GSoC Applicant: Introduction

[Estefania Ojeda]

Hello MDAnalysis team,

I am Estefania Barreto-Ojeda. Last year Ph.D. student in Biophysical Chemistry at the University of Calgary.  I'm interested in solving problems in biophysics, in particular membrane curvature. There is a project I've been working on and would like to integrate into MDAnalysis, if possible.

 

Selected issue #3209 on GitHub. 

Cheers, 

E.

 

[Lily Wang]

Dear Estefania,

Welcome to MDAnalysis! Thank you for introducing yourself. As there is only a week left until the GSOC deadline, please feel free to share your proposal with us while you’re working on the issue. That way mentors can provide feedback and ask questions before submission.

If you are unfamiliar with MDAnalysis and Google Summer of Code, we suggest you read the blog post  and the FAQ . We recommend to do the Quickstart Tutorial and read the User Guide to get a better sense of what MDAnalysis does and how it is used.

Cheers,

Lily

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[Estefania Ojeda]

Hi Lily,

I expect to get the issue solved soon. I'll share the details of the project in the next few days.

Thanks!

My GitHub: https://github.com/ojeda-e

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Estefania Barreto-Ojeda

PhD Candidate Biophysical Chemistry

Centre for Molecular Simulation

VP Finances - BGSA

University of Calgary, AB, Canada.

http://bit.ly/30Y2LWj

[Estefania Ojeda]

Hi Lily,

Now that the PR was merged I would like to provide more details about my proposal and ask you a couple of questions.

- Proposal.
I have been working on a python workflow to calculate membrane curvature out of trajectory + coordinate files from CG MD simulations. The calculation is performed using phospholipid head groups. The backbone of the code is there, it works, it's fast (it runs 2.5K frames in <1min with each frame comprising ~5K lipid headgroups) and it is automated to some extent. Essentially, it calculates the mean ($K_M$) and Gaussian curvature ($K_G$), and it plots the resulting values of $K_M$ and $K_G$ in contours or imshow using matplotlib. However, the next step I was considering was to translate the Python code from functional to object-oriented. And this sense, GSoC with MDAnalysis is a great opportunity to make this happen. Another point is that after working on the PR that was recently merged I have a better understanding of how pytest works, so I could also write the test for it. 

In summary, I would like to write a curvature_analysis.py and test_curvature_analysis.py to calculate membrane curvature in terms of mean and gaussian curvature descriptors.

I think it would be super cool. Happy to share your feedback and opinions.

- Questions
As part of the applications process I should:
1) Introduce my self on the mailing list [Checked]
2) Close an issue of MDAnalysis. [Checked, issue #3209 and PR #3219]

3) Student Registration at https://summerofcode.withgoogle.com/student-signup/

4) Proposal Submission.
For the last one, I am not sure where to find the guidelines and I would appreciate your help with it in case you are ok with my proposal. 

I'm open to discussing my idea in more detail and provide a timeline if you consider it appropriate.

Thanks!

[Lily Wang]

Hi Estefania,

That sounds like it would be a great addition to MDAnalysis. GSoC does ask for a full-fledged proposal, and you can find guidelines for this in the FAQ,  wiki and Google’s own guide. Our evaluation criteria are here. Basically we look for:

1. impact (what does the new functionality do for users of MDAnalysis? Is it something that’s been missing?)
2. feasibility (you can do it in the GSoC time frame)

3. good use of resources (a good match between your project, your background, and mentors’ expertise)

Your project could describe the equations and workflow you propose to use, for example. If you write up a draft before the submission date and show us, mentors will be able to give feedback, which also usually results in a stronger application. You could also ask questions on our Discord for a more casual messaging space. I hope that helps!

Cheers,

Lily

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[Estefania Ojeda]

Hi Lily,

thanks for your kind reply, your help is very appreciated here!

I have a draft of the proposal ready for review. You can find it in this google doc.  
Looking forward to hearing back from you soon!

Cheers,

Estefania.

[Estefania Ojeda]

Hugo, Lily, Richard: Thanks for all your feedback and comments!

I modified the proposal according to the questions/concerns that were raised. Main changes are

- Reference of similar existing tools added (introduction, page 2).
- Challenges and limitations section was updated ( using leafletfinder in bent membranes or extending to other box types, page 7).

- Milestones updated (one added: cookbook/tutorials, page 8)

- Timeline updated (page 10).

I left the thread of comments that discusses leaflet identification using leafletfinder vs parsed by the user, in case questions were not sufficiently answered and I should provide more details.

A question from Hugo on page 6 is still open. 

Here the doc for a second review. 

Thanks!

[Estefania Ojeda]

Hello MDAnalysis team.

I added some lines and references to answer the most recent comments (mainly from Lily and Hugo).

The doc is ready for (hopefully) the last review!

Best,

[Richard Gowers]

Hello

Thanks for the update.  Make sure you have completed the application on https://summerofcode.withgoogle.com/ the deadline is very soon.

Richard

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[Estefania Ojeda]

Thanks,

I will submit the proposal briefly.

Best,

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Estefania Barreto-Ojeda

PhD Candidate Biophysical Chemistry

Centre for Molecular Simulation

[Estefania Ojeda]

Although apparently all steps are completed and the proposal is submitted, haven't received any notification yet. 

Would you please confirm the application status?

Thanks

VP Finances - BGSA

University of Calgary, AB, Canada.

http://bit.ly/30Y2LWj

[Oliver Beckstein]

Hi Estefania,

I see your proposal in “Final” status.

Oliver

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Oliver Beckstein (he/his/him)

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[Estefania Ojeda]

Thanks for your answer,

I guess the application will be fully submitted after the deadline. 

Best,

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