[gmx-developers] looking for co-mentor for GSoC 2020: TNG format

David van der Spoel spoel at xray.bmc.uu.se
Wed Mar 18 21:17:37 CET 2020

Den 2020-03-18 kl. 19:20, skrev Oliver Beckstein:
> Hello Gromacs Developers,
> As part of Google Summer of Code 2020 with MDAnalysis 
> <https://www.mdanalysis.org/2020/02/22/gsoc2020/#google-summer-of-code-2020>  
> we proposed a project to work on the TNG format. Originally the plan was 
> to just make sure that MDAnalysis can work with TNG but after a chat 
> with Erik at BPS (and in the spirit of the last MolSSI interoperability 
> workshop) we thought that it would be more useful to take a step back 
> and possibly work towards finalizing the TNG format 
> <https://github.com/MDAnalysis/mdanalysis/wiki/Project-Ideas-2020#project-6-implement-tng-support> with 
> the goal to make it usable in any MD analysis code (including 
> MDAnalysis). The preliminary objectives would be:

Great initiative!

>  1. Fully define the API and capabilities of TNG.
The existing functionality or would you add stuff that has been 
disccussed for a long time like energies and other data blocks?

>  2. Write documentation.
>  3. Write a reference library implementation (C or C++).
How would that be different from the existing implementation?

>  4. Write tests.
>  5. Bonus: Write Python bindings (see start in our pytng
>     <https://github.com/MDAnalysis/pytng> library) and integrate with
>     MDAnalysis

> This project outline is not set in stone and we would be more than happy 
> to adapt it according to your expert input.
> We have at least one promising candidate student who is interested in 
> working on this project during 10 weeks this summer.
> We would need at least one knowledgable co-mentor from the GROMACS 
> developer community who could commit to mentoring. See 
> https://google.github.io/gsocguides/mentor/ what is expected of mentors. 
> In short, you would be involved in selecting students, communicating 
> with the student (primarily using mailing lists and issue trackers) on a 
> near-daily basis, help with keeping the project on track, and evaluating 
> the student for GSoC (midterm and final evaluation at pass/fail level). 
> About 5h/week is a realistic minimum.
> We completely understand that in the current global crisis, you might 
> have more urgent things to do. But if you think that you could be a 
> co-mentor for this project, please let us know soon because students 
> have to write their applications; their deadline is March 31 but they 
> can submit applications now and unless we have a GROMACS co-mentor we 
> will not be offering the TNG project so students.
> Thank you!
> Oliver (for the MDAnalysis GSoC 2020 Mentors)
> --
> Oliver Beckstein, DPhil * oliver.beckstein at asu.edu 
> <mailto:oliver.beckstein at asu.edu>
> https://becksteinlab.physics.asu.edu/
> Associate Professor of Physics
> Arizona State University
> Center for Biological Physics and Department of Physics
> Tempe, AZ 85287-1504
> Office: PSF 348
> Phone: +1 (480) 727-9765
> FAX: +1 (480) 965-4669
> Department of Physics: https://physics.asu.edu/content/oliver-beckstein
> Center for Biological Physics: https://cbp.asu.edu/content/oliver-beckstein

David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.

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