SBML parser

Is anyone actively working on an SBML parser? I saw this and this but can’t find any status updates. I am busy building a Julia version of Cobrapy (much more expansive than COBRA.jl, which seems to be restricted to distributed FBA type problems) that needs to be able to read SBML models.

I have no problem developing a parser from scratch e.g. by providing bindings to SBML’s C api (or Python’s api, not sure which is the better route?) but I don’t want to duplicate work if there is already a parser being developed…

Any suggestions etc. are welcome!

Someone just put a binarybuilder thing in about one IIRC? I’d have to dig around.

1 Like

This seems to be the repository where it is used: GitHub - LCSB-BioCore/SBML.jl. CC: @laurentheirendt


Excellent, this is exactly what I was looking for! Thanks!

1 Like

In case anyone has a similar question, lots of things have changed since I asked this question. In addition to the SBML.jl parser package linked to above, Julia also now has a very high quality constraint based reconstruction and analysis package, called COBREXA, as well as a Julia interface to equilibrator_api, called eQuilibrator.jl, in case you want to combined thermodynamics with cobra methods.