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Introduction to Pathway Tools & PGDB Creation

Learn about Pathway Tools software, PGDB creation, and FBA modeling. Explore genome analysis, metabolic pathways, and information resources. Get hands-on training and access support for your bioinformatics projects.

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Introduction to Pathway Tools & PGDB Creation

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

  2. SRI International • Private nonprofit multidisciplinary 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

  3. SRI Organization Information and Computing Sciences Bioinformatics Research Group Biosciences Engineering Systems And Sciences Physical Sciences Education and Policy

  4. FBA Tutorial Goals • Learn basic principles of FBA • Learn to run existing FBA models in Pathway Tools • Learn to develop new FBA models in Pathway Tools • Familiarity with information resources available about Pathway Tools to continue your work

  5. 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 • Analyses of omics data • Analyses of cellular systems (dead-end metabolites) • Reports generated by Pathway Tools • Perform comparative analyses with other organisms • Generate a genome poster and metabolic wall chart

  6. Information Sources • Pathway Tools User’s Guide • /root/aic-export/pathway-tools/ptools/14.0/doc/manuals/userguide.pdf • NOTE: Location of the aic-export directory can vary across different computers • Pathway Tools Web Site • http://bioinformatics.ai.sri.com/ptools/ • Publications, FAQ, programming examples, etc. • Slides from this tutorial • http://bioinformatics.ai.sri.com/ptools/tutorial/sessions/ • BioCyc Webinars • http://biocyc.org/webinar.shtm • Desktop vs Web functionality in Pathway Tools • http://biocyc.org/desktop-vs-web-mode.shtml

  7. Information Sources • Publications • “Pathway Tools version 13.0: Integrated Software for Pathway/Genome Informatics and Systems Biology”, Briefings in Bioinformatics 11:40-79 2010 • “A survey of metabolic databases emphasizing the MetaCyc family”, Archives of Toxicology 2011

  8. Information Sources • BioCyc Web site: Help Menu • Basic Help • Search Help • BioCyc Glossary • Publications • Website User Guide • PGDB Concepts • Guide to EcoCyc • Guide to MetaCyc

  9. Reporting Pathway Tools Problems • E-mail to ptools-support@ai.sri.com • Include: • What operation were you performing when the error occurred? • Error message • Result of [1] EC(2) :zoom :count :all • error.tmp • What Pathway Tools version are you are running? • What platform are you running on? • New patches automatically downloaded and loaded with PTools starts up • Auto-Patch • Tools -> Instant Patch -> Download and Activate All Patches

  10. 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 • Software: ptools-support@ai.sri.com • Data: biocyc-support@ai.sri.com • Comprehensive bug reports are required for us to reproduce and fix the problem you reported • Keep us posted regarding your progress

  11. Surveys / Feedback • Please complete survey at end of each day • Your feedback and suggestions on the software are important to us!

  12. 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

  13. 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

  14. 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 • x1980 • Meals • Restrooms

  15. Tutorial Format • Questions welcome during presentations • Lab sessions will take different amounts of time for different people • Refine your PGDB • Read Pathway Tools manuals • Computer logins • Internet connectivity

  16. Introductions • BRG Staff • Attendees • Where are you from? • What genome? • What do you hope to get out of the tutorial?

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