection

containing the property list to which you

are adding the reference, and then click the

section that contains the property list.

The reference is added to the property list

cell. Clicking the hyperlink will display the

section you have referenced.

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4. Right-click within a property list cell and

select Paste Reference from the menu that

appears.

Adding a Link from a Property List to an

External URL

To add a link from a Property List cell to an

external URL or an intranet URL:

1. Right-click within the property list cell to

which you wish to add the reference.

A menu appears.

2. Select Edit Reference.

The Edit Reference dialog appears.

3. Enter the URL and click OK.

The reference is added to the property list

cell. Clicking the hyperlink will display the

URL you have referenced.

Rendering

Rendering is the computer term for converting

objects such as graphics into visual form. Here,

we are using it to describe the export of the

contents of a collection to a PDF or MS Word

file, or to a printer.

E-Notebook provides several options for rendering

the contents of your pages/reaction and

other types of collections. See “Exporting to

Word” on page 26 and “Printing Collections or

Sections” on page 26.

66 Working with Data

Chapter 9


10

Searching

Searching allows you to find information in E-

notebook that meets the criteria you specify. E-

Notebook makes it possible to search for:

• Chemical Structures

• Text

• Collections - Notebooks, Folders, etc.- that

meet specific criteria, such as creation date,

owner’s name, or state.

The Query tab appears.

2. From the More Options list, select the type

of search you want.

3. Select the type of query you would like to

run.

An empty query form is displayed. An

example is shown below:

See the following topics for more information:

• Conducting a Search

• Working with Query Results

• Saving a Query

• Refining a Query

• Search Query Types:

• Simple Text Query

• Advanced Text Query

• Reaction Query

Searching

You can search for information in E-Notebook

that meets the criteria you specify. You can

then save your queries and the results.

To conduct a search:

1. Select Search at the top of the E-Notebook

screen.

4. Specify the parameters that will determine

the search results.

The parameters you can specify are determined

by the type of query you are conducting.

5. Do one of the following:

• Click Search Now to execute the query.

A results list appears.

• Click Save Search to save the query.

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The Collection Tree appears with a new

search, and you are prompted to give the

search a name.

See the following topics for information about

entering the search criteria for the various

types of searches:

• Simple Text Query

• Advanced Text Query

• Reaction Query

Working with Query

Results

shown below.The Collection Tree appears,

with the item displayed.

When you conduct a Search in E-Notebook,

the results are displayed in a list. You can save

the results list, and/or view any item on the list.

Viewing Items in a Results List

To view an item on the results list, click the

name of the item that you want to open, as

Saving a Results List

To save the results list:

1. Click Save Search.

A dialog appears, prompting you to browse

to the location in the Collection Tree where

you would like the results to be saved.

2. Click a collection to select it in the tree and

click Save.

3. The Collection Tree appears, showing the

search results as a new collection. The links

are maintained so that you may browse to

any of the items.

Related Topics

• Conducting a Search

• Saving a Query

• Refining a Search

• Defining different Types of Search Queries

68 Searching

Chapter 10


Saving a Query

When you create a query, you can save it in the

Collection Tree.

To save a query:

1. Click Save Search to the left of the query

form.

A dialog appears, and you are prompted to

select the location where you wish to save

the search.

2. Click a collection to select it as the location,

and click the Save.

The Collection Tree appears, and the query

appears in the tree.

3. You can also rename the query.

NOTE: The last query you created will appear

by default when you enter Search mode again.

Running a Saved Query

To run a query that is saved in the collection

tree:

1. Click Browse at the top of the screen.

The Collection Tree appears.

2. Click the query in the collection tree.

The query form appears in the right frame.

3. Right-click the query form tab and select

Copy Section.

4. Click Search at the top of the screen.

Search mode appears.

5. From the More Options list, select the type

of query that corresponds to the query form

you are copying.

6. Right-click the query form tab menu and

select Paste Section.

Refining a Search

Once you have conducted a search, you can

further refine it - performing a search that is:

• An intersection of two searches.

• A union of two searches.

• The exclusion of one set of search results

from another.

It is possible to refine your search based on

your requirements.

To do this:

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1. From the dropdown list at the top of the

query form, choose any of the following

options:

• Create a New Set of Search Results -

deletes the previous search results and

replaces them with the search results generated

by the new query.

• Refine the Previous Search - uses the previous

search results to limit the collections

in which a search is done. The stored hit

list will contain the intersection of the previous

search results and the results specified

by the new query.

• Refine the Previous Search By Section -

uses the previous search results to limit

the sections in which the search is done.

The stored hit list will contain the intersection

of the previous search results and

the results specified by the new query. If

the current search engine is a collection

search engine, then this option is not

present.

• Exclude Collections from the Previous

Search - excludes collections from the

stored hit list that are part of the previous

search results. The stored hit list is completely

replaced.

• Add to the Previous Search - adds the

results specified in the search query to the

previous search results. Duplicate collections

and/or sections will not be added.

• Remove from the Previous Search -

removes the results specified in the search

query from the previous search results.

2. Fill in the new search criteria.

3. Click the Search Now.

The hitlist appears, modified according to

the option you chose in step 1.

4. If you wish, you may refine your search

further, by selecting another option from

the dropdown list.

You can create these types of search queries:

• Simple Text Query

• Advanced Text Query

• Reaction Query

By Default, the Simple Text Query form is displayed.

To change the type of search, click

More Options and select the desired type of

query form.

Simple Text Query

Using a simple text query, you can search for a

section or collection by specifying the text

associated with it. To create a simple text

query:

1. Click Search in the main menu toolbar.

2. Click the More Options icon and select Simple

Text Query.

3. In the Simple Text Query tab, enter the text

string for which you want to search.

4. Do one of the following:

• Click Search Now to execute the query.

The Result tab displaying a list of pages/reaction

which contain the specified text appears.

• Click Save Search to save the query.

A dialog appears, and you are prompted to

select a location for the saved query. Then, you

are prompted to give the search a name.

70 Searching

Chapter 10


Advanced Text Query

Advanced Text Query allows you to obtain

more precise search results. In addition to

specify the text associated with the experiment,

you can also specify Search Location. You can

also specify the metadata about the experiment

that you want to search. For example, Collection

Name, Owner Name, Creation Date, and

Status.

To create an Advanced Text Query:

1. Click the Search in the main menu toolbar.

2. Click the More Options icon and select

Advanced Text Query.

3. Enter the text and metadata for which you

want to search.

• Click Save Search to save the query.

A dialog appears, and you are prompted to

select a location for the saved query. Then,

you are prompted to give the search a name.

Reaction Query

Using a reaction query, you can search for

structures. You can also specify other criteria

such as reactant name, product name, solvents

and reaction conditions associated with a reaction.

To create a reaction query:

1. Click Search in the main menu toolbar.

2. Click the More Options icon and select

Reaction Query.

4. Do one of the following:

• Click Search Now to execute the query.

The Results tab displaying a list of pages/

reaction, which match the specified criteria,

appears.

3. Enter the structure associated with the

experiment that you want to search.

4. Specify the values for the fields, such as

Reactant Name and field of the reactant

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associated with the experiment that you

want to search.

The Results tab displaying a list of pages/reaction,

which match the specified criteria,

appears

5. Do one of the following:

Click Search Now to save the query.

• Click Save Search to save the query.

A dialog appears, and you are prompted to

select a location for the saved query. Then, you

are prompted to give the search a name.

Related Topics

• Conducting a Search

• Working with Query Results

• Saving a Query

• Refining a Search

72 Searching

Chapter 10


11

Working Offline

You can work in offline mode in E-Notebook

12.0 when server or network connection is not

available. The changes or the data you have

added during the offline mode will get synchronized

as soon as the network or server is

available.

Creating an offline folder

You can create a offline folder:

1. Right-click on the user collection in the

Collection tree.

A menu appears.

2. Select New>Offline.

3. A new Offline folder is created and the

Work Offline appears in the upper corner

of the screen.

except for the first notebook, its reference

needs to be created manually (Copy/Paste

Reference).

Working in the Offline

mode

You can log into offline mode in two ways:

• Click the Work Offline on the upper right

corner of the screen

• While logging to E-Notebook, click Work

Offline.

NOTE: You should have only one offline folder

in the user collection.

NOTE: Once the offline folder has been

created, all notebooks and reaction created

will have a reference in the Offline folder,

You can work in the offline mode after clicking

it. You can see that User Collection contains

only two collections:

• Offline

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• User Configuration

A dialog Box appears showing you the list of

changes at the top of the dialog box, the original

contents and the updated contents, contents

of the new page/reaction page.

You can make changes and additions as you

did in online mode.

To reconnect:

1. Click Connect on the upper right corner of

the screen.

A dialog appears prompting you to enter

the password.

2. As soon as you come online a Synchronization

Change dialog appears:

The changes in a reaction page/page can be

described as:

• Content Changed: The contents in a page/

reaction page is added or changed.

• New reaction page/page: If the reaction is a

new reaction page then the word “Reaction”

is replaced by the type of the newly

created reaction “New Reaction”.

3. You can review the changes done. Click

Show Details.

When the Show Details is clicked for a reaction

that has contents changed or new page/

reaction page. Dialog box appears in which

you can see a list of the changes, the original

contents and the updated contents, contents of

the new page/reaction page. At the top of the

dialog box is a list of the changes.

4. Click Synchronize to update all the changes

that were done when you were offline in the

online content.

When the Synchronize is clicked, the synchronization

process occurs as follows:

5. Click Cancel button to cancel the login.

Limitations to Offline

Working

There are certain limitations to working offline

in E-Notebook.

1. You will not be able to create new notebooks

or any new collection in offline

mode.

2. You will not be able to make any transition

changes.

74 Working Offline

Chapter 11


12

E-Notebook Batch Import Facility

The batch import facility in E-Notebook lets

you import a partial or complete configuration

in a single menu command. This process is

controlled by an import script called the Batch

File, which is an XML file adhering to the

schema described in this document. The batch

file typically refers to additional files, either E-

Notebook content files created with the Export

command (called Content Files) or subsidiary

batch files. This process is initiated by selecting

a collection in the E-Notebook collection

tree (which will be referred to as the Parent

Collection) and choosing the Import command.


The root element must be a . There are

no attributes defined for the batch element. A

batch may contain zero or more of any of the

following elements, interspersed in any order,

except as dictated by the dependencies

between the imported collection and section

types.






The import element causes a single file to be

imported. This file may contain any content,

including section types, collection types, collections,

or sections. There are no attributes

defined for the import element. Each import

element may contain a element, if

none is specified, the target is the parent collection.

Each import element must contain a

element.


The target element describes where in the E-

Notebook collection hierarchy the imported

content is to be placed. This element must contain

one of the following elements, depending

on what sort of content is being imported:




A collectionType element indicates that the

relationships for a previously imported collection

type are to be imported. The name

attribute specifies the name of the collection

type for which relationships are to be imported,

Chem & Bio Office 2010 User Guide 75

E-Notebook


and the collectionType element must include a

collection element which specifies by position

the first (and only) collection which defines

that collection type. For example:




Collection Types/

Binder.xml



A indicates a reference to a

collection contained within the Parent Collection.

This element must contain a name or

position attribute, but is invariably used with a

name. For example, this may be used to create

a grandchild of the Parent Collection, as follows:


Section Types.xml




General Information.xml


Assuming Section Types.xml describes a collection

named Section Types and that General

Information.xml describes a section type, this

will create a Section Types collection,

and within that, a General Information

section type.

The E-Notebook collection hierarchy distinguishes

between the nodes, called collections,

and the links between the nodes, called references.

Every reference has one container collection

and one target collection, and a

collection may be referred to as the target of

any number of references. Thus, the

describes a reference, but if a

specifies a reference, it is assumed

that the target is the reference’s target collection.

A may contain a

element explicitly to indicate

that the target is the collection, not the reference,

but this is optional unless one wishes to

further specify a collection contained within

this collection. For example, to specify deeper

levels in the collection hierarchy, one might

use:









Deeper Folder.xml



The source element contains text which specifies

the path of the file to be imported. This is

interpreted relative to the batch file.


The log element contains text which is written

to the client log file, if logging is enabled. If

76 E-Notebook Batch Import Facility

Chapter 12


logging is not enabled, this element is ignored.

Example:

General Information section

type created


The alert element causes a message to be displayed.

This element must contain the text to

be displayed, and may have a title attribute

which specifies the title of the message box,

and may have a buttons attribute which may be

0 or 1. If the buttons attribute is 0 or not specified,

the message box will have an OK only. If

the buttons attribute is 1, the message box will

have OK and Cancel, and if Cancel is pressed,

the import process will stop.


The refresh element causes the client to refresh

the display of section and collection type information

to show the effect of any imported

objects. One commonly uses a refresh element

at the end of the import script.

Chem & Bio Office 2010 User Guide 77

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78 E-Notebook Batch Import Facility

Chapter 12


A

System Features

This chapter contains general information

about E-Notebook Workgroup.

Viewing User Information

As an E-Notebook Workgroup administrator,

you can see specific information about the user

who is currently logged in.

1. Click Browse.

2. Right-click any blank area in the Collections

Tree.

A menu appears.

3. Select User Info....

The User Properties dialog box appears. It

contains the following information:

• Login ID – the Login ID of the user who is

currently logged into E-Notebook.

• Password – Depending upon the type of

login authentication your system uses, this

field may be used to change the password

for the logged-in user.

• Administrator – a checkbox that indicates

whether the user has administrative privileges.

This checkbox is visible only if the

logged-in user is an administrator.

Refreshing E-Notebook

If other users add information to E-Notebook

Workgroup, you may need to refresh your

view of E-Notebook workgroup so that you

can see their changes. To refresh E-Notebook

Workgroup:

1. Click the Browse.

The Collection Tree appears.

2. Right-click any blank area in the Collections

Tree.

A menu appears.

3. Select Refresh.

E-Notebook Workgroup information is

updated.

Numerical Units

Tables and property list may contain numerical

properties, which may have default units associated

with them. Your system configuration

determines the default units for any given

property in a table. The following types of

measurements may be specified or displayed in

the permitted units shown below.

For example, there may be a property of mass

and its default units may be grams (g). If you

Chem & Bio Office 2010 User Guide 79

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.

enter a numerical value into the property without

specifying units, the units will be displayed

and stored as grams. You may also enter any of

the permitted mass units shown below, such as

mg or kg.

NOTE: In all cases, the standard units are the

SI units for the given type, which may not be the

units commonly entered or displayed

Type of

Measurement

Standard

Units

Permitted

Units

density kg/m3 g/ml µg/ml

mg/ml µg/l

mg/l g/l kg/l

kg/m3

length m m Å nm µm

mm cm

mass kg g µg mg kg

molality

(quantity per

mass of

solvent or

substrate)

mol/kg

mol/kg mol/g

mmol/kg

mmol/g

µmol/kg

µmol/g

molar mass kg/mol g/mol kg/mol

dalton D kD

molarity

(quantity per

volume of

solution)

mol/m3

mol/l µmolar

mmolar

molar

Type of

Measurement

moles (quantity

of

substance)

normality

(ion equivalents

per

volume of

solution)

Standard

Units

mol

Permitted

Units

mmol µmol

mol

mol/m3 N mN µN

pressure Pa atm Pa kPa

torr bar mbar

temperature K °C °K °F

time s s ms µs min

hr

velocity m/s m/s km/hr

mi/hr

volume m3 ml µl l m3

When you are in Search mode, the table or

property query field allows you to find all

equivalent values entered in various units that

share the same unit type. For example, a search

for a volume of 500 mL will return both 500

mL and 0.5L. The search will assume the

default units for the property if you do not

enter units. Using the same example, if mL

were the default unit for a volume property,

and a search were conducted for a property

value of 0.5, no hits would be returned. A

search for 0.5 L would return both 500 mL and

0.5 L.

80 System Features

Appendix A


Using the Session Manager

In certain situations an E-Notebook session

may be left open. With the Session Manager,

you can end your old session, and release any

collection that may be locked by it.

To access the Session Manager:

1. Right-click any blank area in the Collections

Tree.

A menu appears.

2. Click Session Manager....

The Session Manager appears.

This dialog shows the Users, Session numbers,

and Start Times for each current session.

Ending a Session

If you wish to end a session displayed in the

Session Manager:

1. Click the session in the list.

The session is highlighted.

2. Click the End Session.

A message appears, asking you to confirm

that you wish to end the session.

3. Click Yes.

The session is ended. Any record that was

locked by the session is released.

NOTE: You must have Full Control permission

over your home collection (your user collection)

to end your sessions.

Chem & Bio Office 2010 User Guide 81

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82 System Features

Appendix A


B

Glossary

Terminology

The following terminology is used in the

E-Notebook application and throughout this

guide:

Collection– A set of related items in E-Notebook

Collections are the items that appear in

the E-Notebook Collection Tree.

Collection Listener– Collection Listeners is a

behavior that modifies the behavior of collections,

such as creating, hiding, renaming,

duplicating and moving behaviors. Administrators

assign them to collections.

Collection Type – A collection type defines the

properties of a collection. Each collection type

has a name, an icon for displaying collections

of that type in the collection hierarchy and a set

of business rules that describe what kinds of

operations can be performed on collections of

that type.

Field– Fields are the basis for the forms in

E-Notebook. Each field is based on an add-in

field type. Each field has a type, which

describes the type of data stored in the field,

and a name. Examples of different types of

fields include a property list, a table, a chemical

structure, a spectrum, a Microsoft Word

document. Depending on the type of data

stored in the field, the field may also contain

additional configuration information. For

example, a property list field contains a list of

the properties that can be included in the property

list.

