GSoC Project Idea 4.3: The Virtual Brain (TVB) Edu Pack for clinical case studies reports

html
xml
sql
python

#1

The Virtual Brain (TVB) Edu Pack for clinical case studies reports

About

The Virtual Brain (TVB, thevirtualbrain.org), is an open-source platform to model large-scale brain networks by merging different data sources in a dynamical systems framework.

One of its unique characteristics is the combination of a very powerful set of core functions (written in Python and C++), and a user-friendly web interface, most convenient for educational purposes and dissemination to a wide community.

To enable researchers from various backgrounds a quick start into TVB and brain network modeling in general, an educational module has been developed: TVB-EduPack. EduPack offers two educational functionalities that seamlessly integrate into TVB’s graphical user interface (GUI): (i) interactive tutorials introduce GUI elements, guide through the basic mechanics of software usage and develop complex use-case scenarios; animations, videos and textual descriptions transport essential principles of computational neuroscience and brain modeling; (ii) an automatic script generator records model parameters and produces input files for TVB’s Python programming interface.

A key feature of TVB is the possibility of implementing models of neural activity on the structural architecture of individual brains, and fit these models to the actual brain activity of each subject. This process is called “virtualization”, and is particularly relevant (actually absolutely necessary) in clinical studies involving patient-specific lesions, such as stroke and brain tumor.

Project

This project will be aimed to build EduPacks for specific clinical case studies, already virtualized by the group of the promotor. This means that, in line with the coding spirit of GSoC, the student will have to perform purely coding work, without having necessarily to understand the clinical cases and the details of the computational models. Of course we will be happy to discuss and develop these latter aspects as well for students who are interested.

Technical keywords: Python, C++, XML, SQL, HTML

Mentor: Daniele Marinazzo, PhD & Hannelore Aerts, MSc, U Ghent, Belgium.

Relevant links:
https://www.frontiersin.org/articles/10.3389/fninf.2015.00027/full

https://brainmodes.github.io/EduPack/

https://github.com/liadomide/EduPack

http://www.eneuro.org/content/5/3/ENEURO.0083-18.2018/tab-article-info


#2

Hello Ma’am ,I have completed the whole documentation but I am getting error in installation.
This is creating error in installation -->> ```
git clone git@github.com:BrainModes/EduPack EduPack

Error is ->> 
ssh: connect to host github.com port 22: Connection timed out
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.

#3

Hello,

I have been able to install the library without any problems. I will send a PR to fix the docs.


#4

ok… tell me the repo name also


#6

Dear Dwivedi,
As I told you per email, I suggest that you open an issue on the github repo which hosts Edupack.
I will also look into the issue and get in touch with them.

Also, please specify what your issue is, so that other members of the community can assist you.

Best regards and good luck


#7

Actually another (and maybe more constructive, effective, and educational) approach would be to use the idea behind the original code, but recode the EduPack from scratch (building of course on the TVB package).
The original code stayed pretty much untouched since 2015/2016, so it will inevitably be obsolete to some extent.