DOC PREVIEW
BYU BIO 465 - Overview of the Pathway Tools Software and Pathway/Genome Databases

This preview shows page 1-2-3-27-28-29 out of 29 pages.

Save
View full document
View full document
Premium Document
Do you want full access? Go Premium and unlock all 29 pages.
Access to all documents
Download any document
Ad free experience
View full document
Premium Document
Do you want full access? Go Premium and unlock all 29 pages.
Access to all documents
Download any document
Ad free experience
View full document
Premium Document
Do you want full access? Go Premium and unlock all 29 pages.
Access to all documents
Download any document
Ad free experience
View full document
Premium Document
Do you want full access? Go Premium and unlock all 29 pages.
Access to all documents
Download any document
Ad free experience
View full document
Premium Document
Do you want full access? Go Premium and unlock all 29 pages.
Access to all documents
Download any document
Ad free experience
View full document
Premium Document
Do you want full access? Go Premium and unlock all 29 pages.
Access to all documents
Download any document
Ad free experience
Premium Document
Do you want full access? Go Premium and unlock all 29 pages.
Access to all documents
Download any document
Ad free experience

Unformatted text preview:

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 InternationalBioinformaticsIntroductionsBRG StaffPeter KarpPallavi KaipaMario LatendresseSuzanne PaleyMarkus KrummenackerIngrid KeselerRon CaspiAlex ShearerCarol FulcherAttendeesWhere from, what genome?What do you hope to get out of the tutorial?SRI InternationalBioinformaticsSRI InternationalPrivate nonprofit research instituteNo permanent funding sources1300 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 GroupEcoCycMetaCycPathway ToolsPathway HolesBioWarehouseEnzyme GenomicsSRI InternationalBioinformaticsOutline for TutorialMondayIntroductionPathway/Genome NavigatorPathoLogic tutorial and demoPathoLogic lab session – Make genome input files parsableTuesdayPathoLogic tutorialPathoLogic lab session – Build initial version of PGDBWednesdayPathway hole filler, operon predictor, transport inference parserThursdayEditorsFeedback sessionSRI InternationalBioinformaticsTutorial GoalsGeneral familiarity with Pathway Tools goals and functionalityAbility to create, edit, and navigate a new PGDBCreate new PGDB for genome(s) you brought with youFamiliarity with information resources available about Pathway Tools to continue your workSRI InternationalBioinformaticsSRI’s Support for Pathway ToolsNIH grant finances software development and user supportAdditional grants finance other software developmentEmail us bug reports, suggestions, questionsComprehensive bug reports are required for us to fix the problem you reportedKeep us posted regarding your progressSRI InternationalBioinformaticsAdministrative DetailsPlease wear badges at all timesEscort required outside this room/hallwayLet us know when you are leavingUse E-Bldg EntrancePhone numbers to call from entranceMealsWednesday outing possibleRestroomsSRI InternationalBioinformaticsTutorial FormatQuestions welcome during presentationsLab sessions will take different amounts of time for different peopleRefine your PGDBRead Pathway Tools manualsBuddy system for some computersComputer loginsInternet connectivitySRI InternationalBioinformaticsPathway/Genome DatabaseIntegrating Genomic and Biochemical DataChromosomes,PlasmidsGenesProteinsReactionsPathwaysCompoundsCELLOperons,Promoters,DNA Binding SitesSRI InternationalBioinformaticsTerminologyModel Organism Database (MOD) – DB describing genome and other information about an organismPathway/Genome Database (PGDB) – MOD that combines information aboutPathways, reactions, substratesEnzymes, transportersGenes, repliconsTranscription factors, promoters, operons, DNA binding sitesBioCyc – Collection of 205 PGDBs at BioCyc.orgEcoCyc, AgroCyc, HumanCycSRI InternationalBioinformaticsBioCyc Collection of Pathway/Genome DatabasesPathway/Genome Database (PGDB) – combines information aboutPathways, reactions, substratesEnzymes, transportersGenes, repliconsTranscription factors/sites, promoters, operonsTier 1: Literature-Derived PGDBsMetaCycEcoCyc -- Escherichia coli K-12BioCyc Open Chemical DatabaseTier 2: Computationally-derived DBs, Some Curation -- 12 PGDBsHumanCycMycobacterium tuberculosisTier 3: Computationally-derived DBs, No Curation -- 191 DBsSRI InternationalBioinformaticsTerminology –Pathway Tools SoftwarePathoLogicPredicts operons, metabolic network, pathway hole fillers, from genomeComputational creation of new Pathway/Genome DatabasesPathway/Genome EditorsDistributed curation of PGDBsDistributed object database system, interactive editing toolsPathway/Genome NavigatorWWW publishing of PGDBsQuerying, visualization of pathways, chromosomes, operonsAnalysis operationsPathway visualization of gene-expression dataGlobal comparisons of metabolic networksBioinformatics 18:S225 2002SRI InternationalBioinformaticsPathway/Genome DBs Created byExternal Users600+ licensees -- 50 groups applying software to 100+ organisms Software freely available to academics; Each PGDB owned by its creator Saccharomyces cerevisiae, SGD project, Stanford Universitypathway.yeastgenome.org/biocyc/TAIR, Carnegie Institution of Washington Arabidopsis.org:1555dictyBase, Northwestern UniversityGrameneDB, Cold Spring Harbor LaboratoryPlanned:CGD (Candida albicans), Stanford UniversityMGD (Mouse), Jackson LaboratoryRGD (Rat), Medical College of WisconsinWormBase (C. elegans), CaltechLarge scale users:C. Medigue, Genoscope, 67 PGDBsG. Burger, U Montreal, 20 PGDBs DOE GTL contractors:G. Church, Harvard, Prochlorococcus marinus MED4Larimer/Uberbacher, ORNL, Shewanella onedensisJ. Keasling, UC Berkeley, Desulfovibrio vulgarisFiona 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 genomeCreate an up-to-date computable information repository about an organismPerform analyses on the genome


View Full Document

BYU BIO 465 - Overview of the Pathway Tools Software and Pathway/Genome Databases

Documents in this Course
summary

summary

13 pages

Cancer

Cancer

8 pages

Ch1

Ch1

5 pages

GNUMap

GNUMap

20 pages

cancer

cancer

8 pages

SNPs

SNPs

22 pages

Load more
Download Overview of the Pathway Tools Software and Pathway/Genome Databases
Our administrator received your request to download this document. We will send you the file to your email shortly.
Loading Unlocking...
Login

Join to view Overview of the Pathway Tools Software and Pathway/Genome Databases and access 3M+ class-specific study document.

or
We will never post anything without your permission.
Don't have an account?
Sign Up

Join to view Overview of the Pathway Tools Software and Pathway/Genome Databases 2 2 and access 3M+ class-specific study document.

or

By creating an account you agree to our Privacy Policy and Terms Of Use

Already a member?