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.

Requirements#

MATLAB R2016b or later, which is the oldest release the code still guards for. Continuous integration tests R2024b only, so a recent release is the better-covered choice. No additional MathWorks toolboxes required.
A linear-programming solver: Gurobi (free academic license, recommended) or GLPK, bundled with RAVEN itself, no separate install needed. See Choosing and configuring a solver below.
RAVEN bundles libSBML and the GLPK mex files for Windows, macOS and Linux. BLAST+, DIAMOND and HMMER are not bundled: RAVEN fetches the build for your platform on first use, so the reconstruction functions need internet access the first time they run. downloadRavenBinaries fetches them ahead of time. See Download data and binaries for the full set, where it is cached, and how to prepare an offline machine.

Note

Working offline Download data and binaries covers preparing a machine with no network access ahead of time.

Choosing and configuring a solver#

Solver	LP	MILP	Relative speed	License
GLPK	yes	yes (RAVEN warns; slow on large problems)	1x (baseline)	open source, bundled with RAVEN
SCIP	yes	yes	0.33x	open source; bundled on Windows, a separate install on macOS/Linux
Gurobi	yes	yes	4.2x	free academic license
COBRA Toolbox	yes	depends on the COBRA solver configured	depends on the COBRA solver configured	depends on the COBRA solver configured

MILP-solving functions (getMinimalMedium, ftINIT, some gap-filling algorithms) also run on the bundled GLPK, with a warning that recommends Gurobi: on genome-scale models GLPK can be much slower than Gurobi, SCIP, or a MILP-capable solver through the COBRA Toolbox.

Set the active solver with setRavenSolver, which takes 'gurobi', 'glpk', 'scip', or 'cobra':

setRavenSolver('gurobi');

Gurobi#

Install Gurobi 7.5 or later.
Request and download a license (a free academic license covers most research use).
Place the license file where Gurobi's own installer says to.
Follow Gurobi's MATLAB integration instructions, then run savepath so MATLAB keeps the change after a restart.
setRavenSolver('gurobi').

Through the COBRA Toolbox#

RAVEN can solve through whatever solver the COBRA Toolbox has configured, instead of one of its own bundled options:

changeCobraSolver('glpk');   % or any solver the COBRA Toolbox supports
setRavenSolver('cobra');

ravenCobraWrapper converts a model between the RAVEN struct and the COBRA Toolbox structure; see RAVEN vs. raven-toolbox.

Install#

Warning

Getting 3.0.0b1 specifically This site documents RAVEN 3.0.0b1, a pre-release. Both the Add-Ons manager and the Release download's normal releases page only offer the latest stable release (RAVEN 2.x), not 3.0.0b1: neither method can install what this site documents. Use the Clone with git tab, or the direct archive link in the Release download tab below.

Add-Ons manager

Installs from within MATLAB, with no separate download. Installs the latest stable release, not 3.0.0b1; see the warning above.

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

If MATLAB does not pick up the toolbox after step 2, run matlab.addons.enableAddon("RAVEN") to enable it explicitly.

Release download

Good for offline or managed environments. The RAVEN releases page itself only lists stable releases; 3.0.0b1 is a git tag with no packaged release, so download it directly instead:

Download the 3.0.0b1 archive directly (this works without git).
Extract it to a location of your choice.
In MATLAB, add the RAVEN folder to the path (pathtool), then verify.

Clone with git

Clones the repository, then checks out the 3.0.0b1 tag specifically: a plain git clone alone tracks the develop branch, which can contain changes made after this site's pre-release.

git clone --depth=1 https://github.com/CompMetEng/RAVEN.git
cd RAVEN
git fetch --depth=1 origin tag 3.0.0b1
git checkout 3.0.0b1

Add the folder to the MATLAB path and verify.

Verify#

From the MATLAB command window:

checkRaven

A successful run looks like:

*** THE RAVEN TOOLBOX ***

 > Installation type                    Advanced (via git)
 > Checking RAVEN release               3.0.0
 > Checking MATLAB release              R2024b
 > Set RAVEN in MATLAB path             Pass
 > Save MATLAB path                     Pass

=== Model import and export ===
 > Checking libSBML version             5.20.0
 > Checking model import and export
   > Import SBML format                Pass
   > Export SBML format                Pass
   > Import YAML format                Pass
   > Export YAML format                Pass
   > Export Excel format               Pass

=== Model solvers ===
 > Checking for LP solvers
   > glpk                               Pass
   > gurobi                             Pass
 > Set RAVEN solver                     gurobi

=== Essential binary executables ===
 > Checking BLAST+                      Pass
 > Checking DIAMOND                     Pass
 > Checking HMMER                       Pass

=== Compatibility ===
 > Checking function uniqueness

*** checkRaven complete ***

If MATLAB reports that it could not save the path (common on shared or managed installations where you do not have write access to MATLAB's own pathdef.m), run addRavenToUserPath instead: it writes a startup.m that adds RAVEN to the path on every MATLAB start, without touching the shared path file. addRavenToUserPath('overwrite', false) appends to an existing startup.m instead of replacing it.

Upgrade#

Add-Ons manager

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

Release download

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

Clone with git

The 3.0.0b1 tag does not move, so there is nothing to pull while staying on it. To follow the development branch instead:

git checkout develop
git pull origin develop

develop can contain changes that are not yet released. Then run checkRaven.

Remove#

Add-Ons manager

Go to Add-Ons → Manage Add-Ons and remove RAVEN from the list. Running removeRavenFromPath afterward should report an unrecognized-function error, confirming RAVEN is off the path.

Release download

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

Then delete the RAVEN folder from disk.

Clone with git

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, open an issue on GitHub.