GSoC Blog Post

What is this blog about?

This blog will cover my initial experience about Gooogle Summer Of Code with INCF(Organisation).

The Organization : INCF(International Neuroinformatics Coordinating Facility)

IINCF promotes the field of neuroinformatics and aims to advance data reuse and reproducibility in global brain research.

INCF works on exciting applications of computer science to medical data and serves as an umbrella organization to many projects being carried on throughout the world. The primary reason why INCF seemed like a natural fit to me was because of the following factors:

INCF has participated as a mentoring organization in GSoC since 2011. Interesting and well documented list of ideas (and that too released early around December). A very systematic, well-organized and welcoming community full of passionate highly qualified people from diverse backgrounds.

The Proposal

I started contributing in December 2023 all the way up-to April 2024 and began writing my Proposal around mid-March. After talking to my mentor I quickly made my first draft with a rough estimate of what is to be done. Writing a proposal is an iterative process. I made sure to get feedback from my mentor Ankur Sinha sir in the organisation. Regular feedback from him helped me to fine-tune my details about the time-line, adding more information and making the detailed process as much detailed as it can be.

My Experience?

In the initial phase of learning the basics of Machine Learning, a senior recommended that I watch the lectures of Geoffrey Hinton on Neural Networks. I watched the first few lectures and understood how neural networks are designed by taking reference from our brain. I was determined to know more about it and found out about the NeuroML Project. I started contributing to the NeuroML project by raising a pull request (PR). During this phase, my mentor Ankur Sinha Sir, helped me immensely with great patience in understanding the codebase. Unlike many other open-source projects this is very domain based and a basic understanding of our brain is very important.I kept on commiting to the PR, I worked on refactoring the spikes plotting file to make it more usable. Finally, I submitted my proposal after getting a brief idea of the codebase and my project and also after getting an assurance that I can contribute to the project.

I got selected for Google Summer of Code (GSoC). My GSoC project involves developing an interactive SWC to NeuroML converter in Python. The SWC format is widely used for representing neuronal morphology data, while NeuroML is a standardized format for describing biophysically detailed neuronal models. The converter I'll be working on will simplify the process of converting SWC data into the NeuroML format, making it easier for researchers to integrate morphological data into their computational models.

A SWC to NeuroML converter already exists on the neurosconstruct project developed by my other mentor Padraig Gleeson but it is written in JAVA and a Python based converter will make the PyneuroML project more complete.

One of the key components of my project is the development of an interactive tool that will allow users to visualize and manipulate the neuronal morphology data before converting it to NeuroML. This tool will provide researchers with a more hands-on approach to working with their data, enabling them to make adjustments and explore different scenarios before finalizing their models. To ensure the robustness and accuracy of the converter, I will be testing it against a range of neuronal reconstructions from the NeuroMorpho.org database. This extensive testing will help identify and address any potential issues or edge cases, ultimately leading to a more reliable and efficient conversion process.

I am thrilled to have the opportunity to contribute to the NeuroML community and the broader field of computational neuroscience. With my knowledge of Python, SWC, NeuroML, and some background in computational neuroscience, I am confident in my ability to take on this challenging project. The project will be hosted on the NeuroML GitHub page, ensuring transparency and collaboration within the open-source community. I am deeply grateful to Google for providing this incredible opportunity through the GSoC program and to my mentors, Ankur Sinha and Padraig Gleeson, for their guidance and support.

What's next?

In the coming posts, I plan to post about the technical challenges I will be facing while making through GSoC

I'll also share updates on any personal projects I'm working on and the lessons I learn along the way.

Thank you for joining me on this adventure! I'm looking forward to sharing my thoughts and experiences with you.

Happy reading!