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Bioinformatics Advance Access published online on February 28, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn061
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© The Author (2008). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

In silico Biochemical Reaction Network Analysis (IBRENA): a package for simulation and analysis of reaction networks

Gang Liu 1 and Sriram Neelamegham 1,*

1Department of Chemical and Biological Engineering, State University of New York, Buffalo, NY 14260, USA

*To whom correspondence should be addressed. Dr. Sriram Neelamegham, E-mail: neel{at}eng.buffalo.edu


  Abstract

Summary: We present In silico Biochemical Reaction Network Analysis (IBRENA), a software package which facilitates multiple functions including cellular reaction network simulation and sensitivity analysis (both forward and adjoint methods), coupled with principal component analysis, singular value decomposition and model reduction. The software features a graphical user interface that aids simulation and plotting of in silico results. While the primary focus is to aid formulation, testing and reduction of theoretical biochemical reaction networks, the program can also be used for analysis of high-throughput genomic and proteomic data.

Availability: The software package, manual and examples are available at http://www.eng.buffalo.edu/~neel/IBRENA.htm

Contact: neel{at}eng.buffalo.edu

Associate Editor: Dr. Limsoon Wong

Received on December 7, 2007; revised on February 11, 2008; accepted on February 12, 2008

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