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Error in sbmlimport - Conversion from SBML/XML to stochiometric matrix

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Namrata Tomar
Namrata Tomar on 19 Jun 2015
Commented: Ingrid Tigges on 7 Sep 2015
I am using sbmlimport function to convert KEGG pathway SBML (KGML) file into stochiometric matrix. It has .xml extension, but getting this error -- Error using SimBiology.SBMLReadWrite/sbmlread. A fatal error occurred reading in this file. Error in privatesbmlio (line 26). Error in sbmlimport (line 62) ret = privatesbmlio('read',nargout,{fullfilename, varargin});

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Ingrid Tigges
Ingrid Tigges on 19 Jun 2015
I have 3 questions:
  1. Which MATLAB release are you using?
  2. Does the example from the documentation sbmlobj = sbmlimport('oscillator.xml'); work?
  3. Can you post an example which causes the error here?
Namrata Tomar
Namrata Tomar on 24 Jun 2015
Hello,
  1. I am using Matlab 2014a.
  2. example, m = sbmlimport('lotka.xml'); [M,objSpecies,objReactions] = getstoichmatrix(m1); is working but not for my Kegg Pathway.
  3. I downloaded a kegg pathway- http://www.genome.jp/kegg-bin/show_pathway?map=hsa05230&show_description=show. Code is m = sbmlimport('hsa.xml') but it is giving error.

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Answers (1)

Ingrid Tigges
Ingrid Tigges on 25 Jun 2015
Hi Namrata,
The files from KEGG are not in the SBML format but in the KGML format (see KGML specification information ). SimBiology cannot read in KGML files. There are however tools available on the internet, for example this tool which allow the conversion of KGML files into the SBML format.

  1 Comment

Namrata Tomar
Namrata Tomar on 18 Aug 2015
Thanks .. Can you please let me know how to use it - I have downloaded kgtrans.jnlp. Now how should I proceed?

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