Multiscale Systems Biology Collaboration

Freely available software

openCOBRA toolbox

MATLAB toolbox for constraint-based reconstruction and analysis (COBRA).

CONEOPT

A primal-dual path-following method for cone programming (Matlab)

fastFVA

A tool to compute efficiently flux variability analysis on large-scale biochemical networks

LUMOD

Routines for dense LU factorization and updates (f77).

LUSOL

Routines for sparse LU factorization and updates (f77, f90, and Matlab interface).

PDCO

A primal-dual interior point method for large-scale optimization with convex objective and linear constraints (Matlab).

PNOPT

Proximal Newton-type methods for minimizing composite functions (unconstrained optimization of the sum of smooth and nonsmooth functions) (Matlab).