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237 In order to make wrapper development easier and standardize tool integration into the Workbench, several files containing subroutines are included in the Workbench tree. These files are generally “required” by all Perl wrappers, but the subroutines may be extracted and revised to suit individual needs. While we recommend using the standard subroutines wherever possible, we cannot fully predict the needs of users for other non-standard tool specific routines. This concept is being refined for future releases of the Workbench. The central file for tool integration is the “html.pl” file, which contains the necessary subroutines for communication with BW.cgi (the Workbench core CGI program) and for passing configuration information to the wrapper scripts. This file should be included at the beginning of all scripts using the “require” directive in Perl. Tools wrappers may, however, require only a subset of the subroutines in the html.pl file. Sessions Each time a user accesses the Workbench, a previous analysis session can be resumed or a new one initiated. The role of the sessions is to maintain the state and sequence of operations performed on the Workbench during an interactive session. Sessions can be useful for both recalling previously performed operations as well as for comparison with newer analyses. Essentially, sessions provide the history of the Workbench use and can be updated, erased or permanently stored. Databases Almost all of the relevant biological sequence, structure and literature databases are accessible from the Biology Workbench. The databases are federated by identification of common objects and indexing each database based on these objects. We use the SRS schema (Etzold and Argos, 1993) to store and access the databases allowing them to be queried for multiple objects as well as combinations of objects using Boolean operators on the query construction page. The Workbench also permits nested Boolean queries. To aid the integration of SRS indexed databases, the file “db_config.pl” containing routines for parsing database directories and identifying available databases is provided. These routines also extract important information on specific databases to allow sequence information to be properly imported to the Workbench. A database mirroring program has also been developed for the Biology Workbench, which fetches databases as they are updated in their primary repositories. The indexing and creation of Blastable sequence database files is done locally each time new databases are retrieved. A complete list of all databases available on the Workbench is presented in Appendix A. Analysis Modules
238 The Biology Workbench contains all the commonly used, publicly available analysis modules for the protein and nucleic acid sequences and structures. “Bread-andbutter” modules for biologists such as BLAST and FASTA, programs for aligning multiple sequences such as CLUSTALW and MSA and multiple sequence profile and statistical analysis tools are all a point-and-click away on the Workbench. A complete list of available tools is presented in Appendix B. System Overview Figure 2: Invoking an old session file A typical user session begins with a user-specific login to the Workbench server followed by the invocation of a session. Invoking an old session file places the user in the final state of the most recent prior invocation of that session. The user may then choose one of the analysis tool-sets, namely Protein Tools, Nucleic Acids Tools, and Alignment Tools. Selection of the Protein Tools, for instance, displays a page in
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BIOINFORMATICS: Databases and Syste
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BIOINFORMATICS: Databases and Syste
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To Tish, Emily, Miles and Josephine
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TABLE OF CONTENTS INTRODUCTION ....
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INTRODUCTION Stanley Letovsky Bioin
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for wisdom. Where algorithms tend t
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gain performance by distributing qu
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systems described (OPM, BioKleisli,
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DATABASES
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1 NCBI: INTEGRATED DATA FOR MOLECUL
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figure 1, and all flows into the ID
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There are other sets of data that c
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2. Explicit declaration by the hist
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2. W. J. Wilbur, A retrieval system
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2 HOVERGEN: COMPARATIVE ANALYSIS OF
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Figure 1: Phylogenetic tree of the
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fragment. In some cases, a same gen
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Figure 2: Distribution of families
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the user can visualize all the anno
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Selecting orthologous genes with HO
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Thus, HOVERGEN allows one to do exh
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21. Saitou, N. Nei, M. The neighbor
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3 WIT/WIT2: METABOLIC RECONSTRUCTIO
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protein sequence are used (e.g., OR
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After we have accumulated an initia
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Coordinating the Development of Met
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Availability of the Pathways, Softw
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4 ECOCYC: THE RESOURCE AND THE LESS
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epresented as an instance of the cl
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The Gene--Reaction Schematic The ma
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EcoCyc contains extensive informati
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within compound windows uses a conc
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Figure 4: The EcoCyc linear map bro
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Figure 5: The software architecture
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6. Karp. Frame representation and r
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Introduction 5 KEGG: FROM GENES TO
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Binary relations Figure 1 : Level o
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hierarchical text. The genome map i
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(2) Java applets to search, compare
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can be used for gene function assig
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influenzae lacks the upper portion
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Future Directions Figure 4. KEGG as
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Introduction 6 OMIM: ONLINE MENDELI
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The Entry Each OMIM entry is assign
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Searching OMIM is as simple as typi
