Import XML File to Simbiology

Question

Aditi Kumar 2022-2-20

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此问题的直接链接

https://ww2.mathworks.cn/matlabcentral/answers/1653880-import-xml-file-to-simbiology

回答： Florian Augustin 2022-2-20

Hello,

I am trying to import the attached xml file into SimBiology but receive this error:

Error using SimBiology.internal.sbml.read

Unable to read SBML file. Empty model was returned.

Error in privatesbmlioError in sbmlimport (line 90)

ret = privatesbmlio('read',nargout,{tempFileName})

Error in untitled (line 1)

modelobj = sbmlimport('simulation.xml');

This xml file is from the supplementary information in this paper: https://www.cell.com/molecular-therapy-family/nucleic-acids/fulltext/S2162-2531(17)30153-1?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS2162253117301531%3Fshowall%3Dtrue

How can I fix this error?

I attached the xml file as a pdf file.

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Answer 1

Florian Augustin 2022-2-20

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https://ww2.mathworks.cn/matlabcentral/answers/1653880-import-xml-file-to-simbiology#answer_900190

Hi Aditi,

The SBML model in the supplemental material of the paper you are citing imports without error on my computer in MATLAB versions R2017a - R2021b (current). I don't see an attachment to the question, but the error message you are seeing indicates that the content of the SBML/xml file is invalid. I have seen this error with invalid SBML/xml files that omit the xml prolog:

<?xml version="1.0" encoding="UTF-8"?>

Does your xml file include this declaration? If it is included and the error persists, can you post the Matlab version you are using and attach the xml file?

Thank you,

-Florian