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OpenSourceBrain / OSBv2

An updated version of the Open Source Brain platform
https://www.v2.opensourcebrain.org/
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Add a new adapter to allow repositories which point to BioModels entries #923

Open pgleeson opened 3 months ago

pgleeson commented 3 months ago

There are ~1000 curated models on https://www.ebi.ac.uk/biomodels/, mostly in SBML format.

A good number of these are relevant for neuroscience, e.g. https://www.ebi.ac.uk/biomodels/BIOMD0000000118#Curation

There are new features in pyNeuroML for simulating and translating SBML, and approprriate libraries are included with the latest OSBv2 JupyerLab docker image.

An adapter should be created so BioModels models can be bulk added and listed on OSBv2, and workspaces created with the SBML, SED-ML, etc.

filippomc commented 3 months ago

Need to add the biomodels type to the model spec and generate the code https://github.com/OpenSourceBrain/OSBv2/blob/master/applications/workspaces/api/openapi.yaml.

filippomc commented 3 months ago

MetaCell to create a branch with the model and the glue code; UCL creates the adapter itself

filippomc commented 3 months ago

@pgleeson the base models and code structure has been added in branch feature/biomodels

pgleeson commented 3 months ago

@filippomc Perfect, thanks!