Emergent Session -- Snakebids: Reproducible neuroimaging workflows as BIDS apps

[tkkuehn]

Snakebids: Reproducible neuroimaging workflows as BIDS apps

By Tristan Kuehn, Jason Kai, and Ali Khan, Western University

Preferred sessions: Emergent Session #2 or Emergent Session #5 (But we’re flexible).

Short description and the goals for the session:

Distributing a reproducible neuroimaging workflow that relies on multiple constituent tools is challenging, but made easier by the use of workflow management tools. One such tool, Snakemake, has become increasingly popular but is challenging to use with BIDS datasets. In this session, we introduce Snakebids, an extension to Snakemake that makes it easier to write clear workflows for processing BIDS-formatted data, and exposes those workflows with the standard BIDS App interface.
Our goals are to introduce Snakebids to a wider audience and solicit feedback, feature requests, and/or contributions.

Useful links

Snakebids readthedocs
Snakebids GitHub

Tagging @tkkuehn @kaitj @akhanf

[NaomiGaggi]

Hello @tkkuehn, You have been assigned to the emergent session 10:15-11:15 GMT+1 on June 21, 2022. .

Please confirm that you have seen this reply by giving a thumbs up! This meeting will be recorded hybrid. Whether you are in-person or virtual, this meeting will be held on Crowdcast and streamed into the Gala Room. If in-person, please come to the SEC Armadillo Gala Room 15 minutes before your session to set up. If you are virtual, please join the Crowdcast 10 minutes before your session.

If you are a virtual speaker and did not register for OHBM, please sign this video release form (attached) and email it to ohbmopenscience@gmail.com. Please DO NOT fill out the ID/passport info.

Video_consent_release_2022.odt

[rgbayrak]

You have been assigned to session #5.

[tkkuehn]

Thank you! We'll be in person.

[NaomiGaggi]

Crowdcast link for virtual attendance: https://www.crowdcast.io/e/osr-2022--emergent-5

[NaomiGaggi]

Hello @tkkuehn in the event that I am not there when you are setting up and there are any questions/technical difficulties please send me a message at 17189862634 thank you!!!