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Posts: 7
Location:
University of Connecticut...
Registered:
May 2005
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BioNetGen@VCell release
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06 Oct '06 17:17
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Dear SBML community,
We are pleased to announce the release of BioNetGen@VCell, a software tool
for automatically generating a biochemical reaction network from
user-specified rules for biomolecular interactions on the level of protein
domains. A BioNetGen@VCell service is callable from the Virtual Cell and
runs on a client computer.
The first release of BioNetGen@VCell
1) Ready to be used with the Virtual Cell account: no installation and
registration required.
2) Implements the latest version of BioNetGen 2, in which connectivity of
proteins in the complex can be explicitly specified.
3) Includes
a. iterative network generation of the reaction network from a given
set of seed species according to user-specified reaction rules;
b. Time courses simulation using ODE-based deterministic simulation of
a pre-generated network, SSA-based stochastic simulation of a pre-generated
network, or on-the-fly network simulation and generation;
c. Visualization of simulation results and different data export
options.
4) Provides a capability to pre-equilibrate a network and to restart time
courses simulation from any time point with modified parameter values.
5) Provides compatibility with other modeling and simulation tools (the
Virtual Cell, SBW etc) via export of the biochemical reaction network in
SBML L2 format.
6) Provides detailed information about BioNetGen features, tutorial and
sample files on the website http://vcell.org/bionetgen.
References:
1. W. S. Hlavacek, J. R. Faeder, M. L. Blinov, R. G. Posner, M. Hucka and W.
Fontana (2006) Rules for modeling signal-transduction systems. Sci. STKE
2006, re6. (http://stke.sciencemag.org/cgi/content/abstract/stke.3442006re6)
2.M. L. Blinov, J. Yang, J. R. Faeder and W. S. Hlavacek (2006) Graph theory
for rule-based modeling of biochemical networks. To appear in Transactions
on Computational Systems Biology in the series Lect. Notes Comput. Sci.
Available at http://www.ccam.uchc.edu/mblinov/library/Blinov_LNCS_2006.pdf.
The Virtual Cell and BioNetGen Teams
http://vcell.org/bionetgen
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Michael Blinov
Assistant Professor
Center for Cell Analysis and Modeling
University of Connecticut Health Center
Phone: (860) 679-6081, Fax: (860) 679-1039
URL: http://www.ccam.uchc.edu/mblinov/
E-mail: blinov@uchc.edu
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