FVA tutorial using gurobi solver with Matlab 2020a

[Markus Schulze]

Dear all,

getting in touch with the flux variability analysis, I followed the FVA tutorial but unfortunately encountered troubles using the command 'fluxVariability':

I cannot identify the root cause. I have installed and licensed gurobi to be used as solver according to the tutorial, although it should not be needed.

May it be related to the fact I am using Matlab 2020a and its compatibility with gurobi and/or the FVA command?

Best regards

Markus

[Markus Schulze]

Please find attached now also the system config report.

[Ronan M.T. Fleming]

Hi Markus,

the report has the following, indicating your version may be out of date. Please update and try the tutorial again,

Regards

Ronan 

> Checking for available updates ...
 > There are 7700 new commit(s) on <master> and 0 new commit(s) on <develop> [196b7e @ master]
 > You can update The COBRA Toolbox by running updateCobraToolbox() (from within MATLAB)

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[Markus Schulze]

Hi Ronan,

thanks for your reply.

I have reinstalled the cobratoolbox, checked for udpates and generated the system config report (attached).

Cobra toolbox is now up-to-date, but the FVA tutorial does not work yet.

Can you imagine any further reasons?

Thanks a lot.

Best regards

Markus

[Markus Schulze]

Hello everybody,

I have to update this issue as I am not able to sovle this problem on my own.

So far I have:

- updated git on the latest version 2.30

- reinstalled the cobratoolbox and updated it on the latest version

- and then started the FVA tutorial, but it still is not working!

Can anyone imagine reasons for that? Is it the matlab version 2020a that is not compatible yet with any of the solvers or commands?

Many thanks and best regards

Markus

[Ronan M.T. Fleming]

Hi Markus,

I can confirm there is an issue, even with the latest version of the cobra toolbox and gurobi 911. It may be some issue with the solver because changing to ibm_cplex bypasses the issue.

I am in contact with gurobi about the issue:

https://support.gurobi.com/hc/en-us/community/posts/360057936252-Optimal-objective-from-a-simple-QP-problem-?page=1#community_comment_360013990051

Hopefully they will look at this example.

Regards,

Ronan

changeCobraSolver ('ibm_cplex', 'LP');

changeCobraSolver ('ibm_cplex', 'QP');

To view this discussion on the web visit https://groups.google.com/d/msgid/cobra-toolbox/a912827a-f431-48ed-b86f-a5fb434ea6dfn%40googlegroups.com.

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Mr. Ronan MT Fleming B.V.M.S. Dip. Math. Ph.D.
----------------------------------------------------------------------------
Assistant Professor,
Division of Systems Biomedicine and Pharmacology,
Leiden Academic Centre for Drug Research,
Faculty of Science,
Leiden University.
https://www.universiteitleiden.nl/en/staffmembers/ronan-fleming
&
H2020 Project Coordinator,
Systems Medicine of Mitochondrial Parkinson’s Disease,
http://sysmedpd.eu
&

Senior Lecturer,

[Markus Schulze]

Hi Ronan, 

thanks for your feedback.

I have tried it yet with another, freshly installed and set-up computer using Matlab 2020b. It gives the same error.

Also, I do not have installed the solver 'ibm_cplex'. 

I have now used 

changeCobraSolver ('glpk', 'LP');

changeCobraSolver ('pdco', 'QP');

and this worked with the FVA tutorial and Matlab 2020a, although the solver compatibility is not tested with this version.

Many thanks.

Markus

[Ines Thiele]

Dear Markus

I do not recommend to use glpk.

IBM_ilog has a free academic license.

best ines

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Ines Thiele, PhD

Professor in Systems Biomedicine

ERC grant recipient

NUI Galway Foundation Research Leadership Programme Awardee

Principal Investigator, APC Microbiome Ireland

National University of Ireland, Galway

School of Medicine

School of Natural Science | Discipline of Microbiology
Orbsen Building | Galway, Ireland

 

www.thielelab.eu

NUIG website

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