Pydra: Converting existing scientific workflows to the new dataflow engine Pydra

[yibeichan]

Title

Pydra: Converting existing scientific workflows to the new dataflow engine Pydra

Short description and the goals for the OHBM BrainHack

Pydra is a part of the second generation of the Nipype ecosystem. The goal of this project is to convert existing neuroimaging analytical workflows that are written in other languages to the new dataflow engine Pydra. The main deliverables of the project are comprehensive Pydra workflows that use interfaces from neuroimaging packages such as FSL, SPM, ANTs, AFNI, FreeSurfer.

Goals for the Brainhack:

• Converting Nilearn.glm tutorial to Pydra
• Moving FitLins to Pydra

Link to the Project

https://github.com/nipype/pydra

Image for the OHBM brainhack website

https://raw.githubusercontent.com/nipype/pydra/master/docs/logo/pydra_logo.png

Project lead

Yibei Chen, @Yibeichan, yibei#3755

Mentors: Dorota Jarecka, @djarecka, dorota#4713 Satrajit Ghosh, @satra, satra Chris Markiewicz, @effigies, Chris Markiewicz#5926 Hao-Ting Wang, @htwangtw, hao#7367

Main Hub

Glasgow

Other Hub covered by the leaders

• [ ] Glasgow
• [ ] Asia / Pacific
• [ ] Europe / Middle East / Africa
• [ ] Americas

Skills

Minimal:

• Python
• Git

Optional:

• Familiarity with GLM, BIDS
• Familiarity with Nipype, Nilearn

Recommended tutorials for new contributors

• [ ] Set up a brainhack friendly computing environment
• [ ] A introduction to Bash
• [X] Python: Writing a script
• [X] Python: Data analysis with Python
• [ ] Python: Visualisation
• [ ] Machine learning basics
• [ ] BIDS
• [ ] Machine learning for neuroimaging
• [X] VCS: Using Git and Github
• [ ] VCS: Data management with Datalad
• [ ] Virtualization
• [ ] High Performance Computing: Oracle cloud resource

Good first issues

https://github.com/orgs/nipype/projects/5

Twitter summary

Pydra is a part of the second generation of the Nipype ecosystem. The goal of this project is to convert existing neuroimaging analytical workflows that are written in other languages to the new dataflow engine Pydra.

OHBMHackathon #Brainhack #OHBM2022

Short name for the Discord chat channel (~15 chars)

pydra

Please read and follow the OHBM Code of Conduct

• [X] I agree to follow the OHBM Code of Conduct during the hackathon

[djarecka]

Thank you for submitting the project! We have 35 projects right now, woohoo! But that means the projects pitches will have to be short. We will give you tomorrow 2 minutes to pitch your project, you can have one slide or no slides! If you decide to use a slide, please include the link to the slide here.

And don't worry, you will still have more time to talk about your project during the BrainHack :-)