MicroStation System, MicroLog Version 4.2 - DTU Systems Biology ...

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Data Management and Compiling Databases ASCII Export Window Entries • Date: Date data was saved • Plate Type: GN, GP, YT, FF, etc. required and selected from saved file • Plate Number: number you designated for plate information • Incubation Time: time you designated depending on MicroPlate type • Sample Number: number you designated for plate information • Strain Type: GN-ENT, or GN-NENT, etc., determined by the MicroPlate type • Strain Name: name you designated for plate information • Strain Number: number you designated for plate information • Other: information you add to further describe sample • “+/b/-“ Reactions: results from reading MicroPlate displayed as: o “+” = positive o “-“ = negative o “b” = borderline • 1/0.5/0 Reactions: OD display of results if reactions read manually o 1 = positive o 0 = negative o 0.5 = borderline • Dual Wavelength Data (DWD): O.D. data on printouts if GN, GP, AN, MT or Eco plate is read from a MicroStation Reader = [(590nm–750nm) x – (590nm-750nm) A1] X 1000, where x=any well • Dual Wavelength O.D. (DW): OD difference data if GN, GP, AN, MT, or Eco plate read from a MicroStation Reader = (590nm–750nm) x, where x=any well • 750nm O.D.: Raw O.D. read at 750 nm from MicroStation Reader • 590nm O.D.: Raw O.D. read at 590 nm from MicroStation Reader • 590nm %: O.D. data on printouts if YT, SFN, or SFP plate read from a MicroStation Reader= • 590nm % = (590nm x – A1) x 100, where x=any well • 590nm Filter Position: position 5 • 750nm Filter Position: position 6 • Data Generation Mode: Manual or Reader • ID Result: Message if there is NO ID or Genus species name if ID obtained from reading MicroPlate • ID #1 Name: Genus species name of organism listed as first choice on printout of results • ID #1 SIM: SIM of organism listed as first choice on printout of results • ID # 1 DIS: DIS of organism listed as first choice on printout of results • ID #2 Name: Genus species name of organism listed as second choice on printout of results • ID #2 SIM: SIM of organism listed as second choice on printout of results • ID # 2 DIS: DIS of organism listed as second choice on printout of results • ID #3 Name: Genus species name of organism listed as third choice on printout of results • ID #3 SIM: SIM of organism listed as third choice on printout of results • ID # 3 DIS: DIS of organism listed as third choice on printout of results ASCII Export Window Entries (Unique Entries for FF) • Color Data: O.D. Data on FF printouts for color data = • [(490nm x –490nm A1) -(750nm x –750nm A1)] X 1000, where x=any well. • Turbidity Data: O.D. Data on FF printouts for turbidity data = • (750nmx –750nm A1) X 1600, where x=any well. • Dual Wavelength O.D. (DW): OD readings at 490 nm and 750 nm minus the A-1 well: • (490nm x - 450nm A1), where x=any well. • (750nm x - 750nm A1), where x=any well. • 750nm O.D.: Raw O.D. read at 750 nm from MicroStation Reader. • 490nm O D: Raw O.D. read at 490 nm from MicroStation Reader. • Color Filter Position: 490nm, position 3 • Turbidity Filter Position: 750nm, position 6 Section 7 � Page 22 MicroStation System/MicroLog User Guide Apr 07
Data Management and Compiling Databases Cluster Analysis Cluster analysis uses a mathematical approach to display the relative similarities and differences between strains or species based on pattern matching. It offers a visual method for examining groups using linear dendrograms and two- and three-dimensional cluster diagrams. You can generate cluster analyses on groups of entries in Biolog’s database or your own database. The math behind cluster analysis Dendrograms are generated using a modified UPGMA analysis developed by Biolog (algorithm for constructing rooted phylogenic trees). The algorithm uses DIST values to generate the branching structure of the dendrogram. A DIST value of 14 is usually used as a cutting level to separate genera. This value has been empirically determined to be an appropriate one for most genera of gram-negative bacteria. Once the software generates a preliminary dendrogram, it makes a second pass, rotating all branch points to their most preferred position. This best maintains proximity of related strains or species. If the distance between strains or species adjacent to cut points is less than 14, they are joined with a dashed line that indicates their actual distance. By mathematically removing the linear constraints of the dendrogram, the software can generate two- and three-dimensional diagrams of DIST relationships. All of these cluster diagrams are only approximations of true relationships. With 95 carbon source tests, it would take 95dimensional space to provide fully detailed clustering. As a practical matter, the linear dendrograms and two- and three-dimensional diagrams give very satisfactory representations. Using cluster analysis with IDs 1. Once you get a species ID, click the Cluster Menu selection bar on the Data window. MicroStation System/MicroLog User Guide Apr 07 Section 7 � Page 23
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MicroStation System MicroLog Versi
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LICENSE AGREEMENT Notice: This is a
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Table of Contents Section Title 1.
