[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
> 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:
> 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
> 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>
> 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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