Virtual Cell at UConn

OUTDATED! UNDER RECONSTRUCTION!!!

 


The new SyBiL Build 119 (Shortbread) is available It features further improvement of the user interface and fix of several minor bugs. To start, click here.


The new SyBiL Build 118 (Ginger Snaps) is available with improved user interface. Also minor bugs have been fixed. This makes it more convenient and easier to query Pathway Commons and UniProt, and to convert pathways into models. To start, click here.

The latest presentation.

Flyer about SyBiL

 

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 designed for

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

You need web connection to run SyBiL, as it requires web-start. You also may download it. However, you will need libSBML installed on your computer in order to run it.


To run:

  • - 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.

See detailed manual

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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.