Introduction (ghuser : ooprathamm)

[Pratham Chauhan]

Greetings, My name is Pratham Chauhan. I'm sending you this email to introduce myself and to let you know that I'm interested in working on your package as part of the Google Summer of Code (GSoC) initiative.

I've always been passionate about researching new skills required to solve the problem at hand. When I came across your project, I was impressed by the way you are using your software to try and solve problems related to molecular dynamics simulations. I have intermediate Python skills. I think your project is exactly what aligns with my interests, and it would be a great way for me to expand my knowledge and develop new skills.

Currently exploring your package has been really fun and has got me intrigued.

Thank you for your time.
Best regards,
Pratham

[Estefania Ojeda]

Hello Pratham and welcome to MDAnalysis!

Apologies for the delay in our reply, we do appreciate your interest in our MDAnalysis GSoC program!

If you are familiar with MDAnalysis and you are interested in contributing, please check the contributing section of the User Guide:  
https://userguide.mdanalysis.org/stable/contributing.html 

As per the MDA GSoC FAQ https://github.com/MDAnalysis/mdanalysis/wiki/GSoC-FAQ,  candidates must have code merged to be eligible to apply for GSoC with MDAnalysis (see https://github.com/MDAnalysis/mdanalysis/wiki/GSoC-FAQ#what-should-i-do-for-a-successful-proposal)

If you already have contributions, please let us know you GitHub handle and the issues you have fixed. It is also helpful for GSoC mentors to know which project you would like to work on (see https://www.mdanalysis.org/2023/02/22/gsoc2023/#project-ideas). Or if you have your own idea about a potential project, please also let us know.
 

Our blog post https://www.mdanalysis.org/2023/02/22/gsoc2023/ is the starting point for all GSoC 2023 things. We have a FAQ page as well https://github.com/MDAnalysis/mdanalysis/wiki/GSoC-FAQ  

Cheers,

Estefania

[Pratham Chauhan]

GitHub handle - ooprathamm (github.com)

Providing the list of contributon as asked 

Merged -

1. Fix doctest for MDAnalysis.analysis.psa (Part of #3925) (PR - #4035)

2. [doc] Resolving doc index issue.  (Issue #3998) (PR - #4011)

3. Fix doctest for MDAnalysis.core.topology (Part of #3925) (PR - #4024)

4. filtering warnings (Issue - #3986) (PR - #4010) (GSOC LABEL)

Under Review -

1. solves failing benchmark analysis.rms  (Issue #3520) (PR - #4065)

2. Updates testsuite/MDAnalysisTests/analysis/test_nucleicacids.py (PR - #4051)

I wish to apply for Project 4: Transport property calculations & Project 5: Implementation of parallel analysis in MDAnalysis.

Please guide me through relevant skills required and issues I could see regarding the same.

Thank you for your time.
Best regards,
Pratham

[Project Manager MDAnalysis]

Hi Pratham,

Thank you for sending your contributions and project interests! The skills required for the suggested projects are outlined on the Project Ideas page of the MDAnalysis Wiki. Aside from good knowledge of programming in Python, it is beneficial to have a good grasp of Mathematics/Physics for Project 4 and Parallel Programming/MD for Project 5. For both projects, we recommend learning about writing analysis tools (using AnalysisBase). To explore the projects with some hands-on coding, you can working with the existing diffusion code (related to Project 4) or try out issue 3190 (related to Project 5). 

We look forward to reviewing your proposal.

All the best,
Jenna

Project, Community and Outreach Manager

MDAnalysis * https://www.mdanalysis.org/

a fiscally sponsored project of NumFOCUS

Twitter: @mdanalysis

Github: https://github.com/MDAnalysis

[Pratham Chauhan]

We are all familiar with the problem of fewer computational resources available. The ready-to-go fix I use to use when doing some hands-on was using Google colab. So it comes to my mind when I was using MDAnalysis on my machine locally to have a plugin to easily have this code deployed in a notebook on the cloud.

Features this notebook could provide -

1. Have functions to manage long workflows (or periodic)

2. provide periodic updates for the analysis

3. quickly generate visualizations based on the data (plots etc.)

4. For large datasets provide real-time updates rather than waiting for the completion 

5. A bot to do (2.) after a defined step (Like Twitter Bots)

I know this is not a detailed idea, but I would really like to discuss more on this if felt feasible by the maintainers :)

Sincerely,

Pratham Chauhan 

[Project Manager MDAnalysis]

Hi Pratham,

Thank you for sharing your idea for an original project! Now that the Google Summer of Code proposal period has opened, I would suggest you register as a contributor and submit your project idea as a proposal to seek feedback from the MDAnalysis mentors. Per recent discussion in the #gsoc channel of our Discord server, please upload a PDF (`DRAFT` in the file name) of your proposal - which includes a Google doc link to your proposal - to the GSoC program website. Mentors can then provide feedback directly on your Google doc. When you are ready to submit the final version of your proposal, you can export your Google doc proposal as a PDF and re-upload to the GSoC site.

Keep in mind that you are allowed to submit up to three (3) project proposals. If you would like, you are welcome to submit proposals for Projects 4 and/or 5 as you previously indicated in your interests, in addition to this original project idea.

Best wishes,
Jenna

Project, Community and Outreach Manager

MDAnalysis * https://www.mdanalysis.org/

a fiscally sponsored project of NumFOCUS

Twitter: @mdanalysis

Github: https://github.com/MDAnalysis

[Pratham Chauhan]

Respected MDAnalysis team,

I have submitted a proposal for Project 4: Transport property calculations on GSoC program website. 

It would be really helpful if the respected mentors could review it and provide their feedback and deep insights.

Thank you for your time.

Pratham