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RAVEN (MATLAB)

The RAVEN Toolbox runs in MATLAB and works completely independently — it does not require the COBRA Toolbox, although it can interoperate with it. The canonical reference is the RAVEN installation wiki.

Requirements

  • MATLAB R2016b or later. No additional MathWorks toolboxes required.
  • A linear-programming solver — Gurobi (free academic license, recommended) or GLPK (bundled with the COBRA Toolbox). See Choosing a solver.
  • RAVEN bundles libSBML, BLAST+, DIAMOND and HMMER for Windows, macOS and Linux — no separate installation needed.

Install

The easiest option — installs directly from within MATLAB.

  1. Open the Home tab and click Add-Ons → Get Add-Ons.
  2. Search for RAVEN Toolbox and click Add → Add to MATLAB.
  3. Verify the installation.

Good for offline or managed environments.

  1. Download the latest ZIP from the RAVEN releases page.
  2. Extract it to a location of your choice.
  3. In MATLAB, add the RAVEN folder to the path (pathtool), then verify.

Best option if you want the latest code and one-command upgrades.

git clone --depth=1 https://github.com/SysBioChalmers/RAVEN.git

Add the folder to the MATLAB path and verify.

Verify

From the MATLAB command window:

checkInstallation

A successful run looks like:

*** THE RAVEN TOOLBOX ***

Checking if RAVEN is on the MATLAB path...                                  OK
Checking if it is possible to parse a model in Microsoft Excel format...    OK
Checking if it is possible to import an SBML model using libSBML...         OK
Solver found in preferences... gurobi
Checking if it is possible to solve an LP problem using gurobi...           OK
Checking essential binary executables:
    BLAST+... OK
    DIAMOND... OK
    HMMER... OK
*** checkInstallation complete ***

Upgrade

In MATLAB go to Help → Check for Updates, click Update for RAVEN, then run checkInstallation again.

Close MATLAB, delete the old RAVEN folder, download and extract the new release, and run checkInstallation.

git pull origin main

Then run checkInstallation.

Remove

Go to Add-Ons → Manage Add-Ons and remove RAVEN from the list.

which removeRavenFromPath   % locate the installation
removeRavenFromPath         % clear RAVEN from the MATLAB path

Then delete the RAVEN folder from disk.

which removeRavenFromPath   % locate the installation
removeRavenFromPath         % clear RAVEN from the MATLAB path

Then delete the cloned RAVEN folder from disk.

Getting help

For installation problems, consult the RAVEN wiki or open an issue on GitHub.