BioPAX Hackathon 2009

=Introduction=

=Problems=
 * BioPAX Documentation
 * BioPAX model
 * Paxtools packaging
 * Data export/import
 * BioPAX Best Practices
 * Validation Rules
 * BioPAX Project Cleanup

=Software=

BioPAX Examples

 * [deprecated] browse or 'svn checkout': http://biopax.cvs.sourceforge.net/viewvc/biopax/biopax/examples/
 * http://biopax.hg.sourceforge.net/hgweb/biopax/biopax/file (go to Level3/examples there)

Paxtools

 * Paxtools1:
 * browse or 'svn checkout': http://biopax.cvs.sourceforge.net/viewvc/biopax/Paxtools/
 * download: http://sourceforge.net/projects/biopax/files/ (go to the 'Paxtools 1.0b1' folder)
 * Paxtools2:
 * look how to use Mercurial repository: http://sourceforge.net/projects/biopax/develop
 * browse source files at the new location: http://biopax.hg.sourceforge.net/hgweb/biopax/paxtools/file
 * get the last build (jars): http://sourceforge.net/projects/biopax/files/ (go to 'Paxtools 2 SNAPSHOTs' folder)

BioPAX Validator

 * download: http://sourceforge.net/projects/biopax/files/ (in the 'validator' folder)
 * BioPAX rules: http://sourceforge.net/apps/mediawiki/biopax/index.php?title=BioPAXRules
 * instances:
 * [during the BioPAX Workshop] http://www.biopax.org/biopax-validator/
 * [v1.2b2 - check for updates] at NetPath http://biopaxvalidator.netpath.org/biopax-validator/index.html
 * browse, 'cvs checkout': http://biopax.cvs.sourceforge.net/viewvc/biopax/Validator/
 * http client (example that connects to http://www.biopax.org/biopax-validator/) is now part of PaxTools

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

 * download JAR: http://downloads.sourceforge.net/project/biopax/cytoscape_plugin/biopax.jar?use_mirror=iweb
 * browse, 'svn checkout': http://chianti.ucsd.edu/svn/csplugins/trunk/toronto/rodche/BioPAX/
 * http://chianti.ucsd.edu/svn/csplugins/trunk/soc/arman/PaxtoolsPlugin/
 * http://paxtoolsplugin.svn.sourceforge.net/svnroot/paxtoolsplugin/PaxtoolsPlugin
 * wiki: http://sourceforge.net/apps/mediawiki/biopax/index.php?title=CyPluginBioPAX
 * BiNOM: http://bioinfo-out.curie.fr/projects/binom/

Converters
Converters are now modules in the new PaxTools (so, the same code base) Using BioPAX to build and Annotate models
 * BioPAX Level 1, 2 to Level 3 converter prototype (Upgrader)
 * PSI-to-BioPAX (and back, PSI-MI 2.5) Converter
 * http://vcell.org/biopax

Editors

 * Protege - Ontology Editor and Knowledge Acquisition System
 * http://protege.stanford.edu/
 * download from http://protege.stanford.edu/download/download.html
 * Chisio BioPAX Editor: http://www.bilkent.edu.tr/~bcbi/chibe.html
 * A Cytoscape plugin can be the BioPAX editor as well... (future)

Other

 * "CPath Squared" (cPath2), a new Pathway Commons engine development:
 * http://code.google.com/p/pathway-commons/wiki/cPathSquared
 * http://code.google.com/p/pathway-commons/source/browse/#svn/trunk/cpath2-mvn
 * WonderWeb OWL Validator: http://www.mygrid.org.uk/OWL/Validator
 * OHSU BioPAX Validator: http://www.ohsucancer.com/biopaxvalidator/index.html
 * Ontology Lookup Service (OLS): http://www.ebi.ac.uk/ontology-lookup/
 * OntologyManager (part of PSIDEV Tools): http://psidev.svn.sourceforge.net/viewvc/psidev/psi/tools/
 * PSI-MI 2.5 Validator: http://www.ebi.ac.uk/intact/validator/start.xhtml
 * Cytoscape http://cytoscape.org

=Q&A=