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

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

4. SRI International Bioinformatics Research in the SRI Bioinformatics Research Group BioCyc Database Collection l EcoCyc l MetaCyc EcoliHub Pathway Tools BioWarehouse

5. SRI International Bioinformatics Outline for Tutorial Monday l Introduction l Pathway/Genome Navigator l Omics Viewers Tuesday l PathoLogic tutorial l PathoLogic lab session – Build initial version of PGDB l PathoLogic: Creating protein complexes, operon predictor, transport inference parser l Pathway hole filler (run overnight) Wednesday l Pathway Tools Schema l Model organism database projects l Comparative tools l Feedback session Thursday l Editing PGDBs

6. SRI International Bioinformatics General 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

7. SRI International Bioinformatics 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

8. SRI International Bioinformatics BioCyc Tutorial Overview Mix of lectures and lab sessions All powerpoint slides available at http://www.ai.sri.com/pkarp/talks/2010-07-SIM- Tutorial/ http://www.ai.sri.com/pkarp/talks/2010-07-SIM- Tutorial/ www.mozilla.org firefox www.mozilla.org Chrome

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

10. SRI International Bioinformatics Terminology “Database” = “DB” = “Knowledge Base” = “KB” = “Pathway/Genome Database” = “PGDB”

11. SRI International Bioinformatics Downloading Pathway Tools Obtain license l http://biocyc.org/download.shtml Download directory offers several configurations Choose platform and database configuration l Many combinations of databases available l All databases requires a lot of memory l Use registry to add PGDBs to configuration you downloaded

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

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

14. SRI International Bioinformatics Information Sources BioCyc Web site: Help Menu l Basic Help l Search Help l BioCyc Glossary l Publications l Website User Guide l PGDB Concepts l Guide to EcoCyc l Guide to MetaCyc

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

16. SRI International Bioinformatics 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 l Software: ptools-support@ai.sri.comptools-support@ai.sri.com l 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

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

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

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

20. SRI International Bioinformatics 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 l x1980 Meals Restrooms

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

22. SRI International Bioinformatics Introductions BRG Staff Attendees l Where are you from? l What genome? l What do you hope to get out of the tutorial?