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How OMIM is Curated OMIM is maintai
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7 GDB: INTEGRATING GENOMIC MAPS Int
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in one of two ways: by being wholly
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Figure 3: Universal Coordinate Disp
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Figure 5: Dispersion of linear (lef
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which minimizes dispersion. The opt
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Figure 10: A piece of an "comprehen
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alignments are better for the speci
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Summary 8 HGMD: THE HUMAN GENE MUTA
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Data coverage and structure 101 By
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Conclusions and Outlook 103 Being b
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Introduction 9 SENSELAB: MODELING H
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107 For the purposes of the rest of
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109 users might advocate creating a
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111 The Associations table describe
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Managing the Object Class Hierarchy
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115 In fig. 2, the Objects and Clas
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117 7. Mirsky JS, Nadkarni PM, Hine
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10 THE MOUSE GENOME DATABASE AND TH
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genetics community fostered the ear
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123 Data acquisition for MGD includ
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125 In February 1998, a ‘cDNA and
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Acknowledgments 127 MGD is funded b
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11 THE EDINBURGH MOUSE ATLAS: BASIC
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expression database under developme
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133 For blastocysts the shape of th
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135 which is a cut at an arbitrary
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137 This defines a viewing directio
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139 plate spline [19] or polynomial
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12 FLYBASE: GENOMIC AND POST- GENOM
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143 Genes, including links via publ
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Public Access to FlyBase Data The c
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147 There are two classes of annota
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149 screens to identify direct or i
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13 MAIZEDB: THE MAIZE GENOME DATABA
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The bins map strategy has been empl
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Clicking on one of the orthologous
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* hyper-text linked to MaizeDB enti
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DISSEMINATION TO EXTERNAL DATABASES
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Appendix 2: part of the Query Form
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Introduction 14 AGIS: USING THE AGR
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Horn Fly--Haematobia Screwworm--Coc
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Figure 2 : Main AGIS Menu 167
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Figure 4 : Available Classes and Su
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Figure 6 : Query by Example and Que
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Figure 8 : Hypertext ACEDB Object a
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15 CGSC: THE E.COLI GENETIC STOCK C
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177 described once for that gene an
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FIGURE 1. A Query for an hsdR- recA
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FIGURE 2. A Query for a lacZ-(amber
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183 These are suggestions that dese
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SYSTEMS
Page 196 and 197: Introduction 16 OPM: OBJECT-PROTOCO
Page 198 and 199: 189 OPM is a data model whose objec
Page 200 and 201: The OPM Database Development Tools
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Page 204 and 205: 195 Interface, except that one can
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Page 208 and 209: Acknowledgments 199 Between 1992 an
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Page 212 and 213: 203 In the remainder of this chapte
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Page 216 and 217: BioKleisli in Action: Querying Biom
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Page 220 and 221: References 211 13. NCBI ASN. 1 Spec
Page 222 and 223: Introduction 18 SRS: ANALYZING AND
Page 224 and 225: 215 In SRS, databank structures are
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Page 228 and 229: Figure 1. The SRS Top Page. Figure
Page 230 and 231: Analyzing Data in SRS with Applicat
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Page 234 and 235: Figure 7. A SWISS-PROT entry with i
Page 236 and 237: Figure 8. The results of a query fo
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Page 242 and 243: Introduction 19 BIOLOGY WORKBENCH:
Page 244 and 245: Figure 1. Organization and Flow of
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Page 252 and 253: PROFILESCAN Comparison of protein o
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Page 256 and 257: 247 the Object Request Broker (ORB)
Page 258 and 259: 249 Every database entry is represe
Page 260 and 261: 251 Wrappers with and without State
Page 262 and 263: Discussion 25 3 CORBA and IDL minim
Page 264 and 265: Introduction 21 BIOWIDGETS:REUSABLE
Page 266 and 267: Visualization Solutions 257 Turnkey
Page 268 and 269: 259 The architecture also exploits
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Page 272 and 273: 263 4. Gish, Warren (1994-1997). un
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Page 276 and 277: 267 On the other hand, most users c
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Page 288 and 289: Introduction 23 LABBASE: DATA AND W
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Page 292 and 293: LabBase Details 283 A LabBase objec
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287 sequence-assembly Worker in our
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289 The Worker converts the object
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291 Genome Research and are beginni
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INDEX
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INDEX A of Agricultural Genome Info
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of vertebrate genes, 21-33 developm
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GenBank database query software of,
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Metabolic Pathway Database, 38 Meta
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conversion to ‘gi’ identifiers
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