Virtual Cell at UConn



BioPAX at Virtual Cell

 

SyBiL is short for Systems Biology Linker. Biological pathways, reaction and signaling networks are made publicly availabel in formats standardized to the Biological Pathway eXchange format (BioPAX). Simulation tools for biological pathways are standardized to other Markup languages such as Systems Biology Markup Language (SBML) and Virtual Cell Markup Language (VCML). To take full advantage of scientific advances requires the mapping and integration of simulation markup languages with BioPAX. Sybil is developed to convert models between BioPAX and SBML/VCML.


Sybil is a stand-alone application designed for

  • - visualizing pathway data files in BioPAX format, such as imported from Reactome. 
  • - converting BioPAX file into SBML file.

Download. You need Java and libSBML installed on your computer in order to run it. To run:

  • - download SybilAll.jar. Double click it to launch.
  • - open any BioPAX .owl file, such as from Reactome database.
  • - explore the file both graphically and semantically in BioPAX data tab
  • - set criteria for conversion to SBML in BioPAX to SBML conversion tab
  • - Convert to SBML and use.

 

Sybil is intended to be a part of the Virtual Cell, similarly to BioNetGen@VCell. You will be able to call BioPAX@VCell window from VCell and create a VCell BioModel from BioPAX pathway data.

 

Read more about the proposed way to link Pathway data in BioPAX standard with simulation tools supporting SBML at VCell wiki.

 

BioPAX/Sybil tutorial given at the 2nd q-bio conference, August 6th, 2008, Santa Fe, NM.