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Welcome and Introduction Peter D. Karp, Ph.D. Bioinformatics Research Group SRI International SRI International Bioinformatics 1 Pathway Tools Workshop Workshop format First three days formal presentations Last two days

  1. Welcome and Introduction Peter D. Karp, Ph.D. Bioinformatics Research Group SRI International SRI International Bioinformatics 1

  2. Pathway Tools Workshop � Workshop format � First three days formal presentations � Last two days presentations and hackathon / working groups � Let’s accumulate suggestions for the working sessions � Hold workshops every 18 months SRI International Bioinformatics 2

  3. Workshop Goals � Hear great science � Present new developments in Pathway Tools � Learn what new directions PTools should take � See how other groups are making use of PTools � Learn of PTools extensions being developed by other groups � Work together on new directions � Learn how to program PTools SRI International Bioinformatics 3

  4. Workshop Will be Available Live via Internet � Via WebEx plus Conference Call � WebEx shares the computer’s desktop � Make your presentation from � SRI laptop � Your WebEx-enabled laptop � If you are willing, email your slides to taltman@ai.sri.com for posting on workshop Web site SRI International Bioinformatics 4

  5. SRI Campus is Secure SRI International Bioinformatics 5

  6. Pathway Tools Capabilities � Create and maintain an organism database integrating genome, pathway, regulatory information � Computational inference tools � Interactive editing tools � Query and visualize that database � Use the database to interpret omics data � Comparative analysis tools � Systems biology analyses � Model repository SRI International Bioinformatics 6

  7. Model Organism Databases / Organism Specific Databases � DBs that describe the genome and other information about an organism � Every sequenced organism with an active experimental community requires a MOD � Integrate genome data with information about the biochemical and genetic network of the organism � Integrate literature-based information with computational predictions � Curated by experts for that organism � No one group can curate all the world’s genomes � Distribute workload across a community of experts to create a community resource SRI International Bioinformatics 7

  8. Rationale for MODs � Each “complete” genome is incomplete in several respects: � 40%-60% of genes have no assigned function � Roughly 7% of those assigned functions are incorrect � Many assigned functions are non-specific � Need continuous updating of annotations with respect to new experimental data and computational predictions � Gene positions, sequence, gene functions, regulatory sites, pathways � MODs are platforms for global analyses of an organism � Interpret omics data in a pathway context � In silico prediction of essential genes � Characterize systems properties of metabolic and genetic networks SRI International Bioinformatics 8

  9. Pathway Tools Software: PathoLogic � Computational creation of new Pathway/Genome Databases � Transforms genome into Pathway Tools schema and layers inferred information above the genome � Predicts operons � Predicts metabolic network � Predicts which genes code for missing enzymes in metabolic pathways � Infers transport reactions from transporter names SRI International Bioinformatics 9

  10. Pathway Tools Software: Pathway/Genome Editors � Interactively update PGDBs with graphical editors � Support geographically distributed teams of curators with object database system � Gene and protein editor � Reaction editor � Compound editor � Pathway editor � Operon editor � Publication editor SRI International Bioinformatics 10

  11. What is Curation? Ongoing updating and refinement of a PGDB � Correcting false-positive and false-negative � predictions Incorporating information from experimental literature � Authoring of comments and citations � Updating database fields � Gene positions, names, synonyms � Protein functions, activators, inhibitors � Addition of new pathways, modification of existing � pathways Defining TF binding sites, promoters, regulation of � transcription initiation and other processes SRI International Bioinformatics 11

  12. Pathway Tools Software: Pathway/Genome Navigator � Querying and visualization of: � Pathways � Reactions � Metabolites � Genes/Proteins/RNA � Regulatory interactions � Chromosomes � Two modes of operation: � Web mode � Desktop mode � Most functionality shared, but each has unique functionality SRI International Bioinformatics 12

  13. Obtaining a PGDB for Organism of Interest � Find existing PGDB � In BioCyc � From third party � Create your own SRI International Bioinformatics 13

  14. Pathway Tools Software: PGDBs Created Outside SRI � 2,580+ licensees: 205 groups applying software to 1,750 organisms � Saccharomyces cerevisiae, SGD project, Stanford University � 135 pathways / 565 publications � FungiCyc, Broad Institute -- 23 fungi � Candida albicans , CGD project, Stanford University � dictyBase, Northwestern University � Mouse, MGD, Jackson Laboratory � Drosophila, FlyBase, Harvard University � Under development: � C. elegans, WormBase � Arabidopsis thaliana, TAIR, Carnegie Institution of Washington � 288 pathways / 2282 publications � ChlamyCyc, GoFORSYS � PlantCyc , Carnegie Institution of Washington � Six Solanaceae species, Cornell University � GrameneDB, Cold Spring Harbor Laboratory � Medicago truncatula , Samuel Roberts Noble Foundation SRI International Bioinformatics 14

  15. Pathway Tools Software: PGDBs Created Outside SRI � E. Uberbacher, ORNL 33 Bioenergy-related organisms � G. Serres, MBL and ORNL: 18 Shewanella genomes � M. Bibb, John Innes Centre, Streptomyces coelicolor � TBDB Project, Mycobacterium tuberculosis � F. Brinkman, Simon Fraser Univ, Pseudomonas aeruginosa � Genoscope, Acinetobacter � R.J.S. Baerends, University of Groningen, Lactococcus lactis IL1403, Lactococcus lactis MG1363, Streptococcus pneumoniae TIGR4, Bacillus subtilis 168, Bacillus cereus ATCC14579 � Matthew Berriman, Sanger Centre, Trypanosoma brucei, Leishmania major � Sergio Encarnacion, UNAM, Sinorhizobium meliloti � Mark van der Giezen, University of London, Entamoeba histolytica, Giardia intestinalis SRI International Bioinformatics 15

  16. Pathway Tools Software: PGDBs Created Outside SRI � Large scale users: � C. Medigue, Genoscope, 200+ PGDBs � G. Sutton, J. Craig Venter Institute, 80+ PGDBs � G. Burger, U Montreal, 60+ PGDBs � Bart Weimer, UC Davis , Lactococcus lactis, Brevibacterium linens, Lactobacillus acidophilus, Lactobacillus plantarum, Lactobacillus johnsonii, Listeria monocytogenes � Partial listing of outside PGDBs at http://biocyc.org/otherpgdbs.shtml SRI International Bioinformatics 16

  17. Acknowledgements � SRI � Funding sources: � Suzanne Paley, Ron Caspi, � NIH National Institute of Ingrid Keseler, Carol Fulcher, General Medical Sciences Markus Krummenacker, Alex � NIH National Center for Shearer, Tomer Altman, Joe Research Resources Dale, Fred Gilham, Pallavi Kaipa � EcoCyc Collaborators � Julio Collado-Vides, Robert Gunsalus, Ian Paulsen � MetaCyc Collaborators BioCyc.org � Sue Rhee, Peifen Zhang, Kate Dreher � Lukas Mueller, Anuradha Pujar Learn more from BioCyc webinars: biocyc.org/webinar.shtml SRI International Bioinformatics 17

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