TVB GSOC 2022

[liadomide]

The Virtual Brain: An open-source simulator for whole brain network modeling.

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 bellow can be tailored for 12weeks time window, both full time and part-time, as the features/pages can be build incrementally.

[1] Integrate TVB with Zenodo

Description: TVB (https://www.thevirtualbrain.org/) has a demo dataset currently published on Zenodo (https://zenodo.org/record/4263723#.Ydi-dX1Bzx4).
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: https://req.thevirtualbrain.org/browse/TVB-2607

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

Skills: Python, Zenodo, Jupyter

Mentors: Lia Domide, Paula Prodan, Romina Baila

[2] Separate tool to upload data into TVB

Description: TVB (https://www.thevirtualbrain.org/) has become a complex tool. It exposes REST services also. We are interested to build a separate, from scratch, a new module, to remotely call TVB web service for importing data into TVB. This tool could also be enhanced into encrypting data before upload, validate it, check BIDS compatibility, etc.

Expected results: A new tvb-* package, ready for Pypi, to be able and call TVB rest services for uploading data into a running tvb-distribution. Unit-tests.

Skills: Python, REST, encryption, BIDS

Mentors: Paula Prodan, Romina Baila, Lia Domide

[3] TVB Web page redesign

Description: TVB (https://www.thevirtualbrain.org/) has become a complex tool, with a large web front-end. We have few very complex pages which could benefit from a redesign. One of such pages in the Simulator page. We expect from this project to first understand the current web design and logic of the application, then improve one or multiple pages in TVB through CSS/HTML.
https://www.thevirtualbrain.org/tvb/zwei/image-zoom/122368/26?stage=brainsimulator

Expected results: A static HTML with CSS containing the new design, respecting TVB logic.

Skills: HTML, CSS

Mentors: Romina Baila, Lia Domide, Paula Prodan