Related Experiment Video
Updated: Jul 7, 2026

A Web Tool for Generating High Quality Machine-readable Biological Pathways
Published on: February 8, 2017
In silico Biochemical Reaction Network Analysis (IBRENA): a package for simulation and analysis of reaction networks
1Department of Chemical and Biological Engineering, State University of New York, Buffalo, NY 14260, USA.
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
Related Concept Videos
Coupled Reactions
Energy in adenosine triphosphate or ATP molecules is easily accessible to do work. ATP powers the majority of energy-requiring cellular reactions. Cells...
Protein Networks
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Protein Networks
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Predicting Reaction Outcomes
Measuring Reaction Rates
Ribozymes
Ribozymes can be...
