Introduction & statement of interest for P1 & P5

[Egor Marin]

Hi everyone, my name is Egor, I'm finishing my PhD in structural biology in the Univesrity of Groningen.

I've had much experience in protein crystallography throughout my BSc/MSc (articles here). Having this experience and occasional experience with python/bash for simple scripting/data analysis in experimental science, I'm now transitioning towards more software-related projects.

List of technical things I've done you might check out on my github. The interesting parts would be i) stil-utils "package", with bunch of scripts that greatly simplified my workflow with serial crystallography & increased reproducibility; ii) a contribution to reciprocalspaceship package -- I wrote a parser for specific type of data; iii) insanely useful job processing notification bot ntfy_cryosparc, which parses responses simple PUSH requests from data processing software and sends push notification to a user who created the job via ntfy.sh

For MDAnalysis, I'm particularly curious about 2 projects -- P5 (parallel analysis) & P1 (generalize groups), and not yet sure how to decide between these two. P1 seems pretty straightforward and convenient to use, increasing the analysis reproducibility in general (and I love reproducibility), whereas P5 is closer to my HPC experience & current interests, especially given that I currently have access to a univesity cluster and might test different distributed benchmarks & decide which one is worth using for the backend.

If there's any project prioritization from the devs group that might help me focus on one of the projects for the future proposal, I'd be happy to know that :)

P.S. this is my second open-source contribution, and I'm still impressed how I can follow instructions on "Contribute" page, simply configure the environment and the tests just run smoothly from the first time😯

[Egor Marin]

>and might test different distributed benchmarks & decide which one is worth using for the backend

oh wow, I read the project proposal once again, as well as the pmda library, and now understand that the main idea is to adapt *multiple* backends, which is even more interesting and challenging! But the initial introduction contained an error, sorry about that.

[Project Manager MDAnalysis]

Hi Egor,

Thank you for your introduction, and welcome to MDAnalysis! We are happy to hear that you have had good experiences with the contributing page in the user guide.

Regarding project selection, it is completely up to you to decide which project would best fit your skills and interests. Once you are familiar with the MDAnalysis package, the best way to decide on a project is to explore open issues and start contributing. Since you are interested in Project 1, you may want to specifically check out related issues 1861 and 2188.

As per the FAQ, candidates must have code merged to be eligible to apply to GSoC with MDAnalysis. On the MDAnalysis repository, you can find several issues tagged with "good first issue", "Difficulty easy", or "GSoC Starter". Please bear in mind, you can only attempt one issue tagged as a GSoC Starter. Note also that we do not assign issues to people; we review the first pull request (PR) that solves an issue. Therefore, you can work on any issue you would like that does not already have an open/active PR against it. We also strongly suggest to work on a single issue/PR at a time. Once you have one PR merged, you are of course very welcome to tackle another issue, and so on.

We look forward to your contribution.

All the best,
Jenna

 | Project, Community and Outreach Manager

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[Egor Marin]

Hi Jenna, I wonder, are there any good first issues specific for project 5? 

I looked through the gsoc-starter issues briefly, and couldn't find anything that might look relatable.

If no -- it's not a problem, I can work on any other issue.

E M

[Project Manager MDAnalysis]

Hi Egor,

For Project 5, it would be a good idea to learn more about writing analysis tools (using AnalysisBase). For example, you may want to give issue 3190 a shot.

Best wishes,
Jenna