Form– It is a layout which contains Fields,

Boxes, and possible Form Tools. The term

Form is associated with a Section. When you

click on a Section type you can see the layout

of a Form.

Form Tool– a Form Tool is used to perform particular

function in an E-Notebook section, such

as data analysis or data import/export.

Full Control privilege– The privilege required to

manage the security settings of a collection.

The Full Control privilege includes all of the

features associated with the Read & Write

privilege

History– A list of the versions and transitions

that have been made to a collection.

Home– The collection that appears when you

first log in to E-Notebook. It is the collection

associated with you as a user.

Meta-data– Data that describes other data. For

example, you can use meta-data such as creation

date or owner’s name as parameters

when searching for data and information in

E-Notebook.

Owner, of a Collection– the E-Notebook user

who created the collection.

Property List– A list of data properties corresponding

to a particular section. For example,

Chem & Bio Office 2010 User Guide 83

E-Notebook


the property list in a reaction section may contain

pressure, temperature, etc.

Read privilege– The privilege required to view

a collection in the collection tree, along with its

contents.

Read & Write privilege– The privilege required

to modify the contents of a collection. The

Read & Write privilege subsumes all of the

features associated with the Read privilege.

Region - A geographic area where each user is

associated with his home collection in E-Notebook.

The regional setting determines which

collection type print templates will be used

when the user exports to MS Word or prints.

Table– A section (or part of a section) in which

you can record data in a tabular format.

Template– A collection containing data or

information that you wish to reuse multiple

times. You can use the template as the basis for

new collections.

Section– A set of data. Each piece of datum is

described by a field. For example, a reaction

section might contain a chemical structure

drawing, a table of reactants, a table of solvents,

a table of products and a description of

the procedure used to create the drawing.

Section Listener– Section Listeners is a behavior

that modify the behavior of sections, such

as renaming and moving behaviors. Administrators

assign Section Listeners to various

types of sections.

Section Type– A configuration that contains a

set of fields, form tools and a form. You can

associate section listeners with a section type

to implement business rules associated with

sections of this type.

Transition– Are the actions performed to move

a collection from one state to another.

Transition Listener– Transition Listeners modify

the effect of a transition, usually by performing

an operation that is associated with the

transition. System administrators configure

Transition Listeners.

Version– The contents of a collection saved at a

particular time.

84 Glossary

Appendix B


BioAssay

Desktop & Workgroup


BioAssay Desktop & Workgroup

BioAssay enables research biologists to store,

analyze, and create reports on biological assay

data. This application is optimized for handling

data related to high-throughput screening.

However, it can also be effectively used to

manage data related to low-throughput and in

vivo studies.

Protocols are the basic data entities in BioAssay

application. Protocols contain tables representing

various physical storage entities, such

as plates and wells. Data is actually stored in

these tables. BioAssay lets you define protocols

for storing raw data, summary data, and

aggregate data. In addition to storing data, Bio-

Assay also facilitates curve fitting and data

manipulation.

This figure shows the start page of the BioAssay

application:

What’s New

Excel Analysis. This feature lets you integrate

BioAssay with Excel. For more information,

see “Integrating with Excel” on page 120.

About this Guide

Welcome to the BioAssay Desktop and Workgroup

User Guide. Inside this guide, you will

find a full description of BioAssay, its features,

and complete instructions on how to use them.

This guide is available in print (this file) and

CHM formats.

Logging in to BioAssay

To start the BioAssay client application:

1. Click Start>All Programs>ChemBioOffice

2010>BioAssay 12.0>BioAssay Desktop

12.0. to display the Login dialog box.

2. Enter relevant information in the Username,

Password, Data Source, and Initial Catalog

text boxes. For more information about

these fields, contact your system administrator.

Terminology

• High Throughput Screening (HTS): Testing

thousands of compounds in a short period

of time.

• Low Throughput Screening (LTS): In-depth

screening of fewer compounds.

• Protocol: A collection of database tables

and calculations that hold data about a

given biological experiment.

• Plate: A means of holding multiple samples

in an easily transportable unit.

• Plate Format: The layout of the wells on a

plate.

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• Well Format: The type of contents in a well,

such as Compound, Control, and Empty.

• Aggregate: A calculation that summarizes

multiple results in one number, such as

Average, Maximum, Minimum, Standard

Deviation, and Curve Fits.

• Grouping: A method used in conjunction

with aggregate calculations to summarize

data.

• Primary Protocol Tables: The collection of

tables that are automatically filled and calculated.

• Summary Tables: Tables that provide alternate

ways of summarizing primary data.

• File Import Template: A map that tells how

to take data from a file and place it into an

HTS assay.

• Graph Template: A template that specifies

how to place data in a 2-D graph.

• Browse Table: A table that lets you interact

with data and perform Quality Control

tasks.

• Search Table: A table that lets you search

all protocol data.

• % Inhibition: An experiment to identify

potential drug candidates.

• IC50, EC50, LD50: Measures of compound

potency, which refers to the concentration

in a protocol at which a compound is effective

at the 50% level.

• Valid, Invalid, Not Validated: Measures of

confidence in data. Generally, data that has

less confidence assigned is less visible.

• Curve Fitting: The process of using an algorithm

to determine the line that best fits a

set of points. The parameters of this equation

can then be used in further calculations.

• Picklist: A defined list of items in an assay

from which you may select the desired

item.

Navigation

The user interface of the BioAssay application

is split into two major frames: Navigator and

Content. The following figure displays the user

interface of the BioAssay application:

In the preceding figure, the left-hand side

frame is referred to as the Navigator frame. In

the Navigator frame, projects, and protocols

are organized in a tree structure in the same

way as folders are organized in Microsoft

Explorer. You can navigate through the tree

structure to access the desired protocol.

The right-hand side frame in the preceding figure

is referred to as the Content frame. This

frame displays the content of the following

items, which can be selected in the Navigator

frame:

• Protocols

• Lists

• Plate Formats

• Well Formats

• Picklists

• Field Dictionary

88 BioAssay Desktop & Workgroup

Chapter


In addition to viewing, you can also manage

the content of the above mentioned items

through the Content frame. The Content frame

lets you define and import data into protocols.

The Content frame can also be used to manage

the content of the plates, wells, and picklists in

the following three modes:

• Browse

• Filter

• Edit

There are some common operations, which

you can perform through the Content frame

irrespective of the data being displayed. These

operations are as follows:

• Resizing and Moving Columns

• Sorting Data

• Filtering Data

• Refreshing the Data View

• Printing

• Exporting data to Excel

• Getting Help

Resizing and Moving Columns

You can resize the columns of tables displayed

in the Content frame using the click and drag

method, in the same way as you resize columns

in table/spreadsheet interfaces.

To resize columns in a table in the Content

frame:

1. Move the mouse over the border between

two columns in the table header row, until

the mouse pointer turns into a double sided

arrow, as shown in the following figure:

2. Click the mouse and drag it, while holding

down the mouse button. The column will

resize as you drag the mouse.

3. Release the mouse when the size of the

selected column becomes appropriate, as

shown in the following figure:

In some tables, such as assay data tables, the

columns can also be moved within the table.

To move a column within a table in the Content

frame:

1. Move the mouse over the column header,

which you need to be move.

2. Hold down the mouse button and drag the

column to its new location, as shown in the

following figure:

NOTE: A column line appears when you have

dragged the column to a new column location.

3. Release the mouse button when you have

dragged the column to the proper location,

as shown in the following figure:

This new column arrangement will be saved and displayed when the table is opened in future.

Sorting Data

You can sort the data in any table based on the

content of any of the columns in the table.

After you sort the data based on a particular

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column, the data will appear in the same sorted

manner when you open the table in future.

To sort the data on the basis of a particular column,

click on the column header. To invert the

sort, click the corresponding column header

again.

Filtering Data

You can use the Filter mode of the Content

frame to filter data contained in tables. To use

the Filter mode, click the Filter button in the

toolbar of the Content frame. In the Filter

mode, you are able to filter the table data based

on any criterion. When data of a table is filtered,

only the data matching the entered criteria

is displayed.

To filter the data in a table:

1. Click Filter. A row with a green background

appears at the top of the table.

2. Enter a criterion into the new row, as shown

in the following figure:

The criterion can be entered using drop

down lists, ranges for numerical columns,

or the appropriate characters for text columns.

NOTE: To search for an empty field, type

“NULL” as the value of the field to be searched.

To search for a field starting with one or more

empty spaces, type the appropriate number of

spaces in the search criterion.

3. Click Apply. The filtered and sorted data

appears:

4. Click Clear to remove the filter.

Refreshing the Data View

You need to refresh the Content frame in order

to view the updated data contained in the

tables. This is because, unless you close the

windows in the Content frame and reopen

them, the data contained in the tables is not

updated. To refresh the Content frame, click

the Refresh button.

Printing

The Content frame lets you print any table contained

in BioAssay. To print a table:

1. Click the Print icon. The Print dialog box

appears.

2. Select the appropriate printing options and

click the OK button to print the selected

table.

Exporting Data to Excel

The Content frame lets you export any BioAssay

table to MS Excel. To export a table to MS

Excel, open the table in the Content frame and

click the icon in the menu bar. The Excel

sheet corresponding to the selected table

appears.

Table and Form View

You can view any data table in BioAssay in

either Table or Form view. You can switch

90 BioAssay Desktop & Workgroup

Chapter


etween these views by clicking the appropriate

icon. The Table view can be seen by clicking

the Table icon, while the Form view can be

seen by clicking the Form icon. By default, all

data is displayed in Table view. The following

figures display the Table and Form views of a

table:

Table View

Form View

numerical data, a calculation, or an attachment,

such as a picture or document. After defining

the type of fields contained in a table, you can

import data into the table from files through

the use of a user defined file import template.

Protocol Navigation

The Protocols folder in the Navigator frame

contains any number of protocols that can be

accessed through a folder within the Protocols

folder. You can navigate to the desired protocol

in the Navigator frame through the Protocols

folder. The following figure displays the

Navigator frame along with the Protocols

folder:

Getting Help

The BioAssay User's Guide, provided as Windows

Help files (a compiled HTML format),

can be accessed from the Content frame by

clicking the Help icon available in the menu

bar.

Protocols

Protocols are the basic data entities in BioAssay.

The BioAssay application enables you to

store and analyze assay data through the use of

protocols. The interface provided by BioAssay

for managing assay data is similar to that of

Microsoft Access.

Protocols contain tables in which data is actually

stored. The fields contained in these tables

can be defined as simple text, a piece of

In the preceding figure, The Protocols folder

contains folders, projects, and protocols.

Right-clicking on the projects and/or folders in

the Navigator frame exposes a menu, which

lets you create projects/folders/protocols,

Chem & Bio Office 2010 User Guide 91

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ename the project/folder, or remove a project/

folder.

Right-clicking on a protocol in the Navigator

frame exposes a menu which lets you perform

the following tasks:

• Create new protocol

• Remove a protocol

• Move a protocol

• Duplicate a protocol

• View protocol properties

The Unclassified folder appears by default and

it cannot be deleted because of the following

reasons:

• When a project is deleted, the protocols

contained in that project are moved to the

Unclassified folder

• When a duplicate protocol is created, that

duplicated protocol is placed, by default, in

the Unclassified folder.

Moving a Protocol or Project

To move a protocol or a project:

1. Right-click on the project or protocol,

which is to be moved. A menu is displayed.

2. Select the Move Protocol or Move Project

menu item from the menu. The Move a Protocol

dialog box appears.

3. Select the destination project in the list of

projects within the Protocols folder. The

Destination Project text box will be filled

automatically.

4. Click OK to move the selected protocol to

the destination project.

Duplicating a Protocol

To duplicate a protocol:

1. Navigate to the protocol, which you need to

duplicate.

2. Right-click on the protocol. A pop-up menu

is displayed.

3. Select the Duplicate Protocol menu item

from the menu. A copy of the selected protocol

is added to the Unclassified project in

the Navigator frame. You can rename and/

or move the protocol as per your requirements.

Viewing Protocol Properties

To view the properties of a protocol:

1. Navigate to the protocol whose properties

you need to view.

2. Right-click on the protocol in the Navigator

frame to display a menu.

3. Select the Properties menu item in the

menu. The Protocol Properties dialog box

appears.

4. Click OK to close the Protocol Properties

dialog box.

NOTE: You can also rename the protocol in the

Protocol Properties dialog box.

Protocol Data and Definitions

Protocol data and definitions are accessed by

selecting or clicking the appropriate protocol

in the Navigator frame of the BioAssay interface.

The content of the protocol is displayed

in the Content frame, which shows the following

three tabs:

• Tasks

• Data

• Definition

92 BioAssay Desktop & Workgroup

Chapter


The following figure shows the above mentioned

tabs in the Content frame of the BioAssay

interface:

The Primary Data tables of a protocol are represented

throughout the application using the

blue data table icon. The Summary tables are

denoted by a green data table icon. These

tables are defined under the Definition tab in

the Content frame when the protocol is

accessed. To view the data stored in these

tables, perform a search or click the Retrieve

All button.

Searching Protocol Data

BioAssay lets you perform search operations

over protocol data according to your specified

criteria. To perform search operations over

protocol data:

Protocol Tasks

The BioAssay application enables you to perform

various tasks through the Tasks tab, after

you select a protocol in the Navigator frame.

These tasks are as follows:

• View and manage experimental data

• Manage tables, fields, and file import templates

• Get help using the associated help files

Protocol Data

The data stored in a protocol is accessed by

clicking the Data tab of the protocol in the

Content frame. When you click the Data tab,

the Open Datasource dialog box appears.

NOTE: The term 'datasource' refers to an

internal table that is used to select data. It differs

from the term 'external datasource'

because an external datasource refers to a

view/table that is not a part of the protocol. The

table may belong to a different schema.

1. Select the protocol in the Navigator frame.

2. Click the Data tab in the Content frame. If

the Data tab was already open, click the

Datasource button. The Open Datasource

dialog box appears:

3. Select the table over which you want to perform

the search operation in the Select Datasource

list.

4. Enter your search criteria in the cells corresponding

to the fields displayed. The search

fields vary depending on the data table

selected.

5. Click Search to get the search results.

NOTE: BioAssay performs a like search from

all search dialogs.

Browsing Protocol Data

The data is arranged in hierarchical tables, as

defined in the protocol Definition tab. Doubleclicking

a row in a table exposes the data

related to that row in the next table in the hierarchy.

For example, your protocol may contain

2 tables, a Plates and a Wells table. Doubleclicking

on a row in the Plates table exposes

the data in the Wells table associated with the

Chem & Bio Office 2010 User Guide 93

BioAssay


selected plate. The following figure shows the

data in the Wells table associated with the plate

having plate ID, P1002:

be loaded into the Wells table, as shown in the

following figure:

Tables are arranged in the Data tab according

to the hierarchy defined in the protocol definition.

In other words, tables that are higher in

the hierarchy are found at the top of the data

browser and nested tables are displayed lower.

If the number of tables displayed exceeds 4, a

button lets you bring the hidden tables back

into view.

Changing the selection to a table higher in the

hierarchy cascades the change through the

child tables. Thus, to see data for plate 2

instead of plate 1, click plate 2’s row in the

Plates table. Information related to plate 2 will

NOTE: Data in the tables can be edited

through the edit mode by clicking the Edit icon

in the menu bar.

By default, the table view of data is shown. If a

plate view or a graph is available, the menu bar

that appears above the bottommost table will

show additional icons.

Related Plate Data

In some BioAssay protocols, the table located

at the lowest level in the hierarchical table

structure contains the Plate and MultiPlate tab.

For example, in an IC50 protocol, the Wells

table contains the Plate and MultiPlate tab as

shown in the following figure:

94 BioAssay Desktop & Workgroup

Chapter


The Plate tab lets you view data for a single

plate, as shown in the following figure:

table, the table displays the Graph: Study

Graph tab, as shown in the following figure:

NOTE: The Graph: Study Graph tab is visible

only when you view the protocol tables in the

Data tab of the protocol.

The MultiPlate tab lets you view data for multiple

plates, as shown in the following figure:

Clicking the Graph: Study Graph tab enables

you to view the graph related to the table data

as shown in the following figure:

Related Graphical Data

BioAssay also lets you view table data in

graphical format. To view data in graphical

format, you first need to create a graph template

within the appropriate table. You can create

graph templates by using the Definition tab.

When a graph template is created within a

In order to view data for more than one row at

a time, hold down the Ctrl or Shift keys when

selecting rows. By doing this, you can select

multiple rows and display the results for the

data on one plot, as shown in the following figure:

Chem & Bio Office 2010 User Guide 95

BioAssay


Plate Template Manager

BioAssay lets you create or add plates to the

Plates table of a protocol by using the Plate

Template Manager tool. When creating a new

plate, you need to select an existing plate format.

The newly created plate will inherit well

format and concentration related information

from the selected plate format. When creating

a plate, you can pin or double-click enable the

fields related to that plate.

Pinned Fields

Pinning is a feature using which you can manage

the visibility of data for a field in the Plate

Template Manager window. When a field is

pinned, the well values for that field will

always be visible at the bottom of the well. For

example, if the Well Format field is pinned, its

values appear in the wells of other fields also,

as shown in the following figure:

Double-click Enabled Fields

The double-click enabling feature lets you

select wells containing same values for a field.

When this feature is enabled for a field, double-clicking

on a well selects all other wells

containing the same value for the double-click

enabled field.

