Pathway Tools Tutorial June 4-8

Pathway Tools Tutorial June 4-8, 2007

SRI's Bioinformatics Research Group will be holding a Pathway Tools
tutorial session on June 4-8, 2007 at SRI International in Menlo
Park, CA.

The goal of the tutorial is to teach scientists how to use the Pathway
Tools software to create a Pathway/Genome Database (PGDB) for an
organism of interest, how to interactively update and curate a PGDB,
and how to publish a PGDB on the web, and how to use the Pathway
Tools omics viewers.

Pathway Tools includes a unique combination of bioinformatics
algorithms including a predictor of metabolic pathways, an operon
predictor, and an algorithm for predicting which genes in a genome
code for missing enzymes in predicted metabolic pathways ("pathway
holes").

Each day's tutorial will last from 9:30am-5:00pm. Each day will
combine lectures with lab sessions in which students apply the
software to a sample genome. No programming experience is required
for days 1-4, but a basic knowledge of Unix is helpful, as is
knowledge of a Unix text editor such as vi or emacs.

Day 5 requires programming experience in Perl, Java, or Lisp. Day 5
is optional.

Three example PGDBs are:

o EcoCyc http://EcoCyc.org/
o Yeast pathway database: http://pathway.yeastgenome.org/biocyc/
o Arabidopsis pathway database: http://www.arabidopsis.org/biocyc/index.jsp

Agenda:

Day 1 (June 4)
Introduction to Pathway Tools
Overview of Pathway/Genome Navigator
Pathway Tools Omics Viewers: Cellular Overview, Regulatory Overview, Genome Overview
Querying PGDBs with BioVelo

Day 2
Pathway prediction using PathoLogic
Matching enzyme names to reactions
Pathway hole filler

Day 3
Operon predictor
Pathway Tools schema
Administering Pathway Tools
Pathway/Genome Database Registry

Day 4
Transport Inference Parser
Editing Pathway/Genome Databases

Day 5 (optional)
The Pathway Tools APIs -- Programmatic querying and updating of PGDBs
using the Perl, Java, and Lisp languages.

If you wish, you may bring with you to the tutorial the annotated
genome of an organism for which you wish to build a PGDB, in which
case you will most likely leave the tutorial with a draft version of
the database.

Please reply to Wilma Lenz (lenz@ai.sri.com) to reserve a space at the
tutorial; space is limited. There will be a tutorial fee of $75 to
cover food and other expenses. Please indicate if you will attend Day 5.

For more information about the tutorial please see:

http://bioinformatics.ai.sri.com/tutorial/

Peter Karp
Bioinformatics Research Group
SRI International

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