GSoC 2022 Project Idea 2.1: Developing a tool to easily store data and study details for computational neuroscience research (350 h)

The values of reproducibility and data sharing gain more and more importance in the research community. To make neuroscience studies reproducible and allow for easy data sharing, the Brain Imaging Data Structure (BIDS, https://bids.neuroimaging.io/) standard has been developed. It allows researchers to store their neuroimaging data in a standardized way, speeding up data sharing efforts. Since the development of this BIDS standard, the advantages of using the proposed data structure have been growing steadily: multiple bids-apps have been developed for common data processing pipelines used in the neuroscience community, allowing users to directly load or generate their BIDS-conform data set. Among those apps, is the bids-validator that easily checks the correctness and completeness of all files. BIDS extension proposals (BEPs) have followed for various other modalities used in neuroscience research, such as EEG or PET.

We recently proposed a new standard for storing the necessary data to reproduce a computational neuroscience modeling study. We exemplified our standard by putting a first data set for one of our computational modeling studies using the neuroinformatics platform The Virtual Brain (thevirtualbrain.org/) into the proposed data structure (Triebkorn et al., 2020). We have a first set of scripts allowing the conversion from the modeling and imaging data to the proposed standard but they are so far limited to the specifics of that particular study.

The goal of this project is to develop a user-friendly tool to store study details and data for full reproducibility of computational neuroscience modeling publications. We want to incorporate the existing tools for MRI data, like e.g. bidscoin, into our tool and possibly tools from other modalities.

As an end goal, it would be ideal to have a couple of diverse examples for using the developed tool in the form of computational modeling study publications prepared for sharing in this BIDS-conform standard. To be more user-friendly, the conversion tool should also offer a graphical user interface (Figure 1) where researchers can still add their user knowledge to the conversion tool. One could also aim for developing an extension of the bids-validator app for the newly developed standard to be able to easily check the validity and completeness of files.

For this project, we will need to stay in close communication with the research community. The GSOC contributor will be involved in the ongoing efforts of the neuroscience community to standardize the storage of data, code and simulation details. This will allow the GSOC contributor to build a large network involving different experts for the different modalities of neuroscience research. If successful, this project will represent the groundwork for future computational neuroscience studies offering an easy way to store the accompanying data and code in a standardized way enabling replication.

Lead mentor: Dr. Jil Meier @jilmeier (Charité Universitätsmedizin Berlin) - CET time zone

Co-mentors:

Dr. Michael Schirner @MichaelSchirner (Charité Universitätsmedizin Berlin, CET time zone),

Lia Domide @liadomide (Codemart, software development company based in Romania, EET time zone),

Prof. Daniele Marinazzo @Daniele_Marinazzo (Ghent University, CET time zone),

Prof. Petra Ritter @PetraRitter (Charité Universitätsmedizin Berlin, CET time zone)

Planned effort: 350 hours

Intended skill level: all levels welcome, project can be adapted to the contributor’s level

Pre-requisite skills: basic programming knowledge

Tech keywords: Python, docker, BIDS

Further references:

3 Likes

Hi! I am very interested in this project, could you let me know how I could proceed with this for GSoC?

Hello @jilmeier , @MichaelSchirner , I loved the project to develop a tool to easily store data and study details for computational neuroscience research and I would like to contribute to it.

Could you please tell me the how to proceed to get the background knowledge of this project and I also want to discuss to how to proceed further to develop it
Thank you

Hi @chiral-carbon,
In case you didn’t get your answer already:
I suggest you read as much as you ca about BIDS and TVB projects, and start composing a draft GSOC project proposal.
Then, as early as possible share that proposal draft with us, to get feedback if the direction is good or should be adjusted.
Best,
Lia

1 Like

Hi @tushar_gupta1.

We are happy to hear of your interest in this project.

I suggest you read as much as you ca about BIDS and TVB projects, and start composing a draft GSOC project proposal.
For TVB sources are https://github.com/the-virtual-brain/tvb-root, The Virtual Brain: Delivering practical results. For novel clinical applications., https://docs.thevirtualbrain.org/

Then, as early as possible share that proposal draft with us, to get feedback if the direction is good or should be adjusted.

Best,
Lia

Thank you for your response. I highly appreciate it .
I will certainly go through all the links you provided me with and then send you proposal for
feedback

Thank you once again

I’m Aya, a postgraduate computer science student with a pharmaceutical sciences undergraduate degree. I’m interested in scientific research, especially in applying computational methods to the biomedical field. I have read through the project description and the references provided, and the project idea grabbed my attention. As the BIDS concept of standardizing brain imaging data to make them easily accessible across different scientific groups is fascinating and aligns with the core principles of science and research. That’s why I’m excited to contribute to this project and would like to start building my proposal draft in the upcoming days.

Thank you

Hi @Aya_Alaa. We are happy to find about your interest in this project.
Please proceed to write your GSOC proposal. We would appreciate if you share the draft early with us, so that we can give you feedback before the final submit.
Best, Lia.

1 Like

Can I still submit a proposal for GSOC project@2 I am super excited about it and need to know that I still have time to be considered as a potential candidate to work on the project !

1 Like

Hi everyone, My name is Favour James from Lagos, Nigeria.

I am participating in GSOC for the first time and I would love to contribute to this project.
Please I would love guidance on how to understand the topic more and how to create a proposal for solving the problem. Thanks.

1 Like

Hi @Deependra_Singh ! Cool to hear that you are excited about our project! Sure, there is still time to submit your proposal until the 19th of April Google Summer of Code . We would appreciate if you share a draft of the proposal early with us such that we can give you feedback before the final submit. Hope to hear from you soon! Kind regards, Jil

Hi @Favourj-bit ! Great to read that you would like to contribute to our project! The deadline to submit your proposal is 19th of April Google Summer of Code . We would appreciate if you share a draft of the proposal as soon as possible with us such that we can give you feedback before the final submit. For preparing the proposal, please read the information provided in the links carefully and just start writing down your approach/ideas of how we could solve the project. Feel free to contact us via email as well. Hope to hear from you soon! Kind regards, Jil