A COBRA toolbox extension for quantitative flux coupling analysis

Compressed biological systems of tens of thousands of biochemical reactions by a hierarchical organization of pathways which speeds up the downstream analysis up to \(3\times\) in addition to saving memory and storage space

  • Project name: QFCA

  • Project homepage: https://web.stanford.edu/~boyd/papers/qfca.html

  • Operating system(s): Platform independent

  • Programming language: MATLAB

  • Other requirements: Gurobi optimizer (optional for improved performance)

  • License: GNU GPL v3.0

  • Any restrictions to use by non-academics: License needed

A COBRA toolbox extension for context-specific metabolic network reconstruction

Accelerated the state-of-the-art in genome-scale metabolic network reconstruction more than \(10\times\) by convex optimization techniques such as factorization, approximation, and regularization

  • Project name: SWIFTCORE

  • Project homepage: https://web.stanford.edu/~boyd/papers/swiftcore.html

  • Operating system(s): Platform independent

  • Programming language: MATLAB

  • Other requirements: The COBRA and Bioinformatics toolboxes for MATLAB; use of Gurobi or CPLEX is optional for improved performance (free academic licenses are available for both)

  • License: GNU GPL v3.0

  • Any restrictions to use by non-academics: License needed

A Julia package for sparse quantitative flux coupling analysis

Developed a registered Julia package which quantifies the redundancies in genome-scale metabolic networks and provides local sparse certificates which are both efficiently verifiable and interpretable