If no field is double-click enabled, the doubleclick

behavior applies only to the currently

selected field. Fields that are pinned and double-click

enabled, are represented by the following

icon:

Creating a New Plate

To create a new plate:

1. Create a plate based (IC50) protocol.

2. Import data into the protocol using a file

import template.

3. Right click a row in the Plates table when

the Data tab of the protocol is open. A popup

menu is displayed.

4. Select the Create Plates menu item. The

Add Plate dialog box appears.

NOTE: Although you can select different

values in the drop down lists corresponding to

Rows and Cols, the selections will be ignored.

Letters and numbers designation must be made

in the plate format definition.

In the preceding figure, the values of Well Format

are displayed in lower section of each well

corresponding to the Concentration field.

Fields that are pinned are represented by the

following icon:

5. Type a name for the plate in the Name text

box.

6. Select a plate format in the Plate Format

drop down list. The number of rows and

columns will be automatically populated

based on the plate format selected.

7. Click OK. The Plate Template Manager window

appears.

NOTE: In the Plate Template Manager

window, the Well Format tab is selected by

default. In addition, the Well Format field will

be pinned and double-click enabled by default.

96 BioAssay Desktop & Workgroup

Chapter


You can edit the well values and toggle the

pinning or double-click enabling settings as per

your requirements.

8. Click OK to add the plate to the Plates table.

Editing the Plate Fields

To edit the plate fields:

1. Click a field's tab in the Plate Template Manager

window. For example, click the Concentration

tab.

2. Click Edit. The Concentration dialog box

appears.

3. Type a concentration value in the text box

corresponding to the Add button.

4. Click Add to add the value to the New list

box.

5. Click OK. The new concentration value will

appear within the Concentration list in the

Plate Template Manager window.

6. Select a well and click the new concentration

value in the Concentration list. The

value of the selected well changes to the

new concentration value.

7. Click OK.

NOTE: Plate values in a Wells table can be

edited under the Plate tab. To edit a plate value,

double-click on a cell and click the Edit button

in the Details dialog box. After editing, click the

Save button to save the changes.

• Select Toggle Pin or Toggle Double Click

from the Edit -> Layer menu in the menu

bar.

• Click the Pin/ Double Click Layer toolbar

button to display the Pin/ Double Click Layers

window and select the fields to be

pinned or double-click enabled. Thereafter,

click the OK button.

Protocol Definitions

BioAssay lets you define protocols for storing

data. You can access the interface for defining

protocols by clicking the Definition tab in the

Content frame. The Definition tab appears in

the Content frame only when you select a protocol

in the Navigator frame. The Definition

tab lets you define the protocol's structure and

the calculations that can be performed over the

protocol's data. The protocol tables must be

defined before importing data.

For more information about defining tables for

an assay, see “Defining Tables and Fields” on

page 100.

When the Definition tab of a protocol is

opened, the protocol structure is displayed in

the Content frame, as shown in the following

figure:

Pinning and Double-click Enabling Fields

To pin or double-click enable a field, you can

perform one of the following tasks:

• Right click on the field's tab in the Plate

Template Manager window and select Toggle

Pin or Toggle Double Click, as per your

requirements.

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The hierarchical tree in the Content frame of

the protocol groups information in six ways,

which are as follows:

• Primary Tables

• Calculation Tables

• Summary Tables

• Additional Tables

• File Import Templates

• Graph Templates

Primary Tables

In BioAssay, the primary tables contained

within protocols are arranged in a hierarchical

tree structure. A primary table situated lower in

the tree contains rows which hold aggregate

data of a row in a higher table. For example, a

plate based protocol has at least two tables:

Plates and Wells. The Plates table is higher on

the tree than the Wells table. This makes sense

because each plate contains several wells. The

Plates table defines plate attributes, such as

barcode, while the Wells table holds data associated

with a particular well, such as the well

ID.

Each field falls under the appropriate table in

the tree. Clicking on a table name or field name

prompts the application to display details about

the table or field under the appropriate tab in

the right-hand section.

Parent Tables

Every primary table in a protocol, except the

table at the top of the hierarchy, has a parent.

The parent table is the table found in the next

highest level in the protocol tree. For example,

in the above figure, the Plates table is a parent

of the Compounds table. Since, the Plates table

is located at the top of the hierarchy, it does not

have a parent.

Every parent table holds information summarizing

the data contained in tables below itself.

For example, the Plates table contains a Plate

ID field because all the data in the Compounds

table have a common Plate ID.

Child Tables

Every primary table in a protocol, except the

table at the bottom of the hierarchy, has a

child. Child tables contain data that is related

in some way to the data in the corresponding

parent table. For example, the Compounds

table in the above figure is a child of the Plates

table. When you click on a row of the Plates

table, the details of the compounds in that particular

plate appear in the Compounds table.

Calculation Tables

Calculation tables in BioAssay are used to calculate

data for a protocol, in ways that may not

fit into the standard protocol hierarchy. For

example, the standard protocol hierarchy may

be Plates->Wells, but you would like to run

some calculations over the same compound

that is placed on multiple plates. In such cases,

you need calculation tables.

NOTE: The basic difference between calculation

tables and summary tables is that calculation

tables are used for performing calculations

on specific data derived from various tables

whereas summary tables are used for obtaining

the overall picture of a protocol. For example,

calculation tables may use data from only two

tables, but summary tables must use data from

all the tables in a protocol to provide the overall

picture.

Calculation tables contain one or more grouping

fields in addition to calculation fields. The

grouping fields indicate which data should be

used in a calculation. For example, if the

Experiment ID is used as the grouping field,

calculations are made for each Experiment ID.

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Without the grouping field, calculations would

be based on all valid data recorded for the protocol.

Summary Tables

Summary tables in BioAssay are used to

summarize data for a single protocol. Calculations

in the primary tables of a protocol are

usually based on grouped data, such as data for

an individual plate. Therefore, you can not

obtain the overall picture of the protocol using

primary tables.

Summary tables allow you to select fields from

different primary tables and perform calculations

over the selected fields. For example, by

taking averages and standard deviations of data

in more than one plate, you can visualize the

overall picture of the protocol.

Additional Tables

Additional tables are tables that contain data

related to the rest of the data in a BioAssay

protocol. However, unlike summary tables, the

data contained in additional tables are not

linked to the data contained in other tables.

Additional tables can contain any number of

fields. These tables allow you to enter additional

data, which is mapped to the protocol

but is not associated with fields of other tables.

File Import Templates

BioAssay includes a wizard, which enables

you to design templates called File Import

Templates. These templates define how data

should be imported into protocol tables. The

advantage of creating a template is that you

need to specify the format of a data file only

once and reuse the template in future for

importing data into protocol tables.

The format of a data file includes parameters,

such as the type of delimiter used and the number

of header lines in the file being imported.

You must define at least one File Import Template

for any file being imported.

For more information about using the File

Import Template wizard, see “File Import

Templates” on page 111. For more information

about importing data, using a defined File

Import Template, see “Importing Data” on

page 115.

Graph Templates

Graph templates are used to plot data. After

creating a graph template within a protocol

table, you can plot data by clicking on the

Graph: Study Graph tab in Data view of the

protocol table. For more information, see

Related Graphical Data under the section

“Browsing Protocol Data” on page 93.

Graph templates include information related to

both data and the way of displaying that data.

For more information about creating graph

templates, see “Creating a Graph Template” on

page 122.

Protocol Security

Protocol security in BioAssay is mostly related

to the permissions for viewing and modifying

information related to protocols. The user who

creates a protocol is automatically given

appropriate permissions for the protocol. However,

all other users must be explicitly added to

the Protocol Security list, which defines the

permissions granted to each user.

There are three levels of protocol security for

users. The following table describes those

three levels:

Security

Change

Data

Description

Edit, add, and delete protocol

data.

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Security

Validate

Data

Change

Protocol

Definition

Description

Validate data already present

in protocol data tables.

Edit, add, and delete table

definitions, file import

templates, and graph

templates.

6. Click OK. The new protocol is inserted in

the Navigator frame under the selected

project.

NOTE: The protocol definition must be complete

and at least one file import template must

be added to the protocol before you can import

data.

For information about granting permissions to

users for accessing a particular protocol, see

“Defining Security” on page 110.

Designing a New Protocol

BioAssay lets you design your own customized

protocol using pre-defined protocol templates.

In order to design a new protocol, you

must know the type of protocol template to be

used and the kind of data to be imported into

the protocol. The table included below

describes the various types of protocol templates

available in BioAssay.

You need to select the desired template when

creating a new protocol. To create a new protocol:

1. Navigate to the project within which you

need to create a new protocol.

2. Right-click the project in the Navigator

frame to display a pop-up menu.

3. Select the New Protocol menu item. The

New Protocol dialog box appears.

4. Type a name for the new protocol in the

Protocol Name text box.

5. Select the protocol template to be used in

the Choose a template for the protocol list

box.

Defining Tables and Fields

In BioAssay, you need to define protocol

tables and the corresponding fields before you

can import data into the protocol. You can

define any number of tables in a BioAssay protocol.

When defining tables, you need to specify

how the tables are arranged in a

hierarchical tree structure.

The arrangement of tables depends on the data

and the desired result. If the data of a table

depends on the data in another table, the

dependent table must be higher in the structure

than the other table. Typically, raw data values

are found in a table at the lowest level. The

table structure can be defined most efficiently

by defining the lowest level table first, and

working up to the highest level table.

NOTE: It might be helpful to make a sketch of

the table structure before you start defining the

tables and fields.

There are in-built protocol templates in BioAssay

that will help you to get started with creat-

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ing protocols. See “Designing a New Protocol”

on page 100 for more information.

NOTE: After importing data, you will be limited

to adding new fields and adjusting calculation

definitions.

3. Perform the appropriate action:

If you would like

to...

Rename the table or

edit the table

comments

Then...

Click on the table and

edit the fields in the far

right frame.

Defining a Primary Protocol Table

To define tables:

1. Locate the protocol in the Navigator frame

within which you need to define a primary

table.

2. Click the protocol and click the Definition

tab in the Content frame. The protocol definition

appears:

Add a parent table

Add a child table

Remove a table

Right-click on the

table name and select

Create parent table

Right-click on the

table name and select

Create child table

Right-click on the

table name and select

Remove table

4. Click Save Changes after you have finished

performing the table related tasks.

Defining Fields in a Table

After defining a table, you need to define the

fields of that table. However, if you have used

a template or a duplicate protocol, some fields

may already exist.

NOTE: When defining tables and fields, if you

use a pre-defined template or a duplicate

protocol, the table that you need to define may

already exist. Depending upon the template

chosen, the contents of the frame will differ.

NOTE: Templates do not define calculations,

they only insert a field with type calculation.

After tables are created, the table fields must

be defined before data can populate them.

To define fields:

1. Locate the table within which you need to

define fields.

2. Right-click the table to display a pop up

menu.

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3. Select the New Field menu option as shown

in the following figure:

If you would like

to...

Then...

Move a field from a

lower table to a higher

table

Right-click on the

appropriate field

name and select Move

Up To...

NOTE: You can also define a field by editing an

existing field.

To edit an existing field:

a. Click on the appropriate field in the tree.

In the right frame, field definition

appears.

b. Edit the appropriate data as required.

After creating or editing a field, you can

perform various tasks, such as moving the

field or removing the field. The following

table lists the various field related tasks that

you can perform:

If you would like

to...

Remove a field

Move a field from a

higher table to a lower

table

Then...

Right-click on the

appropriate field

name and select

Remove Field

Right-click on the

appropriate field

name and select Move

Down To...

Move a field up

within a table

Move a field down

within a table

4. Click Save Changes.

Right-click on the

appropriate field

name and select Move

Up

Right-click on the

appropriate field

name and select Move

Down

Field Types

In BioAssay, the protocol tables contain fields,

which can be of various types, such as text and

date. When creating fields within protocol

tables, you need to choose the appropriate field

type from the available field types. The field

options that can be defined for a field vary

according to the field type chosen. The following

table lists the various field types and the

corresponding field options available in Bio-

Assay:

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Field Type

Number (Real)

Number

(Integer)

Text

Date

Elapsed Time

(hh:mm:ss

format)

Yes/No

Picklist Value

Calculation

(Numeric

Output)

Calculation

(Text Output)

Compound ID

Well Index

Plate Identifier

Plate Format

Well Format

Concentration

Attachment

(Data Storage)

Field Options

• Use Scientific Notation

• Decimal Places

• Use Scientific Notation

• Decimal Places

None

None

• Use Scientific Notation

• Units of Time

None

Picklist

• Use Scientific Notation

• Defined calculation

Defined calculation

None

None

None

None

None

Use Scientific Notation

None

Field Type

Attachment

(External

Storage)

None

Field Options

NOTE: The Elapsed Time field is a numeric

field. It is meant to simply store an integer, but

it differs from a simple numeric field in the way

of processing data values that are imported into

it from a file.

NOTE: When you enter a value into the data

grid for an Elapsed Time field, the value is

stored as it is. However, when time values are

imported from a file, the Elapsed Time field

attempts to parse the values into integer number

of time intervals for which the field has

been configured through the Field screen on the

Definition tab. For example, suppose the

Elapsed Time field has been configured for seconds,

and the file contains the following values:

00:00

00:30

00:60

01: 30

On import, the Elapsed Time field will take the

following values:

0

30

60

90

The parsing is done because BioAssay does not

support data and time arithmetic. Once the time

values are represented as numbers, calculations

can easily be carried out on them.

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Indexed Fields

Indexed fields are the fields, which are used to

search data in protocol tables. Indexed fields

help to improve searching speed. However, the

time to taken to import data into indexed fields

is slightly more than the time taken to import

data into a non-indexed field. Examples of

indexed fields are Compound ID and protocol

data fields, which are often searched over.

To index a field of a protocol table:

1. Locate the field in the protocol tables tree in

the Definition tab of the protocol.

2. Click the field to display its details in the

Content frame on the right side.

3. Select the Indexed check box.

4. Click Save Changes.

Key Fields

In BioAssay, key fields are used to perform the

following functions:

• Optimize the data returned such that the

returned data is related only to the row

selected in the previous table.

• Group data for calculations such that only

data with the same value in the key field are

used to determine calculations.

NOTE: If you do not use any key fields in a

plate based protocol, the positive and negative

control averages for every plate will be same.

This is because, in the absence of key fields, all

well data will be used for calculating positive

and negative control averages instead of well

data for a particular plate.

To mark a field as a key field:

1. Locate the field in the protocol tables tree in

the Definition tab of the protocol.

2. Click the field to display its details in the

Content frame on the right side.

3. Select the Key Field check box.

4. Click Save Changes.

Required Fields

Required fields are fields, which can not be

empty. If a field is a required field, you must

give a value to that field before a data import is

complete.

To mark a field as required field:

1. Locate the field in the protocol tables tree in

the Definition tab of the protocol.

2. Click the field to display its details in the

Content frame on the right side.

3. Select the Require Value check box.

4. Click Save Changes.

Allow Editing

BioAssay lets you specify whether users can

edit the data of a particular field in a protocol

table. This feature is enabled when the Allow

Editing check box in the field definition is

selected. If this checkbox is unchecked for a

field, users will not be able to manually edit the

value of the field in the data table.

To allow users to edit the data of a field:

1. Locate the field in the protocol tables tree in

the Definition tab of the protocol.

2. Click the field to display its details in the

Content frame on the right side.

3. Select the Allow Editing check box.

4. Click Save Changes.

Show Field

BioAssay provides you with the option of hiding

some fields of a protocol table when the

table is displayed in data view. This feature

may be useful for fields that are necessary for

certain calculations, but not relevant to the user

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owsing the data. By default, all fields are visible.

To hide a field:

compute the calculation. The following figure

shows the Calculation Wizard dialog box:

1. Locate the field in the protocol tables tree in

the Definition tab of the protocol.

2. Click the field to display its details in the

Content frame on the right side.

3. Uncheck the Show Field check box.

4. Click Save Changes.

Assigning a Calculation to a Field

In BioAssay, four different types of calculations

are available for being assigned to fields.

These four types of calculations are as follows:

• Aggregate: Calculations made on a row's

aggregate data found in a lower table.

• Mathematical: Calculations dependent upon

a user defined equation.

• Curve Fit: Calculations made to fit a set of

data to a particular curve.

• Conditional: Calculations that fill a field

based on a set of user-defined conditions.

• External: Calculations that are run externally

on BioAssay data through customized

calculation engines. You can import the

results back into BioAssay.

For more information about defining calculations

and assigning values, click on the type of

calculation in the above list.

The above mentioned calculations can be

assigned to fields by using the Calculation wizard.

The Calculation wizard helps you to

define the calculation and the data used to

To define a calculation for a field:

1. Click the field for which you need to define

calculation. The field type must be either

Calculation (Numeric output) or Calculation

(Text output).

2. Click the Edit Calculation button in the Content

frame to display the Calculation Wizard

dialog box.

3. Select the tab for the appropriate calculation

in the Calculation Wizard dialog box.

4. Select the appropriate type of calculation.

5. Click Next.

6. Select the tables and fields that you want to

use for variables in the calculation. The

fields listed depend on the type of calculation

you are creating and the field type of

field.

• Except for Conditional calculations, only

fields with a field type of Number (Real),

Number (Integer), or Calculation are displayed.

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• For Aggregate calculations, only fields in

tables below the current table are displayed.

• For Mathematical, Conditional and Curve

Fit calculations, only fields in the current

table or tables higher than the current table

are displayed.

