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

html
xml
sql
c-plusplus
python
#1

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

About

TheVirtualBrain (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.

TVB has already been successfully employed in a wide range of case studies, including different
experimental paradigms in healthy subjects, and different types of brain diseases.

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 tumour.

To facilitate the reproducibility of these results, and to provide robust starting points for further
research, we aim to build a set of webpages containing all the information to reproduce clinical
applications, including videos of the workflow from a GUI perspective, and notebooks with code.
In line with the coding spirit of GSoC, the student will have to perform purely coding work (mainly in Python to build the notebooks), 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.

NB, small changes were made to this text on Feb 27, on request of the mentors.

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

Relevant links:
https://www.frontiersin.org/articles/10.3389/fninf.2015.00027/full
http://www.eneuro.org/content/5/3/ENEURO.0083-18.2018/tab-article-info
http://docs.thevirtualbrain.org/demos/Demos.html
https://www.youtube.com/playlist?list=PLVtblERyzDeIATvaoHp-bBtksF25zm8p1

1 Like
#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.

1 Like
#8

Students could see a small code prototype and demo screenshot on this task:
https://req.thevirtualbrain.org/browse/TVB-1975

#9

Weekly Report

  1. What did you get done this week?
  • Went through general TVB framework documentation, read Educase Video and Manuscript. Set up environment. Download required packages. Reproduce the examples.

    1. What do you plan on doing next week?
  • Get more familiar with tvb framework functions. Talk to mentor about Educase project.

    1. Are you blocked on anything?
  • No.

Simone Liu

1 Like
#10

Thanks Simone, glad to hear that!

INCF has created a new private category, called GSoC 2019, for students and mentors. I have posted a welcome topic there, with the name and number of the project. Please let me know if you can access it.

d.

#11

Hi Daniele,

Thanks for letting me know. I don’t think I have GSoC 2019 in my category. Could you tell me the step I need to be added in that category?

Thanks,
Simone

#12

Hi! I’ve added you to the GSoC_Students group. You should now be able to mark your posts with ‘GSoC_2019’ which is private to this year’s students and mentors

Best,
Malin