Learn how easy it is to sync an existing GitHub or Google Code repo to a SourceForge project! See Demo

Close

#36 SBMLToolbox - convertSBMLToCobra - bug models without kineticLaws

SBMLToolbox-4.0.1
closed
nobody
SBMLToolbox (1)
5
2014-07-15
2013-08-05
Matthias König
No

I wanted to report a SBMLToolbox bug (in 4.1), but unfortunately it is not possible to create a ticket in the SBMLToolbox section (see screenshot attached -> I am logged in SourceForge, but do not have the create ticket option). Here is the only option for me to create a ticket. So please move it to the SBMLToolbox section.

BUG REPORT
There is a problem in convertSBMLToCobra, if SBML models do not have kineticLaws (which is quit often the case, especially for FBA networks).


Error in convertSBMLToCobra (line 122)
parameters = modelSBML.reaction(i).kineticLaw.parameter;

Error in demo_example_1 (line 9)
[model] = convertSBMLToCobra(modelSBML, defaultBound);


The patch is:

% Bug Fix for SBML models without kinetic laws
if isempty(modelSBML.reaction(i).kineticLaw)
    parameters = [];
elseif isfield(modelSBML.reaction(i).kineticLaw,'parameter')
    parameters = modelSBML.reaction(i).kineticLaw.parameter;
else
   parameters = [];
end

Sorry for posting in the wrong section. Probably the settings for reporting tickets have to be changed, so that all logged in users can post and not only people in the group.

Greetings Matthias

1 Attachments

Discussion

  • Sarah Keating
    Sarah Keating
    2013-08-05

    Hi Matthias

    I'm sorry you were not able to create a ticket in the SBMLToolbox tracker. We will look into that.

    However, you are reporting the bug to the wrong people :-)

    The function convertSBMLToCobra is not part of SBMLToolbox - it in fact comes from the COBRA Toolbox.

    Sorry for any confusion.

    Sarah

     
    Last edit: Sarah Keating 2013-08-05
  • Hallo Sarah,
    thanks for the fast answer. Wanted to quickly report the bug, but choose
    the wrong forum ;).
    Greetings Matthias

    On 8/5/2013 6:25 PM, Sarah Keating wrote:

    Hi Matthias

    I'm sorry you do not able to create a ticket in the SBMLToolbox tracker.
    We will look into that.

    However, you are reporting the bug to the wrong people :-)

    The function convertSBMLToCobra is not part of SBMLToolbox - it in fact
    comes from the COBRA Toolbox.

    Sorry for any confusion.

    Sarah


    [tickets:#1] SBMLToolbox - convertSBMLToCobra - bug models without
    kineticLaws

    Status: open
    Labels: SBMLToolbox
    Created: Mon Aug 05, 2013 03:48 PM UTC by Matthias König
    Last Updated: Mon Aug 05, 2013 03:48 PM UTC
    Owner: nobody

    I wanted to report a SBMLToolbox bug (in 4.1), but unfortunately it is
    not possible to create a ticket in the SBMLToolbox section (see
    screenshot attached -> I am logged in SourceForge, but do not have the
    create ticket option). Here is the only option for me to create a
    ticket. So please move it to the SBMLToolbox section.

    BUG REPORT
    There is a problem in convertSBMLToCobra, if SBML models do not have
    kineticLaws (which is quit often the case, especially for FBA networks).


    Error in convertSBMLToCobra (line 122)
    parameters = modelSBML.reaction(i).kineticLaw.parameter;

    Error in demo_example_1 (line 9)
    [model] = convertSBMLToCobra(modelSBML, defaultBound);


    The patch is:

    % Bug Fix for SBML models without kinetic laws
    if isempty(modelSBML.reaction(i).kineticLaw)
    parameters = [];
    elseif isfield(modelSBML.reaction(i).kineticLaw,'parameter')
    parameters = modelSBML.reaction(i).kineticLaw.parameter;
    else
    parameters = [];
    end

    Sorry for posting in the wrong section. Probably the settings for
    reporting tickets have to be changed, so that all logged in users can
    post and not only people in the group.

    Greetings Matthias


    Sent from sourceforge.net because you indicated interest in
    https://sourceforge.net/p/sbml/tickets/1/

    To unsubscribe from further messages, please visit
    https://sourceforge.net/auth/subscriptions/

    --
    Matthias Koenig
    Computational Systems Biochemistry
    Institute of Biochemistry
    Charité - Universitätsmedizin Berlin
    http://www.charite.de/sysbio/people/koenig/
    Tel: + 49 30 450 528 197
    Email: matthias.koenig@charite.de
    http://scholar.google.com/citations?user=xD9IjnYAAAAJ&hl=en

     
  • Sarah Keating
    Sarah Keating
    2013-11-20

    This was sorted so I am closing it.

     
  • Sarah Keating
    Sarah Keating
    2013-11-20

    Ticket moved from /p/sbml/tickets/1/

    Can't be converted:

    • _milestone: 1.0
     
  • Sarah Keating
    Sarah Keating
    2013-11-20

    • status: open --> closed
    • Version: 1.0 --> SBMLToolbox-4.0.1
    • Priority: --> 5