7. Click Next.

8. Specify the value for limiting the results.

9. Click Finish.

Aggregate Calculations

Aggregate calculations are calculations that are

performed on a data set resulting in one figure

that is representative of the whole data set.

Therefore, aggregate calculations must be

included in a table higher than the location of

the data set.

The default aggregate calculations are as follows:

• Mean: Takes an average of all aggregate

data.

• Standard Deviation: Finds the standard

deviation of all aggregate data.

• Sum: Computes the sum of all aggregate

data.

• Maximum: Returns the maximum value in

the aggregate data.

• Minimum: Returns the minimum value in

the aggregate data.

The aggregate calculations can be accessed

using the Aggregate tab in the Calculation

Wizard dialog box. When you click the Edit

Calculation button in the field definition, the

Calculation Wizard dialog box appears.

To insert an aggregate calculation to a field:

1. Select the appropriate calculation in the

Aggregate tab of the Calculation Wizard dialog

box.

2. Click Next. The Input Values page appears.

3. Select the table where the data to be used

for the calculation is located, in the Table

drop down list.

4. Select the field where the data to be used

for the calculation is located, in the Values

drop down list.

5. Click Next. The Define Conditions page

appears.

6. Add a condition if you would like to use

only those data points that meet the condition.

To add a condition:

a. Click Add.

b. Select a field where the data must fulfill

the condition.

c. Select a mathematical equality symbol.

d. Finish the condition by entering the

value that the data must fulfill.

7. Click Next button. The Finished screen

appears.

8. Select the number of decimal places that the

result should be limited to, in the Limit

result to drop down list.

9. Click Finish.

Mathematical Calculations

Mathematical calculations are calculations that

are performed using a defined equation containing

variables that are related to table data.

Therefore, mathematical calculations must be

made on data in the same table in which the

calculation is inserted or any table higher than

that table. BioAssay contains some pre-defined

mathematical calculations, which are as follows:

• % Inhibition: Returns the % inhibition calculated

using the following formula: (100 *

((Value - LowControlAverage) / (HighControlAverage

- LowControlAverage))).

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• Log(x): Returns the log of a value.

• 10^x: Returns the inverse log of a value

(base 10).

• Addition: Returns the sum of two values

derived from a data table.

• Subtraction: Returns the difference between

two values derived from a data table.

• Multiplication: Returns the product of two

values derived from a data table.

• Division: Returns the quotient when one

value derived from a data table is divided

by another one.

• Percentage: Returns the percentage result

using the following formula: ((first value/

second value)/100)

• Half Life: Returns the result of the following

formula: (Time * ln(2)) / (ln(100 /

PctRemaining)).

• Z' Factor: Returns the result of the following

formula: 1 - ((3*SDPosCtl +

3*SDNegCtl) / abs(AvgPosCtl -

AvgNegCtl))

• Normalization: Returns the result of the following

formula: (100 * (Value - LowCtl) /

(HighCtl - LowCtl))

When you click the Edit Calculation button in

a field definition, the Calculation wizard

appears. Clicking the Mathematical tab provides

access to the mathematical calculations.

When performing a mathematical calculation,

you can use two options, which are as follows:

• Use a default equation

• Define a new equation

Use a Default Mathematical Calculation

To use a default mathematical calculation:

1. Click the Mathematical tab in the Calculation

Wizard dialog box. The Select Calculation

page of the Calculation Wizard appears.

2. Select the calculation that you would like to

use.

3. Click Next. The Calculation Parameters

page appears.

4. Select the values that should be used for the

variables in the equation. This involves first

selecting a table and then a field in that

table from the drop down list boxes.

5. Repeat step 4 for all the variables listed in

the Equation Parameters table.

6. Click Next. The Finished page appears.

7. Select the number of decimal places to

which the result should be limited, in the

Limit result to drop down list.

8. Click Finish.

Define a New Mathematical Calculation

To define a new calculation:

1. Click the Mathematical tab in the Calculation

Wizard dialog box. The Select Calculation

page appears.

2. Click New. The Edit Custom Function dialog

box appears.

3. Enter a name for the calculation in the

Function text box.

4. Enter an equation for the calculation in the

Equation text area. General information

about defining an equation is provided in

the help section of this dialog box. Supported

operators are found under the Operators

tab and predefined functions are listed

under the Functions tab.

5. Click OK. The Select Calculation page of the

Calculation Wizard dialog box appears.

6. Select the calculation, which you defined in

the third step.

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7. Click Next. The Calculation Parameters

page appears.

8. Select the values that should be used for the

variables in the equation. This involves first

selecting a table and then a field in that

table from the drop down list boxes.

9. Repeat step 8 for all the variables listed in

the Equation Parameters table.

10.Click Next. The Finished page appears.

11.Select the number of decimal places to

which the result should be limited, in the

Limit result to drop down list.

12.Click Finish.

Curve Fit Calculations

Curve Fit calculations are calculations that are

used to fit data to an equation so that a curve is

generated in a graph plot. Therefore, calculations

must be made on data in the same table in

which the calculation is defined or any table

higher than that table.

When you click the Edit Calculation button in

a field definition, the Calculation Wizard dialog

box appears. Clicking on the Curve Fit tab

provides access to the Curve Fit calculations.

The list will contain the curve fits that are

applicable for the given table, based on the

graph templates that have been set up and the

curve equations that have been defined for

those graphs. If the list does not contain any

values, go back to the Graph Templates section

and set up the graphs and curve fits that you

wish to perform. For more information, see

“Creating a Graph Template” on page 122.

To define a Curve Fit calculation for a field:

1. Select the curve parameter to be used for

the calculation in the Insert Value section

within the Curve Fit tab. The options displayed

will be limited to curve parameters,

which are related to the selected Curve Fit

calculation.

NOTE: If no predicted values were defined in

the Curve Fit calculation definition, there will

be no options in the corresponding drop down

list when the Predicted option is selected.

2. Click Next. The Finished dialog box

appears.

3. Select the number of decimal places to

which the result should be limited, in the

Limit result to drop down list.

4. Click Finish.

Define a New Curve Fit Calculation

To define a new Curve Fit calculation:

1. Create a graph template.

2. Click the Curve Fits tab in the definition of

the graph template to display the Add or

Remove Curve dialog box.

3. Click New. The CurveFit Template dialog

box appears.

NOTE: For more information about creating

new models, see the topic, “Defining a New

Model” under “Curve Fit Calculations” on

page 108.

4. Enter a name for the calculation in the

Name text box.

5. Select the model to be used in the Defined

Models list.

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6. Enter parameter information under the

Parameters Tab, as shown in the following

figure:

To enter parameter information:

a. Select Variable or Constant in the Type

column, for each parameter.

b. Enter a numerical value or select a value

from the drop-down menu in the Value

column.

7. Enter additional calculation options under

the Advanced tab.

8. Enter the desired predicted values for variables

under the Predicted tab

To enter predicted values:

a. Click Add. The New Predicted Value dialog

box appears.

b. Enter a name for the predicted value.

c. Select which value is given (X or Y).

The value not provided is the value

which is predicted.

d. Enter a value for the variable.

e. Click OK to close the New Predicted

Value dialog box.

9. Click OK in the Curve Fit Template dialog

box. The Add or Remove Curve dialog box

appears.

10.Select the curve you have just defined and

click the Add to List button.

11.Click OK.

Defining a New Model

To define a new model:

1. Click New under the Model tab in the Curve

Fit Template dialog box. The User-Defined

Model dialog box appears.

2. Enter a name for your model in the Name

text box.

3. Enter an equation in the Equation text box.

Equation definition tips and conventions

can be found in the lower half of the window.

4. Click Validate Equation to ensure that the

equation entered is written in the correct

syntax.

5. Click OK. The new model is listed under the

Model tab.

Editing a Curve Fit Calculation

To edit a Curve Fit calculation:

1. Select the Curve Fit calculation that you

need to edit within the Available Curves list

in the Add or Remove Curve dialog box.

2. Click Edit. The CurveFit Template dialog

box appears.

3. Edit the name for the calculation in the

Name text box, if necessary.

4. Select a different model, if required.

5. Edit the parameter information under the

Parameters tab, as shown in the following

figure:

To edit parameter information:

a. Select Variable or Constant in the Type

column, for each parameter.

b. Enter a numerical value or select a value

from the drop-down menu in the Value

column.

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6. Edit the calculation options under the

Advanced tab.

7. Click OK in the Curve Fit Template dialog

box. The Add or Remove Curve dialog box

appears.

8. Select the curve you have just edited and

click the Add to List button.

9. Click OK.

Conditional Calculations

Conditional calculations allow you to fill a

field based on the contents of other fields in a

protocol. Conditional calculations are the only

calculations that may output either a text value

or a numeric value. In order for a conditional

calculation to hold a text value, the filed type

of the corresponding field must be defined as a

Calculation (Text Output) in the Field Type

section of the field definition.

To define a conditional calculation:

1. Click Edit Calculation in a field definition to

display the Calculation Wizard dialog box.

2. Click the Conditional tab. The Conditional

tab page appears.

3. Click Next. The Define Output Values page

appears.

4. Choose a value that will be placed in the

field when none of the conditions are met

(the default value).

5. Add as many conditions and output values

as you need by clicking the Add button and

filling in the table. In the above example,

the Then Output column will contain the

value, In Range if the value of the Successful

Curves field is between 1 and 5, and will

contain the appropriate out of range message

if it is high or low.

6. Click Next to display the Finished page.

7. Click Finish.

External Calculations

The calculation engine of BioAssay lets you

perform calculations externally and include it

in a protocol definition as if it were native to

the calculation engine.

To define an External calculation:

1. Click Edit Calculation in a field definition to

display the Calculation Wizard dialog box.

2. Click the External tab. The External tab

screen appears.

3. Click Configure Calculation. The following

dialog box appears:

4. Select the field whose average you need to

calculate.

5. Click OK.

6. Click Next. The Finished page appears.

7. Select the number of decimal places to limit

the result.

8. Click Finish.

Defining Security

Users, other then the creator, must be given the

appropriate permissions to access and edit protocols.

To give a user permissions to a protocol:

1. Open the appropriate protocol definition.

110 BioAssay Desktop & Workgroup

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2. Click on the Security tab in the Content

frame.

NOTE: The Security tab is accessible only to

an administrator user.

3. Enable the Lock valid data check box.

4. Click Edit Protocol Security. The Protocol

Security dialog box appears.

You can add or delete a user or group from

the security list.

To add a user or group to the protocol security

list:

a. Select the user or group in the Available

list.

b. Click Add.

c. Select the check boxes corresponding to

the permissions you would like to give

the user or group. For more information

about your options, see “Protocol Security”

on page 99.

To remove a user or group from the protocol

security list:

a. Select the user or group in the table (on

the right).

b. Click Remove.

5. Click OK.

Importing and Viewing Data

In order to import data into a BioAssay protocol,

you must define the protocol tables first.

The only way to import data into a BioAssay

protocol is to use the File Import wizard and

file import templates. Therefore, a file import

template compatible with the data being

imported must also be defined before importing

data.

File Import Templates

File import templates are used to import data

from a file and populate user-defined tables

with that data.

To define a file import template:

1. Open the protocol definition.

2. Right-click the File Import Templates folder

in the tree to display a pop-up menu.

3. Select the New Template menu item. The

File Import Template Wizard dialog box

appears.

4. Enter a name and description for your file

import template.

NOTE: File import templates contain a default

name. If you do not rename your file import

template, you may lose it later.

5. Click Next. The File Format Information

page appears.

6. Select a file delimiter. The following

options are available:

• Commas

• Tabs

• Spaces

• Tecan

• Other

7. Select the type of file you are importing.

The following table describes the available

file types:

File Type

Columnar

(Excel-

Type)

Description

A series of columns; each

column contains the values for

one variable.

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File Type

Plate Block Raw data is arranged in a

block or blocks, sometimes

separated by header lines; the

block may be arranged to

coincide with plate arrangement,

or it may be in a

columnar format.

Custom

File Type

Description

Enables you to select a custom

file importer.

8. Complete the details related to your file

type.

• Columnar:

• Specify if your data file has header lines

(lines not containing actual data). If there

are header lines, enter the number of

header lines in the text box.

• Specify how you want to treat empty values

in your data. You can either leave

those fields blank, or fill them with the

last non-blank value encountered in the

file. For example, your data file may contain

the following data:

• Even though all the above data apply to

compound AB-00001, the compound name

is not repeated for clarity.

Compound ID

AB-00001 34.5

AB-00001 56.4

AB-00001 67.8

Result

• All results are properly associated with the

correct compound id.

• Plate Block:

• Check the available boxes to indicate

which sections are present in your plate

block file. Enter the number of rows in

each category.

• Custom File Type:

• Select the customized file importer. You

can also configure it by clicking the Configure

button.

NOTE: When you click the Configure button, a

DOS window flashes and disappears.

Compound ID

AB-00001 34.5

56.4

67.8

Result

9. Click Next.

• If you have selected a Columnar type file,

the Other Options page is displayed. In

this page, you can specify whether you

want to truncate the resultant data. You

can also specify the action that should be

taken when the input data is in incorrect

format.

• If you have selected a Plate Block file, the

Other Options page is displayed. In this

page, you can select how many values

appear for each well in your file. The fol-

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lowing table describes the available

options:

Option

A single

value for

each well.

Multiple

values for

each well -

separate

data blocks,

separate

fields.

Description

A standard protocol which

measures a single value for

each well. There may be data

for multiple plates in a single

file, but each well has just one

number associated with it.

A protocol where multiple

values are measured for each

well. In the most common

case, a reader reads at 2

different wavelengths and

outputs a data block for each

wavelength.

NOTE: If you have selected a Custom File

type, the Map Fields page is displayed.

Continue from step 11.

10.Click Next. The Map Fields page appears.

11.Assign values to the fields in the selected

table by selecting the type of value to populate

the field. Choices depend on the type of

file you have chosen and the type of file

being imported. For a description of

options, see “File Import Data Source

Options” on page 114.

12.Click Finish.

Multiple

values for

each well -

separate

data blocks,

same field.

A kinetic protocol where

multiple values are measured

for each well at different time

points. All the values will go

in the same field, but there are

many values for each well.

Multiple

values for

each well -

columnar

format,

separate

fields.

Multiple

values for

each well -

columnar

format,

same field.

A protocol where multiple

values are measured for each

well, and the data is arranged

in a columnar format similar

to an Excel file.

A kinetic protocol where

multiple values are measured

for each well at different time

points, and the data goes into

the same field.

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Plate Block Data Format

• A: 1 line at the top of cf file

• B: 2 lines before plate block data

• C: 2 columns before plate block data

• D: 4 lines after plate block data

• E: 3 lines of plate block data

File Import Data Source Options

The file import data source options are as follows:

• Leave Blank

• Field Type: Columnar (Excel) or Plate

Block

• Description: No data is imported into

this field.

• System Assigned

• Field Type: Columnar (Excel) or Plate

Block

• Description: The application automatically

assigns a value for this field (e.g.

Well Format for a plate linked protocol).

• Data in File Column Number

• Field Type: Columnar (Excel)

• Description: Data is found in a column in

a data file - enter the column number to

the right.

• Use Filename Data

• Field Type: Columnar (Excel) or Plate

Block

• Description: Data is part of the filename.

• Use Default

• Field Type: Columnar (Excel) or Plate

Block

• Description: A default value should be

entered for this field - enter the default

value to the right.

• Prompt Me

• Field Type: Columnar (Excel) or Plate

Block

• Description: During import, you will be

prompted for the value of this field.

• Upload File

• Field Type: Columnar (Excel) or Plate

Block

• Description: For attachment fields only.

The file itself will be uploaded to the

database, into the field.

• Plate Block Data

• Field Type: Plate Block

• Description: Data is the data found in the

plate block.

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• File Header Cell

• Field Type: Plate Block

• Description: Data is in a particular cell in

the File Header Block - enter the cell to

the right.

• Block Header Cell

• Field Type: Plate Block

• Description: Data is in a particular cell in

the Block Header Cell - enter the cell to

the right.

• Block Footer Cell

• Field Type: Plate Block

• Description: Data is in a particular feel in

the File Block Footer Cell - enter the

cell to the right.

• Block Column Cell

• Field Type: Plate Block

• Description: Data is in a particular feel in

the Block Column Cell - enter the cell to

the right.

• Use Import Time

• Field Type: Columnar (Excel) or Plate

Block

• Description: Uses time on your machine

when file is imported.

• Use Current User

• Field Type: Columnar (Excel) or Plate

Block

• Description: Uses username of user who

imports file.

Importing Data

You can import data into a protocol using

Import File Wizard after defining the protocol

primary tables and a File Import Template

compatible with the data file being imported.

To import data into a protocol:

1. Open the protocol by selecting it in the

Navigator frame.

2. Click the Import a data file link in the Tasks

tab. The Import File Wizard dialog box

appears.

3. Select an import template in the Import Template

list.

4. Click Next. The Select Data File (s) page

appears.

5. Click Browse to select the data files, which

you would like to import.

6. Click Next.

7. Enter the appropriate information, if the

wizard asks. This page may differ depending

on the File Import Template being used.

If the wizard does not ask for additional

information, continue from step 9.

8. Click Next. The Import File page appears.

9. Select the appropriate import option as per

your requirements.

10.Click Finish. The appropriate table is populated

with data. If some fields in the protocol

tables are calculations, those

calculations are performed by the application

and the results are displayed. You can

view the table data in the Data tab of the

protocol.

