NeuroCAUSAL - an platform for storage, sharing, synthesis & meta-analysis of clinical data

[vborghe]

Title

NeuroCAUSAL - Development of an Open Source Platform for the Storage, Sharing, Synthesis and Meta-Analysis of Clinical Data

Short description and the goals for the OHBM BrainHack

We wish to work with clinicians, neuroimagers, and software developers to develop an open source platform for the storage, sharing, synthesis and meta-analysis of human clinical data to the service of the clinical and cognitive neuroscience community so that the future of neuropsychology can be transdiagnostic, open, and FAIR.

Following the steps of what enable similar transition in functional neuroimaging, we are breaking down the over-ambitious goal in two stages:

1. Create a sort of spin-off of Neuroquery that only covers lesion-related data hence allowing causal inferences
2. A Neurovault kind of tool facilitating sharing of clinical data, which shall benefit from a sort of “neuropsyhcological BIDS formatting guidelines” (OHBM poster #2066 seems to have read our minds)

Project lead

Isil Bilgin @complexbrains time zone: Europe / GMT+1 - discord: Isil Pedro Pinheiro-Chagas @pinheirochagas time zone: Americas / PDT - discord: Pedro Valentina Borghesani @vborghe time zone: Americas / EDT - discord: vborghesani Sladjana Lukic @Sladja13 time zone: Americas / EDT - discord: Sladjana

Main Hub

Americas

Other Hub covered by the leaders

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

Link to the Project

https://github.com/neurocausal

Image for the OHBM brainhack website

https://neurocausal.github.io/images/author/inverted-logo_huf11703388d6cc09ec62cec26261f7e3e_54804_148x148_fit_box_2.png

Skills

We are very heterogeneous in our own skills sets & levels and welcome all sorts of contributions 😄

The ontological issues we are facing require familiarity with neurology and/or cognitive science. These are contentious matters in the field and a perfect solution is not realistic: we seek the good compromise that will make this platform a useful tool for the broad community interested in the future of neuropsychology.

The technical issues will benefit from people familiar with tools to scrap data from texts, train/test predictive models, generally speaking converting to code our pipeline of papers selection > model fitting > function-to-structure mapping visualization (example).

We are aware we just started scratching the surface and will need lots of help on all fronts 🙏

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
• [X] Python: Visualisation
• [X] Machine learning basics
• [X] BIDS
• [X] 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

coming soon

Twitter summary

A transdiagnostic, open, and FAIR neuropsychology? Sounds interesting? Join @ppinheirochagas @complexbrains @NoLaB_Lukic @vborghesani in building https://neurocausal.github.io #OHBMHackathon #Brainhack #OHBM2022

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

neurocausal

Please read and follow the OHBM Code of Conduct

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

[djarecka]

@vborghe - thanks for testing

@anibalsolon - what should I do now? when exactly the CI is run?

[djarecka]

btw. i changed slightly the template that it's clear that we want Hub next to a leader names

[anibalsolon]

@djarecka now, after we review the info in the issue, the label 'Hacktrack: Good to go' must be added!

[djarecka]

oh, ok, so the label is the key! What happen if the author wants to update something later?

[anibalsolon]

The issue can be edited, and the CI will be triggered. So the trigger is "issue created or edited" and will only consider issues with the label Good to go.

[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 :-)

[vborghe]

We can't wait! here is our slide, with 1 animation. If you have to remove it please let us know and we will provide a static version. Thanks!

[vborghe]

@djarecka could you confirm whether the shared slide (with animations) is OK? I can provide a static one and/or in any other format - how are they going to be displayed? Thanks!!

[vborghe]

Here is the static slide