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Overview of the Pathway Tools Software and Pathway/Genome Databases

Overview of the Pathway Tools Software and Pathway/Genome Databases. Introductions. 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?

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Overview of the Pathway Tools Software and Pathway/Genome Databases

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  1. Overview of the Pathway Tools Software and Pathway/Genome Databases

  2. Introductions • 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?

  3. SRI 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 1987

  4. SRI Organization Information and Computing Sciences Bioinformatics Research Group Biopharmaceuticals And Pharmaceutical Discovery Engineering Systems And Sciences Physical Sciences Education and Policy

  5. Research in the SRIBioinformatics Research Group • EcoCyc • MetaCyc • Pathway Tools • Pathway Holes • BioWarehouse • Enzyme Genomics

  6. Outline 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 session

  7. Tutorial 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 work

  8. SRI’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 progress

  9. Administrative 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 • Restrooms

  10. Tutorial 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 connectivity

  11. Pathway/Genome Database Integrating Genomic and Biochemical Data Pathways Reactions Compounds Proteins Operons, Promoters, DNA Binding Sites Genes Chromosomes, Plasmids CELL

  12. 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, HumanCyc Terminology

  13. BioCyc 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 DBs

  14. Terminology –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 networks Bioinformatics 18:S225 2002

  15. 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 aeruginosa Pathway/Genome DBs Created byExternal Users

  16. Terminology • “Database” = “DB” = “Knowledge Base” = “KB” = “Pathway/Genome Database” = “PGDB”

  17. Why Create PGDBs? • Extract more information from your genome • Create an up-to-date computable information repository about an organism • Perform analyses on the genome and pathway complement of the organism, e.g., analyses of omics data • Perform comparative analyses with other organisms • Generate a genome poster and metabolic wall chart

  18. Sequence Project Workflow Raw Sequence PathoLogic Phred P/G Editors Pathway Tools Phrap P/G Navigator GeneMark/Glimmer WWW Publishing Analyses BLAST, BLOCKS

  19. MetaCyc: Metabolic Encyclopedia • Nonredundant metabolic pathway database • Describe a representative sample of every experimentally determined metabolic pathway • Literature-based DB with extensive references and commentary • Pathways, reactions, enzymes, substrates • Jointly developed by SRI and Carnegie Institution Nucleic Acids Research34:D511-D516 2006

  20. MetaCyc Data

  21. Family of Pathway/GenomeDatabases EcoCyc CauloCyc AraCyc MtbRvCyc HumanCyc MetaCyc

  22. Omics Viewer • Import gene expression, proteomics, metabolomics data • Obtain pathway based visualizations of omics data • Numerical spectrum of expression values mapped to a color spectrum • Steps of overview painted with color corresponding to expression level(s) of genes that encode enzyme(s) for that step

  23. Environment for Computational Exploration of Genomes • Powerful ontology opens many facets of the biology to computational exploration • Global characterization of metabolic network • Analysis of interface between transport and metabolism • Nutrient analysis of metabolic network

  24. Pathway Tools Implementation Details • Allegro Common Lisp • Sun, Linux, Windows platforms • Ocelot object database • 300,000+ lines of code • Lisp-based WWW server at BioCyc.org • Manages 205 PGDBs

  25. The Common Lisp ProgrammingEnvironment • Gatt studied Lisp and Java implementation of 16 programs by 14 programmers (Intelligence 11:21 2000)

  26. Survey • Please complete survey at end of each day

  27. PGDB(s) That You Build • Before you leave • Tar up your PGDB directory and FTP it home, email it home, or copy it to flash disk • We will create a backup copy of your PGDB directory if the directory is still there at the end of the tutorial • Delete the PGDB directory if you don’t want us to back it up • We will not give the backed up data to anyone else

  28. Summary • Pathway Tools and Pathway/Genome Databases • Not just for pathways! • Computational inferences • Operons, metabolic pathways, pathway hole fillers • Editing tools • Analysis tools: Omics data on pathways • Web publishing of PGDBs • Main classes of users: • Develop PGDB to extract more information from genome for genome paper • Develop a model-organism DB for the organism that is updated regularly and published on the web

  29. Information Sources • Pathway Tools User’s Guide • /root/aic-export/ecocyc/genopath/released/doc/manuals/userguide1.pdf • Pathway/Genome Navigator • Appendix A: Guide to the Pathway Tools Schema • /toot/aic-export/ecocyc/genopath/released/doc/manuals/userguide2.pdf • PathoLogic, Editing Tools • NOTE: Location of the aic-export directory can vary across different computers • Pathway Tools Web Site • http://bioinformatics.ai.sri.com/ptools/ • Publications, programming examples, etc. • Slides from this tutorial • http://bioinformatics.ai.sri.com/ptools/tutorial/

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