Searching for and Viewing Data in Tables

To search for and view your data:

1. Click the Data tab. The Open Datasource

dialog box appears.

The left hand side shows the data tables that

are available for opening. By default, the

topmost table in the Primary Data tables

hierarchy is selected. From here, you can

browse your primary assay data, make

changes, and validate data. Other tables that

may be available are calculation tables,

summary tables, additional tables, and a

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flattened view of your primary called data

called "All Primary Data - Read Only".

When you select these tables, the fields on

the right hand side change.

2. Enter search criteria and click the Search

button or click the Retrieve All button to

retrieve all data. The Search By List button

lets you search for a list that you have saved

earlier. For more information, see “Compound

Lists” on page 145.

Viewing and Browsing Data

After data has been retrieved, data is browsed

in a hierarchy. To view data in a child table,

click the plus sign (+) in the left most column

of the data table. If there is no plus sign, there

is no child data associated with the data you

are viewing.

Validating Protocol Data

When protocol data is first imported, the letter

N appears in the left most column in the data

table. This indicates that data has not been validated

yet.

To validate protocol data:

1. Open the protocol data tables that contain

the data to be validated. The data tables can

be accessed using the Data tab in the Content

frame when the protocol is opened.

2. Select the data to be validated.

3. Select Actions --> Change Validity menu

option from the menu bar. The Change

Validity dialog box appears.

4. Select the validity you would like to assign

to the selected data. The following table

describes the available validity options:

Validity

Option

Not Validated

Icon Description

N

No validation

decision

has

been made.

Valid V Data is

found to be

valid.

Invalid I Data is

found to be

invalid.

Invalid data

is not used in

calculations

or curve fits.

Request

Review

R

Data must be

reviewed

before

making a

validation

decision.

Used in

Calculations?

Yes

Yes

No

Yes

5. Select the appropriate cascading options.

The available options are as follows:

• Cascade validity change to detail

records: Apply the same validity decision

to records summarized by the selected

record

• Override current invalid records:

Change invalid records summarized by

the selected data to the new validation.

6. Click OK.

116 BioAssay Desktop & Workgroup

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Importing Data from External Data Source

Data can be imported from an external data

source into BioAssay by using the feature,

Structured Data Manager (SDM). Apart from

facilitating data import from external sources,

SDM also lets you validate the data contained

in external sources and populate the protocol

data table based with the result of validation.

In order to ensure that data is imported efficiently,

SDM classifies BioAssay users into

three groups and clearly distinguishes the roles

that can be performed by these users. The three

groups of users recognized by SDM, are as follows:

• Administrator

• Protocol Administrator

• End User

Administrator

Only users of the Administrator group are

allowed to define external data sources, which

can be used for importing data into BioAssay.

When defining an external data source, an user

of the Administrator group needs to provide

information related to the external data source.

This information includes various entities,

which are as follows:

• Map data source return values to protocol

fields

• Run external data source manually

• Specify whether the changes made to the

external data source parameters would take

effect after updation or after next data

import.

End User

The SDM feature of BioAssay allows users of

the End Users group to perform various functions,

which are as follows:

• Run external data source manually

• Specify whether the changes made to the

external data source parameters would take

effect after updation or after next data

import.

Defining a New External Data Source

To define a new external data source:

1. Right-click on the External Datasources

folder in the Navigator frame and select the

New Datasource menu option. The New

External Datasource window appears:

• Data Source Name

• Connection String

• SQL Query

• SQL Parameters

• SQL Return Values

Protocol Administrator

The SDM feature of BioAssay allows users of

the Protocol Administrator group to perform

various functions, which are as follows:

• Add an external data source to a protocol

• Set data source parameter values

2. Enter appropriate information in the Name

and Description fields.

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3. Select a database type in the Data Source

Type drop down list.

4. Click the icon corresponding to the Connection

String field.

• For data source type, Oracle, the following

Configure Connection String window

appears:

• For data source type, SQL Server, the following

Configure Connection String

window appears:

5. Enter relevant information in the Data

Source, Initial catalog, User ID, and Password

fields.

6. Click OK.

7. Enter a relevant SQL query in the SQL field

to fetch data from an external application or

database.

The SQL query should be in one of the following

forms:

• SELECT value FROM table

• SELECT value1, value2……. FROM

table

NOTE: Use appropriate parameter marker

with parameters in where clause.

8. Click OK.

9. Click the + icon within the Parameters section

to add a new row to the table displayed

within the Parameters section.

10.Enter relevant information about the parameters

supplied through the SQL query.

11.Click the + icon in the Return Values section

to add a new row to the table displayed

within the Return Values section.

12.Enter relevant information about the return

values supplied through the SQL query.

13.Click OK. The newly defined external data

source appears within the External Datasources

folder in the Navigator frame.

Adding and Mapping an External Data

Source to a Protocol

To add and map an external data source to a

protocol:

1. Create a plate-based protocol.

2. Add relevant fields to the Plates table so

that these fields can hold the values

returned by the mapped external data

source.

3. Right-click on the Plates table within the

Primary Data Tables folder to display a popup

menu.

4. Select the New Datasource menu option.

The Select External DataSource window

appears.

5. Select an external data source in the Data

Source list box and click the OK button. The

New External DataSource window appears.

118 BioAssay Desktop & Workgroup

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6. Modify the data in the first row of the

Parameters table corresponding to the

Query Value column.

NOTE: The Query Value field is the only field

through which you can pass different values to

the external database through the SQL query

and observe the result of the query.

7. Select the appropriate fields in the drop

down list corresponding to the Protocol

Field column in the various rows of the

Return Values table. These fields will hold

the data returned by the SQL query, which

is defined in the external data source.

NOTE: The external data source within the

Navigator frame is called the parent data

source, while the mapped data source within the

protocol is called the child data source. After

mapping an external data source to a protocol,

when you make changes to the parent data

source, the changes get propagated to the child

data source. However, if you make changes in

the return values of the parent data source, the

changes get propagated but are not reflected

until the protocol administrator edits the child

data source and assigns the return values to a

field within the protocol.

8. Click OK.

Running the External Data Source Manually

To run the external data source manually:

1. Click the Data tab to display the Open Datasource

dialog box.

2. Click Retrieve All to display the data view

of the protocol.

3. Select Actions > Get Data: [External data

source name] menu item. The Run External

Data Source window appears.

4. Change any data in the Query Value column

of the Input Parameters table.

5. Click Preview to view the changes in return

values due to the change in input parameters.

6. Click OK. The changed data appears in the

data view of the protocol.

NOTE: An end user can also specify that the

data table will be automatically populated during

updation or data import, by selecting the

appropriate check box in the Configure Data-

Source window. For example, by enabling the

Run when data is imported check box, a user

can ensure that data table will automatically

updated by external data during data import.

NOTE: When the Run when data is imported

check box is enabled, the data fetched by external

data source will take precedence over data

imported from a file.

For example, suppose you have two fields in a

protocol: Animal Response and Animal Diet.

You have connected the protocol to an external

datasource and enabled the Run when data is

imported check box. You have also created a

file import template for importing data into the

protocol.

Now, if you perform a file import operation to

populate the protocol fields, the Data Preview

window will display the data fetched by the

file import template. However, the protocol

fields will be actually populated with data from

the external data source when the import operation

is completed.

Validating Data

To validate data using SDM:

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1. Define the external data source so that it

contains a SQL query, which validates data

based on some condition.

2. Run the external data source with different

input values to check validity.

Integrating with Excel

1. The Excel Integration feature is available

only in BioAssay Desktop 12.0.

BioAssay provides Excel Integration 1 feature.

You can select rows of data from the primary

data tables, export the data to an Excel spreadsheet,

and perform operations on the exported

data.

A configuration interface lets you specify how

the data is organized when it is exported to

Excel. For example, you can specify the columns

that are to be exported, sorting order of

the columns, and macro to run once the data is

imported into Excel.

After manipulating the exported data in Excel,

you can import it into BioAssay using the Bio-

Assay File Importer. The BioAssay File

Importer allows you to load data directly from

Excel or choose how existing data is dealt with

when data is imported. The choices for dealing

with existing data are as follows:

• Overwrite: Overwrite existing data with

new data.

• Don’t Overwrite: Do not overwrite any

existing data. This is equivalent to the current

file import data merge algorithm

employed by the BioAssay File Importer.

• Warn: The user is warned if data is about to

be overwritten. At this time the user has the

option to cancel the action, if desired.

To integrate BioAssay with Excel:

1. Create a plate based IC50 protocol.

2. Create a file import template and import

data into the protocol.

3. Create a file import template for Excel analysis.

a. Right-click the File Import Template

folder in the protocol definition tree and

select New Template. The Template Name

page of File Import Wizard appears.

b. Enter template name and description.

c. Click the Next button. The File Format

Information page appears.

d. Specify the number of header lines in

the Columnar (Excel-Type) tab.

e. Click the radio button, Fill field with last

non-empty value encountered.

f. Click the Next button. The Other Options

page appears.

g. Click the Next button. The Map Fields

page appears.

h. Select the fields and enter values for the

selected fields.

i. Click the Finish button.

4. Right-click on the Plates table in the protocol

definition tree and select New Excel

120 BioAssay Desktop & Workgroup

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Analysis. The Excel Analysis Configuration

dialog box appears:

12.Click the Data tab.

13.Click Datasource -> Retrieve All.

14.Select a row in the Plates table.

15.Select Action -> Run Excel Analysis. The

Select Excel Analysis dialog box appears.

16.Click the OK button. The exported data

appears in the selected Excel file.

NOTE: The BA_Analysis_Results worksheet

appears only if you are using a macro. You can

make changes to the data in this worksheet and

import the updated data into BioAssay.

5. Enter name and description for the Excel

analysis.

6. Locate an Excel file using the Browse button

and select it so that file path appears in

the Excel WorkBook text box.

7. Specify the macro name in the Excel Macro

text box.

8. Select the file import template that you created

for Excel analysis.

9. Select the fields to be exported; all the protocol

tables and their fields are listed in the

Fields section. In the right section the

selected fields appear:

10.Click the OK button.

11.Create a database attachment field in the

Plates table. The field name should the

name of the Excel analysis that you created,

followed by ‘_Rslt’. For example, if the

name of the Excel analysis is Exe1 then the

database attachment field should be

Exe1_Rslt.

17.Click the BA_Prompt_Me worksheet.

18.Enter values corresponding to the fields displayed.

19.Click Continue to BioAssay in the dialog

box that appears on the Excel worksheet.

The Excel Analysis dialog box appears.

20.Click the Yes button. The Data Preview window

appears.

21.Click the Load All button. A success message

appears.

22.Click the OK button. The changes made to

the data in the Excel file will be reflected in

the Plates table.

Data Manipulation and Curve

Fitting

In BioAssay, any set of data can be plotted and

fit to a curve if desired. The only constraint is

that both fields being plotted are found in the

same table.

In order to plot your data, you must first design

a graph template for your protocol. Graph templates

define the data being plotted, the location

from where the graph template is

accessed, and the physical properties of the

graph.

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Creating a Graph Template

Graph templates are used to plot data in a protocol.

These templates define the following

properties of the resultant graph:

• The data that is to be plotted

• Physical properties of the graph, such as

error bars, gridlines, graph type, and data

point markers

• The location from where the graph template

can be accessed

• The curve equations that will be fit to the

data by default

To create a new graph template:

1. Browse to the definition of your protocol

and right-click a primary table to display a

pop-up menu.

2. Select the New Graph Template menu item.

The graph template details open in the right

frame.

3. Enter the name and other details as follows:

• Template Name: A name for the template.

• Comment: Additional comments for the

template.

• Summary Table: The table in the protocol

where the graph images will be stored.

For instance, if you are preparing a graph

of activity versus concentration for each

compound, you would select the Compounds

table as the Summary Table, and

the data table would contain the activity at

each concentration.

• Data Table: The table from where the

plotted data is taken. This will typically be

the direct child table of the Summary

Table.

• X-Axis: The field from which the application

should populate the X-axis.

• Y-Axis: The field from which the application

should populate the Y-axis.

When you enter the above details, the following

screen appears:

4. Click Conditions to limit the points that are

included in your graph. For instance, you

may wish to include only points where the

Y-axis value is above 0.

5. Click Graph Storage to define how to store

images of the graphs in your data table. You

can store the full image, or strip the titles

and legends from the stored image. These

stored images are recreated when the data is

recalculated.

6. Click Curve Fits to change the list of curve

equations that are fit to the data by default

when calculations are done. The set of

curves that you define here will be available

for use when you set up Curve Fit calculations.

You can either use the default equations

or create your own.

NOTE: To define a new calculation, see

“Mathematical Calculations” on page 106.

7. Click Display Options and define the graph

display options.

8. Click Save Changes.

Plotting Data using a Graph Template

In BioAssay, you can plot data using a graph

template after defining the graph template in

the Definition tab. There are two ways to dis-

122 BioAssay Desktop & Workgroup

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play the graphs that have been defined using

the graph templates:

• Graph images

• Interactive graphs

Graph Images

Graph images are image fields, which store

graphs. When defining a graph template for a

graph image, you must indicate which table is

the summary table for the graph. Image fields

for storing the graph are then added to the summary

table. When calculations are performed,

a small and a large image of the graph are

stored in the image fields. By default, the

graphs are shown as hyperlinks with the text

"Graph", as shown in the following figure:

NOTE: The graphs can be displayed by double

clicking the hyperlink or right-clicking and

choosing Show Pictures from a pop-up menu.

Interactive Graphs

When defining a graph template for an interactive

graph, you must indicate the location from

where the data for the graph template should

come. If the data for the graph template is

defined to be available from a table, a button

for that graph will appear in the display bar, as

shown in the following figure:

Using Annotation in Graphs

An annotation refers to a collection of text that

is added to a graph in order to provide some

extra information about the graph. For example,

when plotting a bar graph, you can insert

text into the bars in order to identify the compounds

to which the respective bars are related.

The Graph Annotation feature in BioAssay lets

you insert and delete annotations within the

graph plots.

NOTE: You cannot add annotations to graphs

within the calculation tables.

Inserting Annotation

To insert an annotation:

1. Plot a graph in the Data tab of a protocol by

using graph templates.

2. Right-click on an empty area of the graph

and click Insert Text. The Enter text dialog

box appears.

NOTE: Empty area refers to a place within the

graph plot that does not include data points or

axes. However, you can insert text within a bar.

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3. Enter text in the available text box and click

the OK button. The entered text will be displayed

at the location where you rightclicked

to insert text. The entered text is

persistent. Therefore, you can navigate

away from the graph and view the annotation

again.

the equation as close as possible to the data

points. The following figure shows the

graph after fitting the curve:

Deleting Annotation

To delete an annotation:

1. Click on the annotation present in the

graph. The BioAssay Modules dialog box

appears:

2. Click Yes to delete the text.

Fitting Data to a Curve

The graphing interface of the BioAssay application

will fit any data to any curve as long as

the curve is defined in the application. By

default, two curves are defined in BioAssay:

• Sigmoidal-dose response

• One phase exponential decay

For more information about how to define a

new curve fit equation, see “Curve Fit Templates”

on page 124.

If the correct curve is already defined, you can

fit data to the curve. To fit data to a curve:

1. Click Curve after plotting the data in the

Data tab to display the Add or Remove Curve

dialog box.

2. Highlight the name of the curve in the Available

Curves list box.

3. Click Add to List. The name of the curve

appears in the Curves to Display list box.

4. Repeat step 2 and step 3 until all the curves

that you want to plot are listed in the Curves

to Display list box.

5. Click OK. All curves listed in the Curves to

Display list box are added to the plot, fitting

NOTE: The graph characteristics, such as

scaling type and distance between the fitted

curve and data, are defined in the Graph

Options dialog box.

NOTE: After fitting the data to a curve, the

Data tab will display equation parameter values

and curve fit statistics.

Curve Fit Templates

Curve fit templates are listed in the Available

Curves list box within the Add or Remove

Curve dialog box. To access the Add or

Remove Curve dialog box, click the Curve button

in the menu bar of any plot. For more

information about using a template that is

already listed, see “Fitting Data to a Curve” on

page 124.

Creating a New Template

To create a new curve fit template:

124 BioAssay Desktop & Workgroup

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1. Click New in the Add or Remove Curve dialog

box. The CurveFit Template dialog box

appears.

2. Enter a name for the template in the Name

text box.

3. Highlight the model to be used. For more

information about creating new models, see

“Defining a New Model” under “Curve Fit

Calculations” on page 108.

4. Enter Parameter information under the

Parameters Tab.

a. Select Variable or Constant, in the Type

column, for each parameter.

b. Enter a numerical value, or select a

value from the drop-down menu in the

Value column.

5. Enter additional information under the

Advanced tab.

6. Click OK. The name of the new template

will be listed in the Available Curves list

box.

Editing a Template

The edit template interface is similar to the

interface for creating new template. To edit a

template, click the Edit button in the Add or

Remove Curve dialog box. The CurveFit Template

dialog box opens with the fields populated

according to the current template settings.

Viewing the Plotted Data

When you plot data in BioAssay, the Data tab

available in the menu bar of the plot, displays

the plotted data along with information about

any curves fitted to the data. The Data tab itself

contains three tabs, which are as follows:

• Equation

• Data Statistics

• Fit Statistics

Equation

The Equation tab displays the equation in

which the data is fit. The x and y variables

define the x and y coordinates for the fitted

curve. The values for other parameters in the

equation are assigned to fit the data in the best

possible way. The final values are recorded in

the Parameter Values table.

