GSoC 2023 Project idea 1.1 Integrate TVB with Zenodo (175/350 h)

GSoC
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There are several modeling studies using brain network models which incorporate biologically realistic macroscopic connectivity (the so-called connectome) to understand the global dynamics observed in the healthy and diseased brain measured by different neuroimaging modalities such as fMRI, EEG and MEG.

For this particular modelling approach in Computational Neuroscience, open source frameworks enabling the collaboration between researchers with different backgrounds are not widely available. The Virtual Brain is, so far, the only neuroinformatics project filling that place.

All projects below can be tailored for a 12-week time window, both full-time and part-time, as the features/pages can be built incrementally.

[TVB] (https://www.thevirtualbrain.org/) has a demo dataset currently published on [Zenodo] (tvb-data - Extended Dataset | Zenodo).

We use it by manually downloading it, unzip then use inside tvb code and web GUI.

We intend to use Zenodo API instead.

The task is mainly for part-time, if only the above feature will be used, but it can be extended if needed with other external datasources for full-time applicants.

More details here or here.

Expected results: A set of classes , with demo Jupyter notebook, and unit tests.

Skill level: Junior+/mid

Required skills: Python, Zenodo, Jupyter

Time commitment: Flexible (175/350 h)

Lead mentor: Lia Domide

Project website: https://req.thevirtualbrain.org/browse/TVB-2607

Backup mentors: Romina Baila

Tech keywords: Python, Zenodo, Jupyter

3 Likes
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Hi, I’ve read the project description and am extremely interested to participate in GSoC with this project. I’ll be very grateful if you let me know further steps of contribution.

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Hi, I want to contribute to this project could anyone plz guide me about further steps to be a confident applicant. Thanks

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Hello @INCFComms

This project seems interesting and feasible. I have reviewed the GitHub PR mentioned in the post, and I believe I can develop a framework that supports downloads from Zenodo and other repository management systems.

I am working on understanding the directory and framework structure of the tvb-root repository. In the meantime, could you please provide more information on the next steps for contributing?

Thank you.

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Hi @all

To everyone interested in this project, I propose the following concrete steps:

  • read about Zenodo programatic API - is there a Python package? maybe you can do a very small code example that you play with to make sure it is understood

  • scan through tvb documentation (official website, github repos, technical doc, etc) - not more than few hours, just to make an idea on what we do

  • then start directly to work on your GSOC proposal. I think both Google itself, and also INCF have well established templates to start with. We had good experience in the past with Google docs, shared with us the mentors to review early and potentially comments on its content.

Have a great day,
Lia.

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Cool that you got to tvb-root repo already!
Concretely, you could see the current loading of data in code like here tvb-root/connectivity.py at master · the-virtual-brain/tvb-root · GitHub
Regarding next steps, I left few comments bellow, as a generic comment. I hope that message helps, otherwise give me a sign where to put more details

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Cool that you like this project!
I left a generic reply just minutes before.
Let me know if that helps, otherwise give me a sign where to put more details.

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Hello @liadomide

Thanks for the comments.

I have gone through the Zenodo and Datalad APIs; There is a third-party library to work with Zenodo pyzenodo3. We can modify some code from here to support the downloading functionality. I used the Record class as a parent and implemented the download method for the child class; it worked fine for the sample dataset.

I also looked into datalad API as it was mentioned in the GitHub pr comment_link.

datalad has an official python module up on PyPI, which can perform downloading from remote URLs. documentation.

I’ve started to look into the Ebrains project and fairgraph.

Regarding the GSOC proposal, How should I share the google document with you?

Thanks.

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Hi @abhi-glitchhg,
My email address is ldomide@gmail.com
Pls share the google doc with me when you want feedback.

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Hi @all,
Please don’t wait until the last moment to submit your proposals to GSOC.
Technical problems my occur at any time.
If you submit a PDF, you can still change it until the deadline if a better version is produced.

1 Like