addReaction.m and initCobraToolbox .m [help]

Holmes
2012-12-17
2013-05-30
  • Holmes
    Holmes
    2012-12-17

    2 issues while installing COBRA toolbox:

    1. From where do I download addReaction.m file as mentioned in the link below?
    http://benheavner.com/systemsbio/index.php?title=Installing_COBRA_toolbox_for_MATLAB#COBRA_toolbox_download_and_installation

    2. Following is one of the steps for installation (given on the same page)  which I am not able to follow:
    Since we haven't installed the Tomlab solvers, you will get warnings if you try to initialize the Cobra Toolbox. To fix this, edit the initCobraToolbox.m file in the Cobra toolbox as follows: First, comment out lines 20, and 21. Next, change line 27 from "%CBTDIR = 'Z:\Pub\SOFTWARE\COBRAToolbox';" to "CBTDIR = 'C:\Program Files\MATLAB\R2010a\toolbox\COBRAToolbox-1.3.5';". Finally, comment out line 28. Save the changes.

    Line number 20 and 21 in initCobraToolbox.m are these:
    20. %% add cobra toolbox paths
    21. pth=which('initCobraToolbox.m');
    Line number 20 is already commented and I don't think 21 should be commented.

    Also I cannot locate line 27 mentioned in the step above.

    May I know exactly which lines are to be commented? Kindly tell me the specific lines and not the line numbers.

    Thank you.

     
  • Ben Heavner
    Ben Heavner
    2012-12-17

    That's my wiki page, not an official COBRA thing at all.

    I'm out of the office at the moment, but will send you the files tomorrow.

    -Ben

     
  • Holmes
    Holmes
    2012-12-22

    Hello,

    Sorry I did not realise that it is your wiki page and not official COBRA page. 
    I'm still stuck with the installation. I would be really nice if you could help me with it.

    Thanks.

     
  • Ben Heavner
    Ben Heavner
    2012-12-23

    No problem - I'm away for the holidays at the moment. What's the best way to contact you when I get back? Let me know via b heavner at gmail dot com.