Data Statistics

The Data Statistics tab defines various statistics

for both the X and Y values.

Fit Statistics

The Fit Statistics tab records statistics, which

define how well the equation, found under the

Equation tab, fits the table data. The information

found under this tab will help you to determine

if the data is meaningfully fit to the

curve.

Manipulating Data Points

BioAssay lets you manipulate Data points of a

plot in several ways when viewing the plot

(For more information on how to view plots,

see “Plotting Data using a Graph Template” on

page 122). This feature may be useful in

removing outliers in order to produce a better

curve fit.

You can include or exclude data points from

the plot, specify points as invalid, or specify

points as not validated. By marking the points

beforehand, you can perform an operation on

more than one points at a time. The operations

can be performed using the Point Status Button

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Panel or through the context menu, which

appears on right-clicking on the graph.

NOTE: By default, active data points appear in

blue whereas inactive data points appear in

red. All data points are active by default.

To manipulate Data points in a plot:

1. Click the points, which you need to manipulate.

The size of the clicked points

increase, indicating that they have been

marked.

NOTE: You can select all the data points by

clicking the Mark All button. To unmark all the

data points, click the Unmark All button. These

functionalities of marking/unmarking all data

points are also available in the context menu of

the graph.

2. Click on the appropriate button to manipulate

the marked points as per your requirements.

The buttons available are as follows:

• Marked -> Exclude

• Marked -> Include

NOTE: The above buttons temporarily exclude

or include data points from the graphing interface

irrespective of the validity status and do

not affect the recalculation. To include/exclude

selected data points, you may also right-click on the

graph and select the appropriate option from the

context menu.

• Marked -> Invalid

• Marked -> Not Validated

NOTE: The above buttons permanently invalidate

data points or mark them Not Validated.

These buttons also affect the recalculation. To

validate/invalidate selected data points, you may

also right-click on the graph and select the appropriate

option from the context menu.

NOTE: Points invalidated from the graphing

interface are also marked as invalid in the data

tables and are excluded from calculations.

However, you can include the invalidated

points to the graphing interface by marking

them and then clicking the Marked -> Include

button.

NOTE: You can display the plots for more than

one row by selecting multiple rows in the corresponding

table. The items of selected rows are

displayed in the Active Data Series list box.

Manipulating Detail Points

At times, you may need to plot the aggregate

value of one field against all values of another

field. In the same graph, if you plot the individual

values of the former field then the points

corresponding to these values will be called

Detail points.

For example, you may plot data values of Concentration

field in X axis and aggregate value

of Raw Value field in Y axis. In the same

graph, you may also plot the points wherein the

individual values of the Raw Value field map

with the values of the Concentration field.

These points will be called Detail points.

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By default, the Detail points are white in color

whereas the Data points are filled with a solid

color. Unlike Data points, the Detail points are

inactive by default.

To manipulate Detail points in a plot:

1. Create a graph using aggregate value of a

field in Y axis.

2. Open the Graph Options dialog box.

3. Click the Protocol Data tab.

4. Select the Show detail data points check

box.

5. Click OK. The BioAssay Modules dialog

box appears.

6. Click Yes.

7. Right-click on the graph plot and click

Select Detail Point in the context menu. The

Detail points are activated and you can

manipulate the Detail points in the same

way as you manipulate Data points. For

more information, see “Manipulating Data

Points” on page 125.

• Protocol Data: Defines display characteristics,

such as plot color, plot type, and data

point style.

• Additional Content: Defines information

related to error bars and curve extensions.

To access the Graph Options dialog box, click

the Options button in the menu bar of a graph

plot or click the Display Options button in the

definition of a graph template.

Graph Options General Tab

The graph options under the General tab allow

you to specify whether a plot is a line graph or

a bar graph. These options also allow you to

remove and add specific parts of a plot, such as

the legend, title, and axes labels. The following

figure shows the General tab of the Graph

Options dialog box:

NOTE: By default, the Select Detail Point

menu item is unchecked and you need to check

it before manipulating Detail points. After you

click the Recalculate button, the Select Detail

Point menu item returns to its default state.

Graphing Options

The various graphing options available in Bio-

Assay can be accessed through the three tabs in

the Graph Options dialog box. These tabs are

as follows:

• General: Defines general plotting characteristics,

such as graph type, title, legend, X

axis, and Y axis.

Graph Type

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You can plot table data in the form of a line

graph or a bar graph by selecting the appropriate

option in the Graph Type section. When

you select the Bar option, the scaling options in

the X Axis section disappear, which indicates

that you can not set these options for a bar

graph.

Title and Legend

This section lets you display title and legend

on a plot. Selecting the check box next to a

Show option, such as Show Title, will display

the corresponding item in the plot. Un-checking

the check box will hide the item. You can

enter a name for the title in the Graph Title text

box and set its font using the Font drop down

list.

In addition, you can specify the location of the

legend on the plot. The options available are as

follows:

• Left

• Top

• Bottom

• Right

Scaling

By default, the graph window will fit itself to

the data being plotted. Therefore, the maximum

and minimum numbers shown on the

scales may vary in each graph. To prevent this,

you can manually lock either or both axes to a

maximum and minimum value in the X Axis

and Y Axis sections.

The Use Field check boxes in the Scaling section

allow you to specify the maximum and

minimum values of axes using table fields

instead of specifying the values directly. The

Max and Min text boxes convert to combo

boxes when you select the corresponding Use

Field check box. You can select table fields

from these combo boxes.

GRAPH OPTIONS PROTOCOL DATA TAB

The graph options in the Protocol Data tab

allow you to select the color and type of the

plot. You can also specify the types of data

points that will be displayed. In addition, you

can specify the color and style of the different

types of points. The following figure shows the

Protocol Data tab of the Graph Options dialog

box:

In the preceding figure, the Data Set Identification

button lets you select the fields that are to

be used to identify datasets. By default, the

datasets are identified based on key fields.

To select a field for identifying datasets:

1. Click the Data Set Identification button. The

Select Fields dialog box appears.

2. Select the field based on which you need to

identify the datasets.

3. Click OK.

4. Click OK in the Graph Options dialog box.

The BioAssay Modules dialog box appears.

5. Click Yes to save the current settings as the

default settings.

6. Select a row in the table containing the

graph and click the Recalculate tab to

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efresh the table data. The following graph

appears:

Additional Content tab of the Graph Options

dialog box:

NOTE: The legend in the graph displays the

current row value of the field, which you chose

to identify the datasets.

Graph Options Additional Content Tab

The graph options in the Additional Content

tab allow you to define error bars and curve

extension. The following figure shows the

Error Bars

Error bars are lines in a plot that specify the

margin of error in a data point. In other words,

error bars specify the range within which a

point lies. BioAssay lets you add error bars to

any plot based on aggregate data or individual

data. However, only one error bar option can

be chosen at one time.

Curve Extension

The Curve Extension drop down list determines

how much the fitted curve should extend

from the data points. The default is 10%,

which means that the fitted curve will extend

10% more from the data points at the two ends

of the curve. Making this value larger will

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extend the curve further, as shown in the following

figures:

for external analysis, you need to create an

external analysis template.

Sample External Analysis

To perform an external analysis using the Sample

External Analysis add-in:

1. Right-click on a protocol table and select

New Analysis Template. The Analysis Template

folder and new analysis template

appears:

NOTE: By clicking the Save As Default button,

you can ensure that the values for error bars

and curve extension are stored as default values.

External Analysis

Bioassay lets you create an add-in to perform

calculations or connect to third party products

to perform analysis. Thereafter, you can store

the analysis results in BioAssay data tables.

BioAssay lets you create the add-in, Sample

External Analysis. Before creating the add-in

2. Right-click on the new analysis template

and select Edit Analysis. The Edit External

Analysis window appears.

3. Specify a name for the external analysis in

the Analysis Name text box.

4. Select Sample External Analysis in the

Select Analysis Add-In list box.

5. Click Configure Add-In to configure the

selected add-in. The ExtAnalysisMain - Customer

Application window appears.

6. Select the fields you need to export to the

external analysis.

7. Click OK. The Edit External Analysis window

appears.

8. Specify the field names in the Return Values

section.

9. Click OK. The external analysis appears

within the Analysis Template folder.

10.Click the Data tab and retrieve all data.

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11.Right-click on a row in the Summary data

table and run the external analysis.

12.Select a control group and click the OK button.

The analysis result appears in the data

table.

A Sample Protocol - IC50

Overview

The IC50 protocol in BioAssay enables scientists

to manage IC50 assay data. An IC50 assay

is a kind of experiment wherein scientists measure

the effectiveness of a drug candidate in

inhibiting a given enzyme’s function.

In the IC50 assay experiment, known concentrations

of an enzyme are combined with various

known concentrations of a drug.

Thereafter, the results are compared to identify

the extent to which the enzyme’s function is

inhibited by the presence of the drug.

In order to allow you to manage IC50 assay

data, this IC50 protocol in BioAssay makes use

of four components, which are as follows:

• Test Instances: Contains information common

to the entire IC50 assay experiment

run.

• IC50s: Refers to the IC50 and log(IC50)

values for each compound.

• Averages: Contains averages of the raw

data resulting in one data point for each distinct

compound ID.

• Raw Data: Refers to the data file, which

describes the conditions in which data was

collected.

In this section, you will learn to manage IC50

assay experiments using the preceding components

of the IC50 protocol. This section covers

the following topics:

• Creating an IC50 protocol

• Setting up plate format

• Setting up the Wells table

• Setting up a File Import template

• Importing the data file

• Setting calculation options

• Positive control average

• Negative control average

• Verifying results

• Normalizing values

• Creating graphs

• Calculating IC50 values

• Adding graph attachment fields

• Viewing data of attachment fields

• Adding a Notes attachment field

• Modifying the File Import template

Creating an IC50 Protocol

To create an IC50 protocol:

1. Open the BioAssay application to display

the BioAssay window:

2. Right-click the (Unclassified) folder to display

a pop-up menu.

3. Select the New Project menu item. The New

Project dialog box appears.

4. Type Demo Project 1 in the text box.

5. Click OK. The new project, Demo Project 1

is displayed under the Unclassified folder in

the Navigator frame of the BioAssay window.

In case the Demo Project 1 project is

not displayed, expand the ((Unclassified)

folder.

6. Right-click the Demo Project 1 project to

display a pop-up menu.

7. Select the New Protocol menu item. The

New Protocol dialog box appears.

8. Type Demo IC50 Protocol in the Protocol

Name text box.

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9. Select the IC50 protocol template.

10.Click OK. The following window appears:

3. Click the Plate Formats folder. In the Content

frame, the existing plate formats

appear.

NOTE: You can click any plate format in the

Name column to view the details of that folder.

You can also right click on the table containing

the detailed data and select Concentration to

view the concentration of the compounds in the

wells.

NOTE: You need to add a new plate format to

the preceding list.

11.Click the Definition tab. The following window

appears:

Setting up Plate Format

To set up a plate format:

1. Expand the Settings folder in the Navigator

frame to display the Plate Setup folder.

2. Expand the Plate Setup folder in the Navigator

frame to display the Plate Formats

folder.

4. Click Edit. The plate formats appear in edit

mode.

5. Click Add in the menu bar to add a new

row.

6. Type FP Cpd IC50 in the Name column and

select 96 Well Plate in the drop down list of

the Physical Plate Type column.

7. Click Save to save the changes.

8. Double-click the FP4 Cpd IC50 plate format

in the Name column. The contents of the

FP4 Cpd IC50 plate format appear.

9. Click Edit to switch to edit mode. You can

click any cell and select the desired compound

placeholder from the drop down list

of that cell.

10.Click Save to save the changes.

11.Select Actions -> View -> Concentration

from the menu bar and edit the concentration

values of the compounds through the

edit mode.

12.Click Save to save the changes.

Setting up the Wells Table

To set up the format of the Wells table:

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1. Click Demo IC50 Protocol in the Navigator

frame. The following window appears:

6. Select the New Field menu item. The following

window appears:

2. Click Raw Value in the Wells table. The following

window appears:

3. Type Parallel Reading in the Field Name text

box.

4. Click Save Changes to save the changes.

5. Right-click the Wells table to display a popup

menu.

7. Type Perp Reading in the Field Name text

box.

8. Select Number (Real) in the Field Type drop

down list.

9. Click Save and Add Another to add another

field.

10.Type Ratio in the Field Name text box.

11.Select Number (Real) in the Field Type drop

down list.

12.Click Save Changes to save the changes.

Setting up a File Import Template

To set up a file import template:

1. Right-click the File Import Templates folder

in the protocol tree to display a pop-up

menu.

2. Select New Template. The File Import Wizard

window appears.

3. Type Plate Reader File in the Template Name

text box.

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4. Click Next. The following window appears:

8. Click Next. The following window appears:

5. Select Tabs in the This file is delimited by

drop down list.

6. Ensure that the Plate Block tab is selected.

You need to set the Plate Block attributes.

To set the Plate Block attributes:

• Select the Plate Header check box.

• Type 2 in the lines before each plate text

box.

• Type 3 in the data block(s) for each plate

text box.

• Select the Data Block Header check box.

• Type 4 in the lines before each data

block text box.

• Ensure that the Data Block check box is

selected.

• Ensure that the value 8 exists in the lines

in each data block text box.

NOTE: The values of the Plate Block attributes

are based on the content of the IC50Data.txt

file.

7. Click Next. The Other Options page

appears.

You need to select the fields to be

imported. To select the fields:

• Select Plate Header Cell; in the Plate ID

drop down list.

• Type 1,2 in the next cell of the Plate ID

row.

• Select Use Default; in the Plate Format

drop down list.

• Select FP Cpd IC50 in the next cell of the

Plate Format row.

• Select Prompt Me in the Scientist drop

down list.

• Select Prompt Me in the Notebook drop

down list.

• Select Data Block Number; in the Parallel

Reading drop down list.

• Type 1 in the next cell of the Parallel

Reading row.

• Select Data Block Number; in the Perp

Reading drop down list.

• Type 2 in the next cell of the Perp Reading

row.

• Select Data Block Number; in the Ratio

drop down list.

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• Type 3 in the next cell of the Ratio row.

9. Click Finish to display the protocol definition.

Importing the Data File

To import the data file:

1. Click the Data tab. The Open Datasource

dialog box appears.

2. Click Retrieve All to display a blank screen

under the Data tab, as shown in the following

figure:

7. Type your name in the Scientist field and

Notebook 1 in the Notebook field.

8. Click Next. The Import File page appears.

9. Click Finish. The Data Preview window

appears.

10.Click Load File to display the Plates table

data, as shown in the following figure:

3. Click the Import File tab. The Select Template

page of the Import File Wizard dialog

box appears.

4. Click Next. The Select Data File(s) page

appears.

5. Click Browse to locate and select the

IC50Data.txt file. After you had selected the

file, the Select Data File(s) page appears

again.

6. Click Next. The Additional Data page

appears.

11.Click the + icon in the first row of the Plates

table to display the Compounds table data,

as shown in the following figure:

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12.Click the + icon in any row of the Compounds

table to display the Concentrations

table data, as shown in the following figure:

4. Click Next. The Input Values page appears.

5. Select Wells in the Table drop down list.

6. Select Ratio in the Field drop down list.

7. Click Next. The Define Conditions page

appears.

8. Click Add. The following dialog box

appears:

13.Click the + icon in any row of the Concentrations

table to display the Wells table data,

as shown in the following figure:

14.Click the icon in the Plates table to close

all the tables.

Setting Calculation Options

To set calculations for the Positive Control

average:

1. Click the Definitions tab.

2. Click the Pos Ctl Average field in the Plates

table. The definition of the Pos Ctl Average

field appears.

3. Click Edit Calculation. The Select Calculation

page of the Calculation Wizard dialog

box appears.

9. Select Compounds in the Tables drop down

list.

10.Select Well Format in the Field drop down

list.

11.Select is in the Is drop down list.

12.Click the... button in the Value column. The

Condition Value dialog box appears.

13.Select Positive Control in the Constant Value

drop down list.

14.Click OK to close the Condition Value dialog

box.

15.Click Next. The Finished page appears.

16.Select 4 in the Limit result to drop down list

17.Click Finish.

To set calculations for the Negative Control

average:

1. Click the Neg Ctl Average icon in the Plates

table.

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2. Click Edit Calculation. The Select Calculation

page of the Calculation Wizard dialog

box appears.

3. Click Next.

4. Select Wells in the Table drop down list.

5. Select Ratio in the Field drop down list.

6. Click Next.

7. Click Add.

8. Select Compounds in the Tables drop down

list.

9. Select Well Format in the Field drop down

list.

10.Select is in the Is drop down list.

11.Click the... button in the Value column to

display the Condition Value dialog box.

12.Select Negative Control in the Constant

Value drop down list.

13.Click OK to close the Condition Value dialog

box.

14.Click Next. The Finished page of the Calculation

Wizard dialog box appears.

15.Click Finish to close the Calculation Wizard

dialog box.

Verifying Results

To verify the results of setting calculation

options:

1. Click the Data tab. The contents of the

Plates table is displayed, as shown in the

following figure:

2. Select the values in the Scientist column in

the Plates table.

3. Click Recalculate. Data in two new columns

appear in the Plates table, as shown in

the following figure:

Data in the two new columns indicate the

negative and positive control average values.

Normalizing Values

To normalize the values:

1. Click the Definitions tab.

2. Right-click the Wells table in the protocol

tree to display a pop-up menu.

