C13 is a tool for quantification of in vivo metabolic fluxes, from carbon labelling experiments. The underlying approach is metabolic flux analysis based on stationary carbon isotope labelling experiments, using fractional enrichment data. The mathematical framework adopted herein is the one developed by Wiechert and de Graaf (1997).
BioOpt is a software application running on Windows command prompt. The program focuses on the flux balance analysis, using linear programming as the mathematical support. Given a biological system model, which includes a set of metabolic reactions, the program is able to calculate all internal mass balance fluxes, reduced costs and shadow prices depending on the constraints and objective defined by the user. Running BioOpt with different parameters allows the user to obtain several kinds of outputs that can help in the analysis of the system.
List of downloadable tools and their links.
Piano performs gene set analysis using various statistical methods, from different gene level statistics and a wide range of gene-set collections. It also contains functions for combining the results of multiple runs of gene set analyses.
The RAVEN Toolbox (Reconstruction, Analysis, and Visualization of Metabolic Networks) toolbox is a complete environment for reconstruction, analysis, simulation, and visualization of GEMs and runs within MATLAB.
The software has three main foci: 1) automatic reconstruction of GEMs based on protein homology, 2) network analysis, modeling and interpretation of simulation results, 3) visualization of GEMs using pre-drawn metabolic network maps.