BioPAX Hackathon 2009

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Introduction

Problems

  • BioPAX Documentation
  • BioPAX model
    • Paxtools packaging
  • Data export/import
  • BioPAX Best Practices
    • Validation Rules
  • BioPAX Project Cleanup

Software

BioPAX Examples

Paxtools

BioPAX Validator

The biopax-validator.war is not provided there anymore, because one can easily generate it as follows:

  1. download the ZIP, unzip, go to the directory
  2. read README.txt (- you may need to put your server's IP in the web.xml, as you did before)
  3. execute: ant war
  4. new biopax-validator.war will be created

To auto-deploy, copy the biopax-validator.war to the Tomcat6 'webapps' directory. (Note: Tomcat should start with special options; please read the README.txt)

Cytoscape Plugins

Converters

Converters are now modules in the new PaxTools (so, the same code base)

  • BioPAX Level 1, 2 to Level 3 converter prototype (Upgrader)
  • PSI-to-BioPAX (and back, PSI-MI 2.5) Converter

Using BioPAX to build and Annotate models

Editors

Other

Q&A