COBRA Toolbox 2 installation

[Santhoshi Basuthkar]

Dear All,

I'm a newbie to Cobra. I request you to please help me with this
installation of COBRA Toolbox version 2. I've downloaded the toolbox
and followed the instructions as given in this webpage:

http://benheavner.com/systemsbio/index.php?title=Installing_COBRA_toolbox_for_MATLAB

However, this webpage pertains to installation of COBRA version 1.3.5
and my system has only a 32-bit processor. I get the following errors
on installation of COBRA Toolbox 2, when I issue the command
initCobraToolbox. Please help me to resolve this issue.

>> initCobraToolbox
Warning: LP solver Gurobi not useable: gurobi_mex not in Matlab path
> In changeCobraSolver at 129
In initCobraToolbox at 40
Warning: LP solver CPLEX through Tomlab not usable: tomRun.m not in
Matlab path
> In changeCobraSolver at 109
In initCobraToolbox at 40
LP solver set to glpk successful
Warning: MILP solver Gurobi not useable: gurobi_mex not in Matlab
path
> In changeCobraSolver at 161
In initCobraToolbox at 53
Warning: MILP solver CPLEX through Tomlab not usable: tomRun.m not in
Matlab path
> In changeCobraSolver at 151
In initCobraToolbox at 53
MILP solver set to glpk successful
Warning: QP solver CPLEX through Tomlab not usable: tomRun.m not in
Matlab path
> In changeCobraSolver at 181
In initCobraToolbox at 65
Warning: qpng solver has not been fully tested - results may not be
correct
> In changeCobraSolver at 191
In initCobraToolbox at 65
QP solver set to qpng successful
Warning: MIQP solver CPLEX through Tomlab not usable: tomRun.m not in
Matlab path
> In changeCobraSolver at 220
In initCobraToolbox at 76
MIQP solver set failed
CB map output set to svg successful

Thanks,
Santhoshi

[Ben]

Hi Santhoshi -

Yeah, I need to update that page of instructions, it's getting more
and more crufty and out of date. I'll add it to the to-do list!

The set of errors you're seeing relate to which linear programming
software is available to COBRA. From what you've posted, you have
successfully installed glpk "LP solver set to glpk successful "

That is actually all you need to be able to do FBA with COBRA using
the command "optimizecbmodel(model)". So, you're good to go.

If you'd like to do other (linear, mixed-integer, or nonlinear)
programming tasks, such as optknock, you need to get other solvers
working, such as Gurobi.

In other words, if you want to do FBA, you can probably ignore those
errors safely, and have a working COBRA install.

-Ben

On Apr 11, 12:44 am, Santhoshi Basuthkar <santhoshi....@gmail.com>
wrote:

> Dear All,
>
> I'm a newbie to Cobra. I request you to please help me with this
> installation of COBRA Toolbox version 2. I've downloaded the toolbox
> and followed the instructions as given in this webpage:
>

> http://benheavner.com/systemsbio/index.php?title=Installing_COBRA_too...

[dr scientist]

Santhoshi,

1. Could you post install questions here:
https://sourceforge.net/projects/opencobra/forums/forum/1228467
Including any follow ups.

2. It looks like everything works with the provided solver (GLPK). If
you want to do anything that GLPK can't then you'll need to figure out
how to install gurobi/gurobimex or tomlab on your system.

run testAll to find out what functions will run with your current
configuration.

3. The basic install instructions are here:
http://opencobra.sourceforge.net/openCOBRA/Install.html I'll update
them to note that errors will be kicked back if you don't have
specific solvers installed.

4. Install instructions for earlier versions of software should rarely
be used for current releases.

On Apr 10, 9:44 pm, Santhoshi Basuthkar <santhoshi....@gmail.com>
wrote:

> Dear All,
>
> I'm a newbie to Cobra. I request you to please help me with this
> installation of COBRA Toolbox version 2. I've downloaded the toolbox
> and followed the instructions as given in this webpage:
>

> http://benheavner.com/systemsbio/index.php?title=Installing_COBRA_too...

[dr scientist]

Ben,

Thanks for maintaing a tips page. If you need help on getting things
up to speed for 2.0 let me know. I don't use MS Windows, but I hear
the latest libSBML release makes that part of the installation much
smoother.

[Santhoshi Basuthkar]

Thanks a lot for the reply Ben. As you mentioned optimizeCbModel model
works for me. Now I've two questions below:

1. Inorder to make informed descisions, how can I know that which
solver is used by each of the functions in Cobra?
2. Are there any help files or installation directions to install the
other solvers?

Thanks,
Santhoshi

> > Santhoshi- Hide quoted text -
>
> - Show quoted text -

[Ben]

Hi Santhoshi,

You can specify which solvers are used in your initcobratoolbox file

There was some discussion about installing gurobi here:
https://groups.google.com/group/cobra-toolbox/browse_thread/thread/21a6b75bdc2ca03f/773e3dc26d0ef220?lnk=gst&q=gurobi#773e3dc26d0ef220

-Ben

On Apr 12, 2:54 am, Santhoshi Basuthkar <santhoshi....@gmail.com>