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


BACKGROUND
The software package, manual and examples are available at http://www.eng.buffalo.edu/~neel/ibrena
Liu
Gang
G
Department of Chemical and Biological Engineering, State University of New York, Buffalo, NY 14260, USA.
Neelamegham
Sriram
S
D000465:Algorithms; D003198:Computer Simulation; D020869:Gene Expression Profiling / Q000379:methods*; D008954:Models, Biological; D015233:Models, Statistical; D025941:Protein Interaction Mapping / Q000379:methods; D020543:Proteome / Q000378:metabolism*; D015398:Signal Transduction / Q000502:physiology*; D012984:Software
D020543:Proteome