Introduction (GitHub: xhgchen) and Suitable GSoC Projects

[Xu Hong Chen]

Hello everyone,

My name is Xu Hong Chen (GitHub: xhgchen) and I am a recent BSc Hons graduate in biochemistry from the University of Alberta who will be studying computer science this fall. I have 2 years of experience in molecular dynamics research with AMBER, during which I completed 3 research projects and trained 2 undergraduates in computational chemistry, so I am excited to contribute to MDAnalysis. I have read through the getting started pages, and I wanted to start a conversation here while I become more familiar with the code.

I am most interested in "Extend MDAnalysis Interoperability," "Molecular volume and surface analysis," and "Transport property calculations." Do you feel these projects are suitable for someone with my background, and is there any project in particular that would be best for me to work on? I am comfortable with basic C and Python and actively taking online CS courses.

Thank you! I look forward to taking part in improving MDAnalysis and following its impact on the scientific community.

Best regards,

Xu Hong

[hugomac...@gmail.com]

Hi Xu Hong Chen

Welcome to MDAnalysis!

Your background makes you very suitable to contribute to MDAnalysis. Any of the above projects would be relevant to your skills, it is up to you to choose one that interests you the most. Something to note is that MDAnalysis has not been formally accepted for GSOC yet this year. 

With regards to contributing:

In the first instance I would recommend our user guide as your first point of call for getting to know MDAnalysis: https://userguide.mdanalysis.org/stable/index.html. The user guide includes a section on how to contribute to the project. We also have several issues on our github repository labelled as "difficulty-easy" and "good-first-issue" which you may have to have a look at as good first time issues.

For questions about the project I would suggest posting on the MDAnalysis discussion (if it is usage based) or developer (if it is about contributing) mailing lists (see our github page for links to both). We also have a discord sever, see here for more details: https://www.mdanalysis.org/#participating.

With regards to Google Summer of Code (GSoC):

Whilst GSoC 2023 has been announced, MDAnalysis has yet to apply as an organisation (the deadline is ~ February), and likely won't hear about whether or not they will be selected until early March. MDAnalysis does plan on taking part again this year, but until Google makes a decision on participating organisations, there is always a chance that we may not be selected.

At this point in time, the only guidance I can provide is the MDAnalysis FAQ for GSoC from last year: https://github.com/MDAnalysis/mdanalysis/wiki/GSoC-FAQ#preparation

I would point you to the "preparation" section (https://github.com/MDAnalysis/mdanalysis/wiki/GSoC-FAQ#preparation). We will most likely have a very similar process to 2022, so at this point in time the best thing folks can do to prepare for GSoC would be to get familiar with, and aim to merge a code contribution against the MDAnalysis code base. We have "gsoc-starter" labelled issues which we deem to be good first issues for first time GSoC contributors (note there is a limit of one "gsoc-starter" issue per contributor per year).

Best regards,

Hugo

[Xu Hong Chen]

Hi Hugo,

Thank you for the thoughtful and thorough response. The tips you provided are extremely helpful, particularly the parts about communication.

I will follow up again about the projects after I have merged a code contribution, but for now, my top choice is "Molecular volume and surface analysis." I think adding these useful features for calculating molecular volume and SASA (solvent-accessible surface area) would be a rewarding experience. Nonetheless, I am also very interested in "Extend MDAnalysis Interoperability" and "Transport property calculations" and I would be happy to work on any of the three projects if all works out. I am hoping to make a pull request within the next week or two, depending on how long it takes me to become familiar with everything.

On the off chance that MDAnalysis is not selected for GSoC, I would still be interested in contributing.

Sincerely,

Xu Hong