3. Select the New Field menu item to display

its definition, as shown in the following figure:

4. Type Normalized in the Field Name text box.

5. Select Calculation (Numeric output) in the

Field Type drop down list.

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6. Click Edit Calculation. The Select Calculation

page of the Calculation Wizard dialog

box appears.

7. Ensure that the Mathematical tab is selected.

NOTE: If the Normalization calculation is not

present, you need to create it using the New

button. The equation for the Normalization

calculation is as follows:

Y = 100 * ((Value - LowCtl)/(HighCtl -

LowCtl))

8. Select Normalization and click the Next button.

The Calculation Parameters page

appears:

• Select Plates in the Table column of the

Highctl row.

• Select Pos Ctl Average in the Field column

of the Highctl row.

• Select Plates in the Table column of the

Lowctl row.

• Select Neg Ctl Average in the Field column

of the Lowctl row.

• Select Ratio in the Field column of the

Value row.

10.Click Finish to display the protocol definition.

11.Click the Average Raw Value field in the

Concentrations table to display its definition.

12.Type Average Normalized in the Field Name

text box.

13.Click Edit Calculation. The Select Calculation

page of the Calculation Wizard dialog

box appears.

14.Click Next. The Input Values page appears.

15.Select Normalized in the Field drop down

list.

16.Click Next. The Define Conditions page

appears.

17.Click Next. The Finished page appears.

18.Click Finish to close the Calculation Wizard

dialog box.

Creating Graphs

To create graphs:

1. Right-click the Compounds table in the protocol

definition tree to display a pop-up

menu.

2. Select the New Graph Template menu item

to display its definition, as shown in the following

figure:

NOTE: The drop down lists in each cell enable

you to select the specified values.

9. Click Next. The Finished page appears.

138 BioAssay Desktop & Workgroup

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3. Type 4 Parameter Fit in the Template Name

text box.

4. Select Average Normalized in the Y-Axis

drop down list.

5. Click Display Options. The Graph Options

dialog box appears.

6. Ensure that the Standard radio button in the

X Axis section is selected.

7. Click OK to close the Graph Options dialog

box.

8. Click Curve Fits. The Add or Remove Curve

dialog box appears.

9. Select Linear Model in the Available Curves

list.

10.Click Add to List. The Linear Model appears

in the Curves to Display list.

11.Click OK to close the Add or Remove Curve

dialog box.

12.Click Save Changes.

13.Click the Data tab to display its contents, as

shown in the following figure:

16.Click Recalculate. The values of the Average

Normalized field appears:

17.Click the Graph: 4 Parameter Fit tab in the

Concentrations table. The resultant graph

appears:

NOTE: Although you have created the graph

template at the Compounds level, the graph

actually appears at the Concentrations level

because the data required for the graph is

contained in the Concentrations table

14.Click the + icon in any row of the Plates

table to display the Compounds table.

15.Click the + icon any row of the Compounds

table.

Calculating IC50 Values

To calculate IC50 values:

1. Click the Definitions tab to display the protocol

definition.

2. Click the IC50 field in the Compounds table

display the field definition.

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3. Click Edit Calculation. The Select Calculation

page of the Calculation Wizard dialog

box appears.

4. Click the Curve Fit tab. The following dialog

box appears:

13.Click Edit Calculation to display the Select

Calculation page of the Calculation Wizard

dialog box.

14.Click the Curve Fit tab. The following dialog

box appears:

5. Select Slope in the drop down list within the

Insert Value section.

6. Click Next. The Finished page appears.

7. Ensure that the value 4 is selected in the

Limit result to drop down list.

8. Click Finish to close the Calculation Wizard

dialog box.

9. Right-click the Compounds table to display

a pop-up menu.

10.Select the New Field menu item to display

the field definition.

11.Type Adjusted R^2 in the Field Name text

box.

12.Select Calculation (Numeric output) in the

Field Type drop down list.

15.Click the Fit Statistic radio button in the

Insert Value section.

16.Select Adjusted R^2 Value in the drop down

list within the Insert Value section.

17.Click Next to display the Finished page of

the Calculation Wizard dialog box.

18.Click Finish to close the Calculation Wizard

dialog box.

19.Click the Data tab.

20.Click the icon in the Plates table to close

all the other open tables.

21.Select the Plate Format column of the Plates

table and click the Recalculate button.

22.Click the + icon corresponding to any row

of the Plates table to display the Com-

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pounds table, as shown in the following figure:

24.Click the Graph: 4 Parameter Fit tab in the

Concentrations table to display the graph,

as shown in the following figure:

You can view the value of IC50 and

Adjusted R^2 in the Compounds table.

23.Click the + icon corresponding to any row

of the Compounds table to display the Concentrations

table, as shown in the following

figure:

Adding Graph Attachment Fields

To add an attachment field:

1. Click the Definitions tab to display the protocol

definition.

2. Click the 4 Parameter Fit graph template in

the Compounds table to display the graph

template definition, as shown in the following

figure:

3. Click Graph Storage. The Graph Storage

dialog box appears.

4. Select the check box, Store a full-size image

of each graph, with legend and titles.

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5. Select the check box, Store a smaller image

each graph, without legend and titles.

6. Type 100 in both the pixels text boxes

below the check box, Store a smaller image

each graph, without legend and titles.

7. Click OK to close the Graph Storage dialog

box. The graph template definition appears:

3. Select the Plate Format column of the Plates

table and click the Recalculate button to

recalculate data of the Plates table.

4. Click the + icon corresponding to any row

of the Plates table to display the Compounds

table, as shown in the following figure:

You can observe that two new attachment

fields have been automatically added to the

Compounds table.

Viewing Data of Attachment Fields

To view the data contained in the attachment

fields:

1. Click the Data tab to display the protocol

tables.

2. Click the icon in the Plates table to close

all the open tables.

You can view the newly added columns in

the Compounds table.

5. Click Recalculate. Hyperlinks are displayed

in the Graph 4 Parameter Fit and Thumbnail

columns, as shown in the following figure:

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6. Double-click any hyperlink in the Graph: 4

Parameter Fit column. The graph for the

corresponding compound appears:

7. Select any cell in the Thumbnail: 4 Parameter

Fit column and right-click to display a

pop-up menu.

8. Select the Show Pictures menu item to display

the thumbnail graph, as shown in the

following figure:

You can view the graphs stored in the

Thumbnail: 4 Parameter Fit attachment

field.

Adding a Notes Attachment Field

To add a notes field:

1. Click the Definitions tab to display the protocol

definition.

2. Right-click the Plates table to display a

pop-up menu.

3. Select the New Field menu item to display

the definition of the new field.

4. Type Extended Notes in the Field Name text

box.

5. Select Attachment (Database Storage) in the

Field Type drop down list.

6. Click Save Changes to save the changes.

7. Right-click the Plates table to display a

pop-up menu.

8. Select the New Field menu item.

9. Type Raw Data File in the Field Name text

box.

10.Select Attachment (Database Storage) in the

Field Type drop down list.

11.Click Save Changes to save the changes.

Modifying the File Import Template

To modify the file import template:

1. Click the Plate Reader File template in the

File Import Templates folder.

2. Click Edit Template to display the Template

Name page of the File Import Wizard window.

3. Click Next. The File Format Information

page appears.

4. Click Next. The Other Options page appears.

5. Click Next. The Map Fields page appears.

6. Select Upload File in the Raw Data File drop

down list.

7. Click Finish to close the File Import Wizard

window.

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8. Click the Data tab to display the data tables,

as shown in the following figure:

22.Click Load All to display the imported data,

as shown in the following figure:

9. Click the icon in the Plates table.

10.Delete all the rows of the Plates table using

the edit mode.

11.Click Save to save the changes.

12.Click the Actions button in the Plates table

menu bar to display a pop-up menu.

13.Select the Import Data File menu item to display

the Select Template page of the Import

File Wizard dialog box.

14.Click Next. The Select Data File(s) page

appears.

15.Click Browse. The Select File(s) to Import

dialog box appears.

16.Locate the IC50Data.txt file and click OK to

close the Select File(s) to Import dialog box.

17.Click Next to display the Additional Data

page.

18.Type your name in the Scientist field.

19.Type Notebook 1 in the Notebook field.

20.Click Next to display the Import File page.

21.Click Finish. The Data Preview window

appears.

23.Double-click any cell in the Raw Data File

column of the Plates table to display the

raw data file in a new window.

24.Click the + icon in the first row of the Plates

table to display the Compounds table, as

shown in the following figure:

25.Click the + icon in any row of the Compounds

table to display the Concentrations

table, as shown in the following figure:

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26.Click the Graph: 4 Parameter Fit tab in the

Concentrations table to display the graph,

as shown in the following figure:

5. Select the desired field and click the OK

button. The compound list appears in the

Navigator section under the Lists folder.

NOTE: If the list contains the same compound

ID more than once, that compound ID will be

saved only once.

Compound Lists

Compound lists are lists of compounds that can

be used in plate templates.

To create a new compound list:

1. Select the rows in a data table containing

the compound IDs of the compounds that

need to be included in the compound list.

NOTE: A Compound list can be created using

the values of any table field, not necessarily,

Compound ID. Also, it can be created by

passing values from a file.

2. Right-click to display a pop-up menu and

select the Save List menu item.

3. Enter name for the list created.

4. Click OK. The Select Field dialog box

appears.

Manipulating Compound Lists

Manipulating compound lists includes various

actions, such as merging two compound lists,

intersecting a list, and subtracting a list.

To manipulate a compound list:

1. Open a compound list by clicking on it in

the Navigator section.

2. Click on the Actions button and select the

appropriate operation. The following

options are available:

• Merge: Produce a new list by combining

two lists.

• Intersect: Produce a list with only those

compound IDs, which are included in both

the original list and the selected list.

• Subtract: Produce a list with only those

compound IDs, which appear in either the

selected list or the original list, but not in

both.

3. Select a list on which you need to perform

the operation.

4. Click OK. The new list appears.

Reporting

The Reporting feature in BioAssay lets you

create reports by using the data stored in the

protocol data tables. In addition, you can create

custom reports using the data returned by SQL

queries.

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In order to create reports, you need to use

report templates. You can either use the existing

report templates or create a new report

template. After creating a report you can preview

and print it. By previewing your report,

you can ensure that the resultant report is in

accordance with your requirements.

The Reporting feature also lets you select the

printers for printing your report. For example,

you can either select the same printer for printing

all the pages of your report or select different

printers for printing different pages.

Creating Reports

To create reports using the data of a BioAssay

protocol:

1. Open the data view of the protocol.

2. Right-click on any cell to display a pop-up

menu.

3. Select the Create Report menu item. The

Report Templates dialog box appears.

4. Select a report template in the Choose a

report template list box.

NOTE: The Choose a report template list box

displays only those report templates that have

been created earlier. To create a report

template, see “Creating Report Templates” on

page 146.

5. Click Print. The Print Options dialog box

appears.

6. Select the Preview item in the Direct to drop

down list.

7. Click Start. The Preview window appears.

8. Close the window to display the Report

Templates dialog box. Follow steps 9 and

10 if the preview report suits your requirements.

Else, select a different report template

or create a new one.

9. Click Print. The Print Options dialog box

appears.

10.Click Start to print the report.

Creating Report Templates

To create a report template:

1. Click New in the Report Templates dialog

box. The New Template dialog box appears.

2. Enter the name and description of the template

in the Template Name and Description

text boxes.

3. Click Design Template. The Choose report

file dialog box appears.

4. Type a file name in the File name drop

down list and click the Open button. The

Welcome page of the Project Wizard dialog

box appears.

5. Click Next. The next page of the Project

Wizard dialog box appears.

6. Accept the default settings and click Next to

display the next page of the Project Wizard

dialog box.

7. Click Choice if you need to change the

printer settings. After setting the printer

options, click OK.

8. Click Next to display the next page of the

Project Wizard dialog box.

9. Chose whether you need to include page

numbers in your report.

10.Select the options for the title as per your

requirements.

11.Click Done. The Choose Object Type dialog

box appears.

12.Choose the table object and click the OK

button. The Choose Source Table Path dialog

box appears.

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13.Select a protocol table and click the OK button.

The Preselection of fields for a line definition

dialog box appears.

14.Expand the protocol table in the Insertable

fields list box.

15.Select a field and click the right arrow icon

to display it in the Columns list box.

16.Repeat the previous step for each field,

which you need to include in the report.

17.Click OK. The Table Contents dialog box

appears.

18.Click the Header Line tab. The Choose a

Table Line Definition dialog box appears.

19.Click OK to display the Table Contents dialog

box again.

NOTE: You can change the layout of a table

line using the Layout button. You can also

specify conditions for the header line to appear

by using the Appearance Cond button.

20.Click OK. The Design project window

appears.

NOTE: You can put a heading to the report

template in the Design project window.

21.Click the File -> Save menu option in the

menu bar to save the file.

22.Close the window to display the New Template

dialog box again.

NOTE: If your report template contains any

image then you need to import that image by

using the Add button in the Static images

section.

23.Click Save to save the report template and

display it in the Report Templates dialog

box. Now, you can use this report template

to create new reports. For creating new

reports, see “Creating Reports” on page

146.

Editing Report Templates

To edit a report template:

1. Select the report template to be edited in the

Report Templates dialog box.

2. Click Edit to display the Edit Template dialog

box.

3. Edit the template as per your requirements.

4. Click Save to save the changes.

Deleting Report Templates

To delete a report template:

1. Select the report template to be deleted in

the Report Templates dialog box.

2. Click Delete to display a message box,

which asks for your confirmation.

3. Click Yes to delete the selected report template.

Creating Custom Reports

BioAssay lets you create two types of custom

reports: List Style and Label Style. In order to

create a custom report you need to use a report

query and report template.

Creating a Report Query

To create a report query:

1. Select Report > Report Queries from the

menu bar of the BioAssay application. The

Generic Reporting SQL Queries window

appears.

2. Click New. The Create a new Generic

Reporting SQL Query window appears.

3. Enter the query name and description.

4. Enter the SQL query in the SQL text area.

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5. Click Create. The new report query that you

created appears in the Generic Reporting

SQL Queries window.

NOTE: The Edit and Delete buttons in the

Generic Report window allow you to edit and

delete SQL queries, respectively.

6. Click Close.

Creating a List Style Custom Report

To create a List Style custom report:

1. Select Report > Generate > List Style from

the menu bar of the BioAssay application.

The Custom Report window appears.

2. Select a report query.

3. Click the Print/Preview/Export button. The

Generating Report dialog box appears.

4. Select a report template and click Open.

The Print Options dialog box appears.

NOTE: If no report template is available, you

can create it by click the Design button in the

Custom Report window. For more information

about creating report templates, see “Creating

Report Templates” on page 146.

5. Select Preview in the drop down list in the

Export Media section.

6. Click Start to view the report.

Creating a Label Style Custom Report

To create a Label Style custom report:

1. Select Report > Generate > Label Style from

the menu bar of the BioAssay application.

The Custom Report window appears.

2. Perform the step 2 to step 6, as mentioned

in the above procedure for creating List

Style custom reports.

Settings

The Settings folder in the Navigator section of

BioAssay lets you configure the settings

related to the following entities.

• Plate Formats

• Well Formats

• Picklists

• External Picklist

• External Datasource

• Field Dictionary

Editing the settings tables

All the entities in the Settings folder present

the same basic user interface wherein data is

stored in tables. By default, the table of a Settings

folder opens in browse mode. While in

browse mode, you can view the data in the

tables, but can not make any changes. To make

changes to a table, you need to switch to edit

mode. Click the Edit button in the menu bar to

open the table in edit mode. In edit mode, the

Add, Delete, Save, and Cancel buttons are visible.

You need to use these buttons to make

changes in the data contained in the tables.

Adding an Entry

To add an entry to the table of a Settings

folder:

1. Click Add in edit mode. An empty row is

inserted into the table.

2. Enter information in the appropriate columns

of the new row.

3. Click Save.

Deleting an Entry

To delete an entry from the table of a Settings

folder:

1. Open the table in edit mode.

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2. Select the row to be deleted.

3. Click Delete.

4. Click Save.

Canceling/Discarding Changes

If you have made changes to the table of a Settings

folder, but have not saved those changes,

you can discard or cancel the changes. To cancel

the changes, which you made to a table:

1. Click Cancel after making the changes to

the table in edit mode. A warning message

appears.

2. Click Yes.

Plate Setup

Plate Formats

Plate formats are used to define the organization

and general content of wells in a plate. The

following attributes can be defined for a plate

format:

• Name: Specifies the name of the plate format

• Physical Plate Type: Specifies the number of

wells to be included in the plate.

After entering values for the above attributes, it

is necessary to define the general content of

each well. To define the general content of

each well, open a plate format by double-clicking

on it. The plate opens with the number of

wells as specified in the Physical Plate Type

attribute. By default, all wells contain the well

format, Compound. You can change the well

format in edit mode. The various well

format options available, are as follows:

• Compound: Refers to a compound can be

inserted in the well.

• Empty: Refers to the well remains empty.

• Positive Control: Specifies that the well is

reserved for a positive control.

• Negative Control: Specifies that the well is

reserved for a negative control.

More well formats can be defined by you. For

more information about editing the entries in

the plate format tables, see“Editing the settings

tables” on page 148.

To define the general contents of the wells in a

plate format:

1. Double-click the plate format to open it in

browse mode.

2. Switch to edit mode by clicking the Edit

button.

3. Click on a well to display a drop down list

containing options for the well format for

that particular well.

4. Select a well format. The well format of the

cell is updated.