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10. Frequently Asked Questions…
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Welcome Section 1 � Page 2 Connec
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2. Installation and Registration In
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Installation and Registration The A
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8. E-mail the User Key File to tech
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MicroStation System/MicroLog Overvi
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Follow directions closely to obtain
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Preparing Samples Preparing an inoc
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Preparing Samples Recognizing fasti
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Preparing Samples Media shorthand:
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Preparing Samples Don’t forget to
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Preparing Samples b. Use a sterile
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Preparing Samples aids in liquefyin
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Preparing Samples Caution! Pipet th
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Preparing Samples Special Procedure
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Preparing Samples Initial culture m
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Reading MicroPlates Set Up tab Sele
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Reading MicroPlates When you’re e
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Reading MicroPlates 2. Enter reacti
Page 53 and 54: Reading MicroPlates Entering sample
Page 55 and 56: Reading MicroPlates Select file nam
Page 57 and 58: Reading MicroPlates Naming Workshee
Page 59 and 60: Reading MicroPlates This arrow show
Page 61 and 62: Reading MicroPlates Using Worksheet
Page 63 and 64: Reading MicroPlates 4. Click Save t
Page 65 and 66: Reading MicroPlates Wells with high
Page 67 and 68: Reading MicroPlates Exiting When yo
Page 69 and 70: Interpreting Results Understanding
Page 71 and 72: Interpreting Results Mismatch Type
Page 73 and 74: Interpreting Results What are those
Page 75 and 76: Interpreting Results NOTE: A1 value
Page 77 and 78: Interpreting Results Slide the scro
Page 79 and 80: Interpreting Results VS. CURRENT MI
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Page 83 and 84: Data Management and Compiling Datab
Page 85 and 86: Combining Data Files Data Managemen
Page 87 and 88: OK, Out, Hold, Atypical Sorting lab
Page 89 and 90: Remember! When building your own da
Page 93 and 94: DATABASE WINDOW Data Management and
Page 97 and 98: Arrow indicates selected entry Data
Page 103: Export Help Mark this choice if you
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Page 111 and 112: Important! • If you test Password
Page 113 and 114: Log-In Privileges Administration an
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Page 117 and 118: 9. Technical Notes In this section:
Page 119 and 120: Making Biolog Universal Growth Agar
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Page 123 and 124: 10. Frequently Asked Questions In t
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Page 127 and 128: Troubleshooting Symptom Cause Solut
Page 129 and 130: Troubleshooting Preparing Inocula S
Page 131 and 132: Troubleshooting MicroStation Reader
Page 133 and 134: Glossary Dendrogram Cluster diagram
Page 135 and 136: Glossary Spore, fungal Sterile, fun
Page 137 and 138: Culture Media Atmosphere Temperatur
Page 139 and 140: Appendices: Notes Notes: Section 13
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Appendix 4: Database Species Lists
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Appendix 5: Program Printouts Appen
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Appendix 5: Program Printouts 1�
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Appendix 5: Program Printouts Funga
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Appendix 5: Program Printouts Print
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Appendix 6: Dangerous Pathogens (DP
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MicroStation System, MicroLog Version 4.2 - DTU Systems Biology ...

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