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 Tutorial Overview Instructors: l Mario Latendresse, Markus Krummenacker Mix of lectures and lab sessions Questions encouraged at any time 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/

5. 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?

6. SRI International Bioinformatics Outline for Tutorial Day 1 l Introduction l Pathway/Genome Navigator l Omics Viewers l Object Groups Day 2 l PathoLogic Day 3 l Editing Pathway/Genome Databases l Introduction to Flux-Balance Analysis l Feedback session

7. SRI International Bioinformatics Introductory 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 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

9. SRI International Bioinformatics Tutorial Format Mixture of lectures and lab sessions l Questions welcome Computer logins Internet connectivity

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

11. 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 Create a steady-state metabolic flux model that makes phenotypic predictions Generate a genome poster and metabolic wall chart

12. SRI International Bioinformatics Installing Pathway Tools 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

13. 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.shtml http://biocyc.org/webinar.shtml

14. SRI International Bioinformatics Reporting Pathway Tools Problems ptools-support@ai.sri.com Comprehensive bug reports are required for us to fix the problem you reported l What platform you are running on l What version of Pathway Tools you are running l The error message l Result of [1] EC(2) :zoom :count :all l What operation were you performing when the error occurred? New patches automatically downloaded and loaded with PTools starts up

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

16. 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

17. 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 l Develop a metabolic flux model

18. SRI International Bioinformatics Go to file intro-to-ptools-and-biocyc.ppt