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GeomScale / dingo

A python library for metabolic networks sampling and analysis
GNU Lesser General Public License v3.0
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Compartments #23

Closed hariszaf closed 1 year ago

hariszaf commented 2 years ago

To model a community, we will need to track down the reactions and their corresponding metabolites, that take place in the extracellular space.

It is my belief that it would benefit our efforts the most, to use models in the Systems Biology Markup Language (SBML) format to this end.

This means both to implement a function for reading such files (the libSBML library will probably be of help for this, but also to add an attribute in our model, e.g. model.extracellular to keep track of these metabolites.

@TolisChal @vissarion what 's your thoughts?

vissarion commented 2 years ago

Adding a function reading such files sounds reasonable. Regarding the attribute another choice would be to create a new class community_model that inherits model and there add the extracellular attribute.

Kundanagrawalofficial commented 1 year ago

The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form that can be exchanged ...