Spec for the parametrization of the neurodesk apps

[yarikoptic]

We are sitting with @michellewang and @bcmcpher (not)bored at the OHBM hackathon and discussing various types of specs already used to describe Apps interfaces, such as (giving fmriprep example) flywheel gears and boutiques. It seems that neurodesk does not have yet any kind of such interface descriptors. Is any work being planned toward it or any interest to join forces to make it happen one way or another? ;)

[stebo85]

Dear @yarikoptic - thank you for thinking of us in this context :)

yes, we would love to join the efforts in specifying interfaces. It would be wonderful to have one general specification that can be used to convert to specific run instructions for brainlife, flywheel, XNAT, QMENTA, HPC (?), Kubernetes (?), and many more.

We initially thought that we could just use boutiques and contribute, so we added this to our to-do list, but haven't got to it yet (NeuroDesk/neurocontainers#217).

One thing we did to get started is: We picked one pipeline (QSMxT) and @astewartau got this to run on

• brainlife (https://github.com/QSMxT/QSMxT-Brainlife)
• flywheel (https://github.com/QSMxT/qsmxt-flywheel)
• QMENTA (https://github.com/QSMxT/qsmxt-qmenta)
• HPC (https://github.com/QSMxT/QSMxT#linux-installation-via-transparent-singularity-supports-pbs-and-high-performance-computing).

to understand what is involved for different platforms. We wanted to use this as a starting point for a more general description and we had one student working on a generator for flywheel and QMENTA: https://github.com/ByronDowney/neurodesk-cloud-platform-api

I am unfortunately not at the OHBM - but I would be keen to join discussions if the timezone difference allows or offline here in github :)

Thank you again and super keen to see what we can do in this space together as a community