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

Michael R Shirts Michael.Shirts at Colorado.EDU
Wed Mar 18 20:33:26 CET 2020

I’m not sure I’m 100% the right person, but I could be involved at some level.   Keep me posted.

Michael Shirts
Associate Professor
michael.shirts at colorado.edu
Phone: (303) 735-7860
Office: JSCBB C123
Department of Chemical and Biological Engineering
University of Colorado Boulder

From: <gromacs.org_gmx-developers-bounces at maillist.sys.kth.se> on behalf of Oliver Beckstein <obeckste at asu.edu>
Reply-To: "gmx-developers at gromacs.org" <gmx-developers at gromacs.org>
Date: Wednesday, March 18, 2020 at 12:20 PM
To: GROMACS Developer List <gromacs.org_gmx-developers at maillist.sys.kth.se>
Cc: Max Linke <max.linke88 at gmail.com>, Richard Gowers <richardjgowers at gmail.com>
Subject: [gmx-developers] looking for co-mentor for GSoC 2020: TNG format

Hello Gromacs Developers,

As part of Google Summer of Code 2020 with MDAnalysis<https://secure-web.cisco.com/1k3k6ClP2T8HoZmsCuxa4t_WSUMfGp-LzKHUuqt0Wkb6SxdKWPo-pbmOBh40x2w80eUbrX16NqCo6AYekG7o1sFNJamogMRZS8W2Gd-R11OM1YRK5uhwhSERo5xcBI1bchkU15xw5sEKmlCYsEqZpSb2lUrrzNrKe8Vk2AofjmlU-w_QUMH1iJiVzN_7nUDz6WHfPFi_lvqqL-cW-P38ZDihGe2egL-V0fU0A9vpmNkmgTyrE5gwcEoDX3_OBodBNMGbHSkjzQ1pL2gh7u9jW3KaIGCnKewKRQh-0lUOVZBWG5xEXIgPoN42Rw0ILCk7K8DwzPly3zHqycWhGHG33yc-GCrC2gs-YpqJoFvM-XTgSN0thduzTwF0m-XKoq-chTl_QdrxY4DD87IR6KENoIWNPyNvDBVj4bwdN7NPANnNd1eZfILokdkFa-Y4QTAlSKYmlM4ISE1GLJO6K-HJXjg/https%3A%2F%2Fwww.mdanalysis.org%2F2020%2F02%2F22%2Fgsoc2020%2F%23google-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:

  1.  Fully define the API and capabilities of TNG.
  2.  Write documentation.
  3.  Write a reference library implementation (C or C++).
  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>

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

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