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BioCyc / Pathway Tools Tutorial: September 22-23, 2008

BioCyc / Pathway Tools Tutorial: September 22-23, 2008
London, England

A BioCyc and Pathway Tools tutorial well be held from September 22-23 at Kings College London. This tutorial is kindly hosted by the Centre for Bioinformatics at King's College London (KCBI).

Day 1 is intended to teach users of Pathway Tools databases such as BioCyc, YeastCyc, MouseCyc, and AraCyc how to make the most of these resources.

Day 2 will address creation of new Pathway/Genome Databases (PGDBs) with Pathway Tools, and how to query PGDBs programmatically.

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"). It also contains tools for painting omics data onto genome-scale visualizations of metabolic networks and regulatory networks.

Four example PGDBs are:

The tutorial is free of charge.

Schedule

September 22 (afternoon): Pathway/Genome Navigator
  • Basic querying
  • Genome Browser including tracks mechanism
  • Omics Viewers
  • Structured Advanced Query Form
  • Comparative Analysis tools

Intended audience: Users of databases such as BioCyc, MouseCyc, YeastCyc.

September 23 (full day): Constructing Pathway/Genome Databases

  • Pathway prediction
  • Pathway-Hole Filler
  • Operon Predictor
  • Transport Inference Parser
  • Querying a Pathway/Genome Database using Pathway Tools APIs

Intended audience: Creators of new Pathway/Genome Databases; those wanting to query PGDBs programatically.

Registration: Free registration is required. Please indicate which day(s) you will attend at Doodle.

Computer and Software

We recommend that you execute a Pathway Tools license agreement before you attend the tutorial, which can be done online at [Pathway Tools License].

Please note that we expect basic familiarity with Pathway Tools Navigator software for this tutorial, such as use of the BioCyc query page.

We recommend that students bring their own laptop computer for use at the tutorial, with Pathway Tools already installed.

Reading

We suggest that you read the following before the tutorial:

  • For both days:
    • Pathway Tools User's Guide Chapters 1-3. This document is present in the Pathway Tools software distribution in directory aic-export/pathway-tools/ptools/VERSION/doc/manuals/

    • "The Pathway Tools Software"

  • Day 2:
    • Pathway Tools User's Guide Chapters 6.1-6.5, 7. This document is present in the Pathway Tools software distribution in directory aic-export/pathway-tools/ptools/VERSION/doc/manuals/

    • "The MetaCyc Database"

Travel

Location: Strand Building, 6th floor, KCBI.