I'd like to inquire about using the bioinformatics exchange to post COMBINE related questions. COMBINE, as describe in Wikipedia is: "COMBINE, the COmputational Modeling in BIology NEtwork, is an initiative to coordinate the development of the various community standards and formats for computational models, initially in systems biology and related fields."

The COMBINE community has grown over the last 10 years, for example there were 100 attendees at the recent COMBINE workshop held in Heidelberg. COMBINE includes a number of standards, including SBML, SBGN, SBOL etc. The feeling is that it would be very useful to have a stack-overflow location where users could ask questions related to any of the COMBINE standards. Rather than try to create our own stack-exchange we wondered whether it would be ok to ask COMBINE related questions to this bioinformatics exchange? Volume would not be large so it wouldn't flood the current exchange.

To be more specific, the COMBINE standards concern modeling (SBML and CellML), pathway visualization (SBGN), relevant ontologies such as Kisao or SBO, and biological description formats such as SBOL and BioPAX. Of all the exchanges bioinformatics appears to be the most closely related.

The kinds of questions that would most likely be posted would include how to use the standards, what software supports the standards, technical questions about the standards, and how to contribute to the standards etc.

Here are some specific questions that could be asked:

  1. How do I specify units in an SBML model?

  2. How do I access libsbml from Python on Linux?

  3. Does every SBML model have to have a volume compartment?

  4. What's the easiest way to learn SBOL, is there an introductory document I can read?

  5. What is the symbol for a small molecule when using SBGN?

  6. What ontology would you recommend I use to describe numerical algorithms for modeling metabolic pathways?

  7. How can I convert SBML into a Matlab function?


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