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either during the current Workbench session or upon resuming the session at a later time. 24 1 Much of the display on the Workbench is tailored to the program outputs of the specific tools. For instance, using an appropriate MIME-type for RASMOL, three dimensional structures of macromolecules can be displayed on a browser window(Vide Fig. 4). Discussion The Biology Workbench is a WWW-based analysis environment which brings highpowered computation into an experimental laboratory. The seamless integration of remote database and computational biology tools forms creates a virtual computer, with WWW browsers as the GUI interface. The platform independent access to tools creates an environment in which all biologists can utilize programs which previously were found only in large laboratories with heavy bioinformatics investments. The future of the Biology Workbench is targeted towards genomics. Several aspects of genome informatics including automated analysis and annotation, newer tools for protein and gene clustering, and tools for fast comparisons across genomes are all under development. Acknowledgments This work was supported in part by NSF grant ASC 89-02829 and by grants from MDL Informatics Corporation. All the computational resources for the public version of the Biology Workbench are provided by NCSA. APPENDIX A List of All Currently Available Biological Databases in The Biology Workbench Nucleic Acid Databases GenBank - NCBI Nucleic Acid Sequence Database (Protein also) GenBankNew - NCBI Nucleic Acid Sequence Database (Protein also) Protein Databases BLOCKS - Aligned Ungapped Highly Conserved Protein Segments NRL3D - Sequence and Annotation Information Taken From The PDB PDBFINDER - Protein Sequences From The PDB PIR - The Protein Information Resource SWISSPROT - Protein Sequences From Geneva And EMBL SWISSNEW - Protein Sequences From Geneva And EMBL
242 TREMBL - Supplement To SWISSPROT Database TREMBLNEW - Supplement To SWISSPROT Database PIRALN - Alignment Database from The Protein Information Resource Literature and Textual Databases ECDC - Information On The E.coli K12 Chromosome ENZYME - Data For Enzymes With An EC Numbers EPD - Eukaryotic Promotor Database FlyGene - Subset Of FlyBase PRODOM - Comprehensive Collection Of Protein Families PROSITE - Dictionary Of Sites And Patterns In Proteins PROSITEDOC - Annotation On Selected Proteins From PROSITE OMIM - The Mendelian Inheritance In Man Data Bank REBASE - The Restriction Enzyme Database SEQANALREF - Sequence Analysis Bibliography Data Bank APPENDIX B List of Currently Available Tools in the Biology Workbench Sequence Management Tools Add New Sequence Edit Sequence View Sequence Delete Sequence Copy Sequence Download Sequence View Scoring Matrices Common Analysis Tools SRS Multiple database searches with Boolean queries FASTA Heuristic database similarity searching SSEARCH Smith-Waterman database searching ALIGN Smith-Waterman pairwise global sequence alignment LALIGN Smith-Waterman pairwise local sequence alignment LFASTA Heuristic pairwise local sequence alignment BESTSCOR Self-comparison similarity scores RANDSEQ Sequence randomization for statistical analysis CLUSTALW Multiple sequence alignment and phylogenetic tree construction
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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
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Introduction 16 OPM: OBJECT-PROTOCO
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189 OPM is a data model whose objec
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Page 204 and 205: 195 Interface, except that one can
Page 206 and 207: 197 Our strategy of providing suppo
Page 208 and 209: Acknowledgments 199 Between 1992 an
Page 210 and 211: Introduction 17 BIOKLEISLI:INTEGRAT
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
Page 226 and 227: 217 Operands also include named set
Page 228 and 229: Figure 1. The SRS Top Page. Figure
Page 230 and 231: Analyzing Data in SRS with Applicat
Page 232 and 233: 223 other databanks, and define spe
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 240 and 241: 23 1 12. Altschul, S.F., Gish, W.,
Page 242 and 243: Introduction 19 BIOLOGY WORKBENCH:
Page 244 and 245: Figure 1. Organization and Flow of
Page 246 and 247: 237 In order to make wrapper develo
Page 248 and 249: the browser window containing a men
Page 252 and 253: PROFILESCAN Comparison of protein o
Page 254 and 255: 20 EBI: CORBA AND THE EBI DATABASES
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
Page 270 and 271: possible because the bioWidget arch
Page 272 and 273: 263 4. Gish, Warren (1994-1997). un
Page 274 and 275: 22 ACEDB: THE ACE DATABASE MANAGER
Page 276 and 277: 267 On the other hand, most users c
Page 278 and 279: 269 Street, City and State into "ma
Page 280 and 281: 27 1 to a running database after ed
Page 282 and 283: 273 database the class Map refers t
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Page 286 and 287: 277 table of 13 columns and 1 milli
Page 288 and 289: Introduction 23 LABBASE: DATA AND W
Page 290 and 291: 28 1 We will use as a running examp
Page 292 and 293: LabBase Details 283 A LabBase objec
Page 294 and 295: When the procedure completes, LabFl
Page 296 and 297: 287 sequence-assembly Worker in our
Page 298 and 299: 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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