[ENH] BEP034 Computational modelling

[MichaelSchirner]

Dear BIDS community,

this PR replaces #850 on BEP034 Computational modelling.

Briefly, in the original PR the new modality comp with datatypes

1. time series (and their derivatives)
2. connectivities
3. model descriptions (equations and parameters)
4. coordinates
5. code

was proposed.

In this new PR we address feedback from the maintainer meeting:

• We now removed the datatype "time series" from the PR and instead will join efforts with the group around issue 713 "Convergence on time series and events" towards making "time series" a BIDS-wide datatype that can also be used in other modalities.
• Furthermore, we will join efforts with BEP017 Generic BIDS connectivity data schema and add the use case "structural connectivity for computational model simulation" to BEP017 to achieve a BIDS-wide connectivity datatype that can be used for different modalities.
• Instead, this new PR now introduces only one new data type "model" with the filename suffixes "_eq" and "_param" and the file extension ".xml" to store the equations and parameters of computational models in LEMS format.
• Lastly, we propose to store the source codes and the machine codes that were used to create computational results in the modality agnostic folder code.

The new PR will be discussed on Jan 11 at 17 CET in the NFDI-Neuro Webinar, please join the discussion.

[sappelhoff]

(NOTE: I'll cross-post this message across several BEP threads)

Hi there, just a quick notification that we have just merged https://github.com/bids-standard/bids-specification/pull/918 and it may be interesting to look at the implications for this BEP.

We are introducing "BIDS URIs", which unify the way we refer to and point to files in BIDS datasets (as opposed to "dataset-relative" or "subject-relative" or "file-relative" links).

If the diff and discussion in the PR is unclear, you can also read the rendered version: https://bids-specification.readthedocs.io/en/latest/02-common-principles.html#bids-uri

Perhaps there are things in the BEP that need adjusting now, but perhaps also not -- in any case it's good to be aware of this new feature!

Let me know if there are any questions, comments, or concerns.

[Remi-Gau]

@MichaelSchirner

Did a bit of cleaning / maintenance to try to get HTML render of the BEP. Not yet possible.

Would require:

• adding xml to the list of extensions in the schema
• adding code as a datatype in the schema

https://github.com/bids-standard/bids-specification/actions/runs/4162995648/jobs/7202841128#step:5:122

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Remember to pull before working again on the BEP.