Multiscale Systems Biology Collaboration

Freely available software

COBRA 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).

lusolZ

Matlab routines for sparse nullspace computations using LUSOL.

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).