Snakebids: Snakemake + BIDS

[akhanf]

Project info

Title:
Snakebids: Snakemake + BIDS

Project leads:
@akhanf, @tkkuehn

Timezone:
UTC-4 (Atlantis)

Description:
Snakemake (url, paper) is a fast-growing open source workflow management system that provides a high level of transparency, reproducibility and adaptability. Despite its wide adoption in the scientific community (>5 new citations per week), Snakemake has not yet had significant uptake in the neuroimaging community.

We have been working on an extension, Snakebids, to ease working with neuroimaging (specifically BIDS) data, and allow the creation of BIDS Apps with Snakemake (e.g. https://github.com/khanlab/hippunfold).

Link to project: https://github.com/akhanf/snakebids

Mattermost handle: @neuroak

Goals for the OHBM Brainhack

• raise awareness of Snakemake in the neuroimaging community
• get user feedback on a recently developed Snakemake+Snakebids tutorial and enhance this tutorial
• maybe brainstorm with Nipype users re: potential bridges between snakemake & nipype

Good first issues:
https://github.com/akhanf/snakebids/issues/51

Skills:

• Python
• BIDS
• BIDS Apps

Chat channel:

• hbmhack-snakebids
  https://mattermost.brainhack.org/brainhack/channels/hbmhack-snakebids

Image for the OHBM brainhack website
(*note: snakemake and bids logos used without permission!)

Project submission

Submission checklist

Once the issue is submitted, please check items in this list as you add under 'Additional project info'

Please include the following above (all required):

• Link to your project: could be a code repository, a shared document, etc. See here
• Include your Mattermost handle (i.e. your username). If you do not have an account, please sign up here.
• Goals for the OHBM Brainhack: describe what you want to achieve during this brainhack. See here.
• Flesh out at least 2 "good first issues": those are tasks that do not require any prior knowledge about your project, could be defined as issues in a GitHub repository, or in a shared document, cf here.
• Skills: list skills that would be particularly suitable for your project. We ask you to include at least one non-coding skill, cf. here.
• Chat channel: A link to a chat channel that will be used during the OHBM Brainhack. This can be an existing channel or a new one. We recommend using the Brainhack space on mattermost, cf. here.
• Provide an image of your project for the OHBM brainhack website

You can also include information about (all optional):

• Someone co-leading the project in the timeslot you have not selected to provide additional visibility.
• Number of participants, cf. here
• Twitter-size summary of your project pitch, cf. here
• Set up a kanban board on your repository to better divide the work and keep track of things, cf here
• Project snippet for the OHBM Brainhack website, cf. here

We would like to think about how you will credit and onboard new members to your project. We recommend reading references from this section. If you'd like to share your thoughts with future project participants, you can include information about (recommended):

• Specify how will you acknowledge contributions (e.g. listing members on a contributing page).
• Provide links to onboarding documents if you have some.

QMENTA has agreed to sponsor the event and provide computational resources through their platform.

• Get in touch with QMENTA through their Brain Innovation Hub Slack space, if you think your project would benefit from their support.

[tiborauer]

Can you, please, provide an image for the website?

[akhanf]

Just added one now, thanks!