5. Click Save.

Well Formats

Well formats define the general content of a

well. When defining plate formats, the well

formats for each well in the plate are selected

from the available well formats. The well formats

that are available, by default, are as follows:

• Compound: Refers to a compound can be

inserted in the well.

• Empty: Refers to the well remains empty.

• Positive Control: Specifies that the well is

reserved for a positive control.

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• Negative Control: Specifies that the well is

reserved for a negative control.

NOTE: The only well in which a compound

from a database can be inserted, is a well with

the Compound well format.

For more information about editing the entries

in the Well Formats table, see “Editing the settings

tables” on page 148.

Picklist

Picklists allow you to limit the values, which

can be assigned to a field. For example, in Bio-

Assay, a default picklist is Scientist. The Scientists

picklist contains four options, as shown

in the following figure:

6. Click Save.

7. Double-click on the row with the name of

the new picklist. A table defining the

entries in the picklist appears.

8. Click Edit to access the edit mode.

9. Click Add to add a new row to the Picklist

Value table.

10.Enter an entry for the picklist.

11.Click Save.

12.Repeat steps 10-12 until all the entries you

choose to define have been entered.

Using a Picklist

To use a picklist in a protocol's table:

1. Define a table (or choose a defined table).

2. Click a field within the table.

3. Set the field type to Picklist Value.

4. Select a picklist name in the Picklist drop

down list.

5. Click Save.

Defining a Picklist

To define a new picklist:

1. Browse to the Picklist folder in the Navigator

frame.

2. Click on Picklist folder. The items in the

Picklist folder appears in the Content frame

on the right.

3. Click Edit to switch to edit mode.

4. Click Add. An empty row is inserted in the

Picklist Name table.

5. Enter a name for the new picklist in the

empty row.

NOTE: After defining a protocol field as Picklist

Value, if you make changes to the field data

then you will have to click the Recalculate button

twice to update the code for the field. This

is a limitation with the Recalculate button.

External Picklists

External picklists lets you define a picklist by

collecting data from external applications.

After defining an external picklist, you can use

it to assign values to protocol fields, which

have field type set as External Picklist Value.

Defining External Picklists

To define an external picklist:

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1. Expand the Settings folder in the Navigator

frame to display the External Picklists

folder.

2. Right-click on the External Picklists folder

to display a pop-up menu.

3. Select the New External PickList menu item.

The New External Picklist window appears.

4. Enter information in the Name and Description

fields.

5. Select a database type in the Database Type

drop down list.

6. Click the icon corresponding to the Connection

String field. If database type is

selected as Oracle, the following Configure

Connection String window appears:

• If database type is selected as SQL Server,

the following Configure Connection String

window appears:

7. Enter relevant information in the Data

Source, Initial catalog, User Name, and Password

fields.

8. Click OK.

9. Click Test Connection to test the validity of

the connection string.

10.Enter a relevant SQL query in the SQL

field, to fetch data from an external application

or database.

NOTE: The SQL query should be in one of the

two forms: SELECT value FROM table

and SELECT key,

value FROM table

11.Click OK.

Using External Picklists

To use the defined external picklist:

1. Open or create a protocol.

2. Create a field with field type, External Picklist

Value. In the Content frame, the Field

Options section appears.

3. Select the defined external picklist in the

Picklist drop down list.

NOTE: If no external picklists had been

defined then the type of the field will revert back

to Text type because it is the default field type.

4. Click Save Changes to save the changes.

5. Click the Data tab to view the data tables of

the protocol. If the Open Datasource dialog

box appears, click the Retrieve All button.

6. Click Edit to switch to the edit mode of the

protocol data table.

7. Access the column with the field type,

External Picklist Value. When you click on

any row of this column, a drop down list

displays the values returned by the SQL

query defined in the external picklist.

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8. Select the appropriate value in the drop

down list corresponding to each row.

9. Click Save in the menu bar to save the

changes.

Editing External Picklists

To edit an already existing external picklist:

1. Right-click on an external picklist within

the External Picklists folder in the Navigator

frame to display a pop-up menu.

2. Select the Edit External PickList menu item

to display the External Picklist window.

3. Edit the values in the various fields as per

your requirements.

4. Click OK.

Deleting External Picklists

To delete an external picklist:

1. Right-click on an external picklist within

the External Picklists folder in the Navigator

frame to display a pop-up menu.

2. Select the Delete External PickList menu

item to display a message box, which asks

for your confirmation.

3. Click Yes to delete the selected external

picklist.

Field Dictionary

Field dictionary is a collection of pre-defined

fields. The Field Dictionary feature in BioAssay

lets you define and group a number of

desired fields, which you need to include in a

protocol table. After defining and adding a

field to the field dictionary, you can include

that field in any protocol table you want. This

reduces the time and effort required to define

the field each time you create a protocol.

Adding Fields to the Field Dictionary

To add a field to the field dictionary:

1. Expand the Settings folder in the Navigator

frame to display the Field Dictionary folder.

2. Click the Field Dictionary folder. In the Content

frame, the Field Dictionary section

appears.

3. Click Add. The New Field Dictionary Entry

dialog box appears.

4. Enter the name and description of the field

in the corresponding text boxes.

NOTE: BioAssay does not allow you to work

with single character field names that are not

valid ASCII characters (letters and numbers).

For example, you can not use the field names, '

(single quote) and " (double quote). The single,

non-ASCII characters get renamed to S_ and

become useless.

NOTE: BioAssay does allow you to use field

names consisting of a combination of two or

more non-ASCII characters, such as # and %.

However, it is recommended that you use only

valid ASCII characters for field names.

5. Select the appropriate field type in the Field

Type drop down list.

6. Select the desired options in the Field

Options section. For example, if you want

that users must enter some value in the field

then enable the Required Value check box.

NOTE: To specify the maximum value that can

be entered in the defined field, select the

appropriate item in the Lock to Result Column

drop down list and enter the maximum value in

the corresponding text box.

7. Click OK. The newly added field is displayed

in the field dictionary.

Using the Field Dictionary

To add a field to your protocol table by using

the field dictionary:

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1. Open a protocol definition.

2. Right-click on a protocol table to display a

pop-up menu.

3. Select the New Field From Dictionary menu

item. The Choose Field Dictionary Entry

window appears.

4. Select the field, which you need to add to

the selected protocol table.

5. Click OK. The selected field gets added to

the protocol table and the field definition is

displayed on the right side of the Content

frame.

NOTE: When you add a field from a field

dictionary, the attributes of the field get locked.

However, the attributes, which appear within

the Field Options section in the field definition

are editable. Examples of field types whose

attributes appear in the Field Options section

include Picklists, External Picklists, and

Concentration.

6. Click Save Changes in the field definition.

Viewing the Field Dictionary

To view the field dictionary:

1. Select a field in the field dictionary.

2. Click View. The View Field Dictionary Entry

dialog box appears.

3. Click OK.

Removing a Field from the Field Dictionary

To remove a field from the field dictionary:

1. Select the appropriate field in the field dictionary.

2. Click Delete. A message box appears and

asks for your confirmation.

3. Click Yes to remove the field from the field

dictionary.

External Datasource

The External Datasources folder, within the

Settings folder, lets you import data from an

external data source into BioAssay by using

the feature, Structured Data Manager (SDM).

For more information, see “Importing Data

from External Data Source” on page 117.

BioAssay Privileges

BioAssay offers various features related to

protocols and the protocol administrator can

grant different access permissions to different

users. For example, a user may be granted permission

to create reports, but may not be

granted permissions to create external picklists

in a protocol. The access permissions are

granted through the use of pre-defined privileges.

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The following table lists the various privileges,

which can be assigned to a user in BioAssay:

Privileges

Description

Privileges

Description

MANAGE_FIELD

_DICTIONARY

Add/edit/delete field

dictionary entries

CREATE_LIST

Create a Compound List

CREATE_PLATE_

FORMAT

Create a new plate format

MANAGE_PICKL

IST

Add/edit/delete picklists

CREATE_PROTO

COL

DELETE_LIST

Create a new protocol

Delete a compound list

MANAGE_PROT

OCOL_ORGANIZ

ATION

Add/edit/delete folders and

projects in tree

DELETE_PLATE_

FORMAT

DELETE_PROTO

COL

EDIT_PLATE_FO

RMAT

EDIT_WELL_FO

RMAT

Delete a plate format

Delete a protocol

Edit an existing plate

format

Edit an existing well

format

MANAGE_REPO

RT_QUERY

MANAGE_REPO

RT_TEMPLATE

MANAGE_SDM_

DATASOURCE

Create/edit/delete report

queries used in custom

reports

Create/edit/delete report

templates

Create/edit/delete/

configure external data

sources using SDM

GENERATE_CUS

TOM_REPORT

Print a custom report

MOVE_PROTOC

OL

Move a protocol in the tree

GENERATE_PRO

TOCOL_REPORT

Print a protocol report

NOTE: For information about assigning privileges,

see “Managing Users Through BioAssay”

on page 165.

MANAGE_EXTE

RNAL_PICKLIST

Add/edit/delete/configure

external picklists

Actions Menu

The Actions menu in BioAssay provides various

options depending on the table or grid

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eing displayed. The following table lists the

options provided by the Actions menu:

Viewing Options

View Details

View Picklist

View Plate Format

View (from the plate

formats grid)

Viewing Commands

Other Options

Autofit

Change Validity

Coloring Options

Copy

Cut

Hide Invalid Data

Hide Pictures

Import Data

Paste

Recalculate

Save List

Select All

Show Coloring

Show Only Valid

Data

Show Pictures

View Details

The View Details menu item in the Actions

menu can be accessed from any protocol data

table, except from a table found at the bottom

of the table hierarchy. The View Details action

opens the data table holding aggregate data for

the current table. You can also achieve this

result by double-clicking on a row in the current

table. This result makes sense because the

data that makes up a particular row in one table

is formed by the data calculated in the next

lowest table.

View Plate Format

The View Plate Formats action is available

from the Plate Formats folder. This action will

open a table defining the chosen plate format.

To view a plate format:

1. Click the Plate Formats folder in the Navigator

frame to display its content in the

Content frame on the right.

2. Select the plate format whose table you

need to view.

3. Click Actions>View Plate Formats from the

menu bar.

View (from the plate format table)

When accessing a plate format, the View

action helps you to populate the cells in the

plate formats table with the selected data. For

example, selecting Actions -> View ->Well

Formats will populate the cells in the table

with the assigned contents, such as Empty or

Compound.

The following options are available in the

View menu:


• Well Format

• Concentration

• Well Name

View Picklist

The View Picklist action is available from the

table containing assay picklist definitions. This

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action will open a table containing the values

available in the currently selected picklist.

To view the values stored in a picklist:

1. Click the Picklists folder in the Navigator

frame to display its content in the Content

frame.

2. Select the row defining the picklist to be

viewed.

3. Select Actions>View Picklist menu item.

AutoFit Off

The following figure shows the display result

when the AutoFit action is inactive:

Other Commands

AutoFit

The AutoFit action is available from any grid

view. If the AutoFit action is active, the grid

will automatically resize to fit in the current

window. If the window is resized, the grid will

resize accordingly.

AutoFit On

The following figure shows the display result

when the AutoFit action is active:

Change Validity

The Change Validity action is available from

any data table. By default, the BioAssay application

assumes that data is not validated. Data

that is not validated is denoted by the letter, N

in the leftmost column of the data table. After

validating some data, it is possible to view only

valid data in the tables. In addition, by using

the Security tab, you can specify that valid data

may not be edited or recalculated.

To change the validity of data in certain rows

in the table:

1. Browse to the table holding the appropriate

data, in the Data tab of a protocol.

2. Select the rows holding the data.

3. Click Actions -> Change Validity from the

menu bar. The Change Validity dialog box

appears.

4. Select the appropriate validity. The validity

options available are as follows:

• Not Validated

• Icon: N

• Description: Specifies that no validation

decision has been made.

• Used in Calculation?: Yes

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• Valid

• Icon: V

• Description: Specifies that data is found

to be valid.

• Used in Calculation?: Yes

• Invalid

• Icon: I

• Description: Specifies data is found to be

invalid. Invalid data is not used in calculations

or curve fits.

• Used in Calculation?: No

• Request Review

• Icon: R

• Description: Specifies that data must be

reviewed before making a validation decision.

• Used in Calculation?: Yes

NOTE: If you are validating data in a summary

table, you can also choose to cascade the

validity change to the summary data by using

the options in the Cascading section.

5. Click OK.

Coloring Options

The coloring options are used to implement

heat maps. The Coloring Options dialog box

lets you select a parameter on which a heat

map will be based and specify the color values

for that parameter. The Coloring Options dialog

box can be accessed using the Actions

menu in a Wells table.

To set coloring options:

1. Browse to a Wells table in the Data tab of a

protocol.

2. Click the Plates tab.

3. Click Actions -> Coloring Options from the

menu bar. The Coloring Options dialog box

appears.

4. Select a parameter on which the heat map

should be based.

5. Enter maximum and minimum values corresponding

to each color.

6. Click OK.

Copy

The Copy action can be used when a table is

accessed in edit mode as well as in browse

mode. This action lets you copy selected information

in a table.

Cut

The Cut action can be used only when a table

is accessed in edit mode. This action lets you

cut selected information in a table.

Import Data

The Import Data action can be performed from

any data table of a protocol by using the File

Import wizard. The wizard assists in importing

data through the use of a defined File Import

Template.

Paste

The Paste action can be used only when a table

is accessed in edit mode. This action lets you

paste the already copied data on a selected area

in a table.

Recalculate

The Recalculate action will run all calculations

defined in the chosen table again. The Recalculate

action is useful when you change a key

piece of data and you are interested to see how

the calculations will be affected by the change.

Save Compound List

The Save Compound List action, available

from a data table or search data table, lets you

save the currently selected rows to a list.

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Select All

The Select All action lets you select all the

rows in a table. The Select All action is helpful

when you need to apply a similar set of actions

to all the rows in a table.

Show Coloring

This action shows the heat map coloring.

When this action is selected, each cell in the

grid will be filled with a color representing a

value defined in the Coloring Options dialog

box.

Show Only Valid Data

The Show Only Valid Data action will display

validated data in a data table of a protocol.

Prohibited Field Names

The keywords that can not be used as field

names in BioAssay are as follows:

A

• ACCESS

• ACCOUNT

• ACTIVATE

• ADD

• ADMIN

• ADVISE

• AFTER

• ALL

• ALL_ROWS

• ALLOCATE

• ALTER

• ANALYZE

• AND

• ANY

• ARCHIVE

• ARCHIVELOG

• ARRAY

• AS

• ASC

• AT

• AUDIT

• AUTHENTICATED

• AUTHORIZATION

• AUTOEXTEND

• AUTOMATIC

B

• BACKUP

• BECOME

• BEFORE

• BEGIN

• BETWEEN

• BFILE

• BITMAP

• BLOB

• BLOCK

• BODY

• BY

C

• CACHE

• CACHE_INSTANCES

• CANCEL

• CASCADE

• CAST

• CFILE

• CHAINED

• CHANGE

• CHAR

• CHAR_CS

• CHARACTER

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• CHECK

• CHECKPOINT

• CHOOSE

• CHUNK

• CLEAR

• CLOB

• CLONE

• CLOSE

• CLOSE_CACHED_OPEN_CURSORS

• CLUSTER

• COALESCE

• COLUMN

• COLUMNS

• COMMENT

• COMMIT

• COMMITTED

• COMPATIBILITY

• COMPILE

• COMPLETE

• COMPOSITE_LIMIT

• COMPRESS

• COMPUTE

• CONNECT

• CONNECT_TIME

• CONSTRAINT

• CONSTRAINTS

• CONTENTS

• CONTINUE

• CONTROLFILE

• CONVERT

• COST

• CPU_PER_CALL

• CPU_PER_SESSION

• CREATE

• CURRENT

• CURRENT_SCHEMA

• CURRENT_USER

• CURSOR

• CYCLE

D

• DANGLING

• DATABASE

• DATAFILE

• DATAFILES

• DATAOBJNO

• DATE

• DBA

• DBHIGH

• DBLOW

• DBMAC

• DEALLOCATE

• DEBUG

• DEC

• DECIMAL

• DECLARE

• DEFAULT

• DEFERRABLE

• DEFERRED

• DEGREE

• DELETE

• DEREF

• DESC

• DIRECTORY

• DISABLE

• DISCONNECT

• DISMOUNT

• DISTINCT

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• DISTRIBUTED

• DML

• DOUBLE

• DROP

• DUMP

E

• EACH

• ELSE

• ENABLE

• END

• ENFORCE

• ENTRY

• ESCAPE

• ESTIMATE

• EVENTS

• EXCEPT

• EXCEPTIONS

• EXCHANGE

• EXCLUDING

• EXCLUSIVE

• EXECUTE

• EXISTS

• EXPIRE

• EXPLAIN

• EXTENT

• EXTENTS

• EXTERNALLY

F

• FAILED_LOGIN_ATTEMPTS

• FALSE

• FAST

• FILE

• FIRST_ROWS

• FLAGGER

• FLOAT

• FLOB

• FLUSH

• FOR

• FORCE

• FOREIGN

• FREELIST

• FREELISTS

• FROM

• FULL

• FUNCTION

G

• GLOBAL

• GLOBAL_NAME

• GLOBALLY

• GRANT

• GROUP

• GROUPS

H

• HASH

• HASHKEYS

• HAVING

• HEADER

• HEAP

I

• IDENTIFIED

• IDGENERATORS

• IDLE_TIME

• IF