BIDS Computational Models Extension Proposal

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Michael Schirner

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Feb 12, 2021, 8:14:58 AM2/12/21
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Dear BIDS enthusiasts,

we implemented TVB (thevirtualbrain.org) as a service on EBRAINS.eu (https://arxiv.org/abs/2102.05888) and we now need to store our computational models in a generic format.

As presently there exists no BIDS for computational models, we created a draft format for storing computational network models and simulation outputs: 


Used concepts:

- model-specification based on LEMS/NeuroML with parsers/transformers for automatic Python and CUDA (GPU) code generation

- adherence to the typical BIDS principles regarding filename/folder structures, simple and generic file types and metadata sidecar files

What would be new for BIDS:

- unique file identifiers that are checksums/hashes of the associated (meta)data to have an automatic validation mechanism for the internal consistency of BIDS data sets (with some associated ideas how BIDS validator Apps could be extended to something like "BIDS provenance tracker Apps")


We are aware that there are efforts towards a generic model description format (https://github.com/ModECI/MDF) in the wider BIDS community. Since we need an immediate solution we will go for the proposed format for now and are happy to collaborate on the MDF in the future.

We look forward to your feedback on the proposal.

Cheers,
Micha Schirner

Petra Ritter

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Jan 5, 2022, 4:13:35 AMJan 5
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Please visit our Webinar where we present the BIDS Computational Models Extension Proposal including a practical Use Case on January 11th at 17:00 CET: https://nfdi-neuro.de/event/nfdi-neuro-webinar-ritter-et-al-bids/
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