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BioPax Workshop, New York 2009


Wednesday 11th November

09.00 - 17.00 BioPAX Hackathon 2009 (ZRC-105)
BioPAX, SBGN and layout exchange workgroup, paxtools workgroup, validator, worked examples and documentation, Cytoscape plugins

Thursday 12th November

9.00 - 10.00 (ZRC-105)
10.00 - 13.00 (ZRC, 12th Floor Conference Room)
BioPax Level 3 Intro - Tutorial Session
10.00 - 13.00 (ZRC, 16th Floor Conference Room)
Data Export Issues and Validation
13.00 pm -15.00
Group Lunch : Rockefeller University, Abby Aldrich Dining Room
15.00 - 18.00 (ZRC-105)
Project Presentations
19:00, Group dinner

Friday 13th November

9.00 - 12:30 (RRL-101)
Project Presentations
13.30 - 14:45
BioPAX level 3 Current Status and Review
BioPAX level 3 Ratification and official release
BioPAX future features discussion
polymerization and small chemical generics
better integration with other ontologies
15.00 - 17:00 (RRL-01)
Hackathon workgroup reports
BioPAX, SBGN and layout exchange
Paxtools and BioPAX validator
BioPAX outreach, integration with publication process
BioPAX governance


Memorial Sloan Kettering Cancer Centre, New York, New York 10065 [1]

ZRC- Zuckerman Research Center, 417 East 68th Street
RRL - Rockefeller Research Laboratories, 430 East 67th Street

Useful Links

List of Participants

Name Affliation Group/Project
Emek Demir MSKCC BioPAX
Chris Sander MSKCC BioPAX
Igor Rodchenkov University of Toronto BioPAX
Carl Schaefer National Cancer Institute Center for Bioinformatics and Information Technology NCI/Nature PID
Peter D'eustachio New York University Reactome
Sarala Wimalaratne University of Auckland CellML
Özgün Babur Bilkent University ChiBE
Martijn van Iersel University Maastricht WikiPathways
Alexander Pico The Gladstone Institutes, UCSF WikiPathways
Suzanne Paley SRI International BioCyc
Augustin Luna NIH MIM
Peter Hornbeck CST PhosphoSite
Anatoly Sorokin University of Edinburgh EPE
Andrea Splendiani Rothamsted Research Ondex
Alejandra Lopez-Fuentes Universidad Nacional Autónoma de México RegulonDB
Irma Martinez-Florez Universidad Nacional Autónoma de México RegulonDB
Robin Haw The Ontario Institute for Cancer Research Reactome
Huaiyu Mi SRI International PantherDB
Gary Bader University of Toronto BioPAX
Avi Maayan Mount Sinai School of Medicine IMID
Michael Honig Columbia University geWorkbench/CNKB
Mirit Aladjem NCI MIM
Margot Sunshine NCI MIM
Keith Allen Syngenta
Julie Leonard Syngenta
Sasha Tkachev Cell Signalling Technology PhosphoSite
Nadia Anwar MSKCC BioPAX
Michael Blinov UCHC BioNetGen
Ashok Reddy UCSD Nature Molecule Pages
Rebecca Tang Stanford University PharmaGKB
Zhenjun Hu Boston University VisAnt
Martina Kutmon University of Ottawa
Oliver Ruebenacker UCHC Using BioPAX to build and Annotate models


Computational Biology Center Memorial Sloan-Kettering Cancer Centre 1275 York Avenue, Box #460, New York, NY 10065

Phone: +1 646 888 2602 or +1 646 888 2606 Fax: +1 646 422 0717 E-mail: