Overview of the
Pathway Tools Software
and
Pathway/Genome Databases
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
SRI International
Bioinformatics
SRI International
Bioinformatics
SRI Organization
Bioinformatics Research Group
Information and
Computing Sciences
Biosciences
Education
and
Policy
Engineering Systems
And Sciences
Physical
Sciences
FBA Tutorial Goals
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Bioinformatics
 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
Why Create PGDBs?
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Bioinformatics

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
Information Sources

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Bioinformatics
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
Information Sources
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Bioinformatics
 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

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
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Bioinformatics
SRI International
Bioinformatics
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
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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
 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
Surveys / Feedback
 Please
 Your
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complete survey at end of each day
feedback and suggestions on the software
are important to us!
PGDB(s) That You Build
 Before
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Bioinformatics
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
Summary
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Bioinformatics
 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
Administrative Details
 Please
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Bioinformatics
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
Tutorial Format
 Questions
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Bioinformatics
welcome during presentations
 Lab
sessions will take different amounts of time
for different people
 Refine your PGDB
 Read Pathway Tools manuals
 Computer
 Internet
logins
connectivity
Introductions
 BRG
Staff
 Attendees
Where are you from?
 What genome?
 What do you hope to get out of the tutorial?

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Bioinformatics