How to generate boolean network from SBML file to be uploaded in BoolNetR
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4.4 years ago
Pluto ▴ 10

I have sbml file and need to creat boolean network to load in BoolNet R Suggestions?

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4.4 years ago
mhucka ▴ 50

The question as worded does not provide enough information to really answer the question, but here are some general notes.

BoolNet is supposed to be able to import and export SBML models that use the Qualitative Models ("qual") package, so if the "sbml file" mentioned in the question uses the "qual" package for SBML, then in theory, BoolNet should be able to read it directly. If BoolNet can't read it, then perhaps it's an older version of the software and it would worth trying to get the latest version. Otherwise, if it's a recent version and BoolNet still fails to read the SBML "qual" model, I would contact the authors of BoolNet directly.

If the "SBML file" mentioned in the question does not use SBML "qual", then unfortunately, it is a much harder problem. There is currently no automated way to convert a regular model into a qualitative model; it requires human intellect to decide how to convert a general model into a qualitative one. (Perhaps some day someone will write an automatic translator, but as of today, I don't believe one exists.)

If you have more questions about Boolean network models and SBML, please feel free to ask people on the sbml-discuss Google group. The developers of SBML "qual" are on that mailing list and may have other suggestions.


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