Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Add a new adapter to allow repositories which point to BioModels entries #923

Open
pgleeson opened this issue Mar 26, 2024 · 5 comments · May be fixed by #928
Open

Add a new adapter to allow repositories which point to BioModels entries #923

pgleeson opened this issue Mar 26, 2024 · 5 comments · May be fixed by #928
Assignees
Milestone

Comments

@pgleeson
Copy link
Member

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.

@pgleeson pgleeson self-assigned this Mar 26, 2024
@filippomc
Copy link
Contributor

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
Copy link
Contributor

filippomc commented Apr 2, 2024

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

@filippomc
Copy link
Contributor

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

@pgleeson
Copy link
Member Author

pgleeson commented Apr 4, 2024

@filippomc Perfect, thanks!

@pgleeson pgleeson added this to the Urgent milestone Sep 2, 2024
@sanjayankur31 sanjayankur31 linked a pull request Nov 27, 2024 that will close this issue
@sanjayankur31
Copy link
Collaborator

PR for this is at #928 . Needs to be tested and merged.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging a pull request may close this issue.

3 participants