GSoC 2023 Project Idea 1.2 Structural Connectivity editor widget (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.

In the TVB ecosystem there is a new repository called tvb-widgets offering UI widgets for Jupyterlab environments. These widgets are compatible with TVB data formats and able to display them in different forms: either a 2D viewer for time series or a 3D viewer for brain surfaces. The purpose of this project is to implement a new widget which would allow users to edit the connectivity matrices involved in a TVB simulation. Necessary features for this widget: display connectivity matrix, normalize matrix, resect connections, resect nodes, change connection weights, save resulted connectivity. Of course, this new widget has to run in a Jupyterlab notebook as well.

Finally, it would be great to have all the widgets linked into the tvb-ext-xircuits repository which is a Jupyterlab extension based on React JS. At the moment, only the PhasePlaneWidget is linked there, but the rest could be added in a similar manner.

Examples of TVB data formats can be found on Zenodo. Connectivity matrices are available there as well.

Check out our Jupyter notebooks to play with the widgets we have available so far.

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

Skill level: Junior+/mid

Required skills: Python, IPywidgets, React JS, Jupyterlab, Jupyterlab extensions**

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, IPywidgets, React JS, Jupyterlab, Jupyterlab extensions

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Exemple of Structural Connectivity displayed (in other TVB tools) can be seen bellow. These can be used as visual reference, to inspire from them:

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Hi @liadomide
My name is Sumit and I am interested in contributing to this interesting project for GSOC23. I work as a Software Engineer with 2+ years of experience in Python under my belt. I went over the description and the Structural Connectivity screenshots attached. I will try out the Jupiter Notebooks to check out existing TVB widgets and revert back if I have more questions.

Do let me know if you have any other domain-specific resources I should go over that will help me with the project.
Thanks,
-Sumit

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Hi @Sumit_Pagar,

I am happy to hear of your interest with this project.
The first steps you already started sound great, please continue with them, and let us know in case you have questions.
Then, I suggest you immediately start composing a GSOC project proposal document. We had good experience in the past with google docs shared with us early - to be able to give feedback.
When we evaluate a project proposal from a GSOC applicant, we look for respecting GSOC rules, but also for signs that the current project was well understood. So whatever you think if helps on that direction, is welcome. It can be that you include small code snippets, just text, drawings - it is your choice.

Best,
Lia.

PS: ldomide@gmail.com for sharing the google doc.

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Hi Lia, Thank you for the tips. I will start working on the idea proposal and send you a first draft soon.
Thanks,
-Sumit

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Hello, @liadomide
I’m Siddhant Dixit, a Computer Science & Engineering student at Indian Institute of Information Technology Dharwad (IIIT Dharwad).

I am interested in the field of Computational Neuroscience and data visualization, I believe this project is an excellent opportunity to learn new skills, work on an exciting open-source project, and contribute to the field of neuroscience. I have experience working with Python and Jupyter notebooks and have worked on a few data visualization projects in the past.

I am highly interested to work on this project in GSOC23.

-Thank you

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Hi @Siddhant_Dixit
I am happy to hear of your interest.
If decided, please go ahead and start working on your GSOC proposal.

Best,
Lia.

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Hi Lia, @liadomide
Thank you for your response and encouragement I have explored about the project needs, and started working on the GSOC proposal and will you send draft soon as suggested.

I noticed that the Google Doc link for “PhasePlaneWidget” in the project description requires permission to access. Could you please check and provide an updated link?

Thanks
-Siddhant Dixit

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Hi @Siddhant_Dixit
Thank you for notifying this issue. I changed permissions on that folder. Let me know if you can view movie related to PhasePlane.
Alternatively, there is this page where the integration with xircuits between PhasePlane can be inspected: Extension tvb-ext-xircuits - HBP Wiki

Best,
Lia.

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@liadomide Yes! The Google Drive link is accessible now. I can see the simulations and workflow.

Thank you

-Siddhant

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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.

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Hi @liadomide ,
My name is Priya Yadav, and I am currently a sophomore pursuing a degree in computer science and engineering. I am reaching out as I am interested in contributing to this project as part of Google Summer of Code (GSoC) 2024. I am familiar with Python and have experience working with Jupyter Lab. While I don’t have professional experience, I have engaged in coding, particularly in areas such as data analysis, machine learning, and Android development.
I’d appreciate your advice on getting started and approaching the project.I believe my skills and interests would match what the project needs.Excited about the possibility of contributing.

Thanks,
Priya Yadav

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Dear Priya,

Thank you for your interest in TVB, INCF and GSOC!

This current thread where you are writing is from last year 2023.

For this year, we have this project proposed:

But please be aware that we do not have yet a validation that we will be accepted to participate with this project. Please follow INCF announcement for year 2024 GSOC acceptance.

Best,
Lia.