Overview of the Pathway Tools Software and Pathway/Genome DatabasesIntroductionsSRI InternationalSRI OrganizationResearch in the SRI Bioinformatics Research GroupOutline for TutorialTutorial GoalsSRI’s Support for Pathway ToolsAdministrative DetailsTutorial FormatPowerPoint PresentationTerminologyBioCyc Collection of Pathway/Genome DatabasesTerminology – Pathway Tools SoftwarePathway/Genome DBs Created by External UsersSlide 17Why Create PGDBs?Sequence Project WorkflowMetaCyc: Metabolic EncyclopediaMetaCyc DataFamily of Pathway/Genome DatabasesOmics ViewerEnvironment for Computational Exploration of GenomesPathway Tools Implementation DetailsThe Common Lisp Programming EnvironmentSurveyPGDB(s) That You BuildSummaryInformation SourcesOverview of the Pathway Tools Software and Pathway/Genome DatabasesSRI InternationalBioinformaticsIntroductionsBRG StaffPeter KarpPallavi KaipaMario LatendresseSuzanne PaleyMarkus KrummenackerIngrid KeselerRon CaspiAlex ShearerCarol FulcherAttendeesWhere from, what genome?What do you hope to get out of the tutorial?SRI InternationalBioinformaticsSRI InternationalPrivate nonprofit research instituteNo permanent funding sources1300 staff in Menlo Park– Founded in 1946 as Stanford Research Institute– Separated from Stanford University in 1970– Name changed to SRI International in 1977– David Sarnoff Research Center acquired in 1987SRI InternationalBioinformaticsSRI OrganizationInformation and Computing SciencesEngineering SystemsAnd SciencesPhysicalSciencesBiopharmaceuticalsAndPharmaceuticalDiscoveryEducation and PolicyBioinformatics Research GroupSRI InternationalBioinformaticsResearch in the SRIBioinformatics Research GroupEcoCycMetaCycPathway ToolsPathway HolesBioWarehouseEnzyme GenomicsSRI InternationalBioinformaticsOutline for TutorialMondayIntroductionPathway/Genome NavigatorPathoLogic tutorial and demoPathoLogic lab session – Make genome input files parsableTuesdayPathoLogic tutorialPathoLogic lab session – Build initial version of PGDBWednesdayPathway hole filler, operon predictor, transport inference parserThursdayEditorsFeedback sessionSRI InternationalBioinformaticsTutorial GoalsGeneral familiarity with Pathway Tools goals and functionalityAbility to create, edit, and navigate a new PGDBCreate new PGDB for genome(s) you brought with youFamiliarity with information resources available about Pathway Tools to continue your workSRI InternationalBioinformaticsSRI’s Support for Pathway ToolsNIH grant finances software development and user supportAdditional grants finance other software developmentEmail us bug reports, suggestions, questionsComprehensive bug reports are required for us to fix the problem you reportedKeep us posted regarding your progressSRI InternationalBioinformaticsAdministrative DetailsPlease wear badges at all timesEscort required outside this room/hallwayLet us know when you are leavingUse E-Bldg EntrancePhone numbers to call from entranceMealsWednesday outing possibleRestroomsSRI InternationalBioinformaticsTutorial FormatQuestions welcome during presentationsLab sessions will take different amounts of time for different peopleRefine your PGDBRead Pathway Tools manualsBuddy system for some computersComputer loginsInternet connectivitySRI InternationalBioinformaticsPathway/Genome DatabaseIntegrating Genomic and Biochemical DataChromosomes,PlasmidsGenesProteinsReactionsPathwaysCompoundsCELLOperons,Promoters,DNA Binding SitesSRI InternationalBioinformaticsTerminologyModel Organism Database (MOD) – DB describing genome and other information about an organismPathway/Genome Database (PGDB) – MOD that combines information aboutPathways, reactions, substratesEnzymes, transportersGenes, repliconsTranscription factors, promoters, operons, DNA binding sitesBioCyc – Collection of 205 PGDBs at BioCyc.orgEcoCyc, AgroCyc, HumanCycSRI InternationalBioinformaticsBioCyc Collection of Pathway/Genome DatabasesPathway/Genome Database (PGDB) – combines information aboutPathways, reactions, substratesEnzymes, transportersGenes, repliconsTranscription factors/sites, promoters, operonsTier 1: Literature-Derived PGDBsMetaCycEcoCyc -- Escherichia coli K-12BioCyc Open Chemical DatabaseTier 2: Computationally-derived DBs, Some Curation -- 12 PGDBsHumanCycMycobacterium tuberculosisTier 3: Computationally-derived DBs, No Curation -- 191 DBsSRI InternationalBioinformaticsTerminology –Pathway Tools SoftwarePathoLogicPredicts operons, metabolic network, pathway hole fillers, from genomeComputational creation of new Pathway/Genome DatabasesPathway/Genome EditorsDistributed curation of PGDBsDistributed object database system, interactive editing toolsPathway/Genome NavigatorWWW publishing of PGDBsQuerying, visualization of pathways, chromosomes, operonsAnalysis operationsPathway visualization of gene-expression dataGlobal comparisons of metabolic networksBioinformatics 18:S225 2002SRI InternationalBioinformaticsPathway/Genome DBs Created byExternal Users600+ licensees -- 50 groups applying software to 100+ organisms Software freely available to academics; Each PGDB owned by its creator Saccharomyces cerevisiae, SGD project, Stanford Universitypathway.yeastgenome.org/biocyc/TAIR, Carnegie Institution of Washington Arabidopsis.org:1555dictyBase, Northwestern UniversityGrameneDB, Cold Spring Harbor LaboratoryPlanned:CGD (Candida albicans), Stanford UniversityMGD (Mouse), Jackson LaboratoryRGD (Rat), Medical College of WisconsinWormBase (C. elegans), CaltechLarge scale users:C. Medigue, Genoscope, 67 PGDBsG. Burger, U Montreal, 20 PGDBs DOE GTL contractors:G. Church, Harvard, Prochlorococcus marinus MED4Larimer/Uberbacher, ORNL, Shewanella onedensisJ. Keasling, UC Berkeley, Desulfovibrio vulgarisFiona Brinkman, Simon Fraser Univ, Pseudomonas aeruginosaSRI InternationalBioinformaticsTerminology“Database” = “DB” = “Knowledge Base” = “KB” = “Pathway/Genome Database” = “PGDB”SRI InternationalBioinformaticsWhy Create PGDBs?Extract more information from your genomeCreate an up-to-date computable information repository about an organismPerform analyses on the genome
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