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Becksteinlab / GromacsWrapper

GromacsWrapper wraps system calls to GROMACS tools into thin Python classes (GROMACS 4.6.5 - 2024 supported).
https://gromacswrapper.readthedocs.org
GNU General Public License v3.0
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JOSS paper #147

Open orbeckst opened 6 years ago

orbeckst commented 6 years ago

Write a short software paper on GromacsWrapper for JOSS.

richardjgowers commented 6 years ago

I'd be interested in this. I'm going to try and get coverage higher (and find any easy bugs)

orbeckst commented 6 years ago

The more coverage the more Unicode issues raise their head....

So yes, more tests would be super!

-- Oliver Beckstein email: orbeckst@gmail.com

Am Aug 11, 2018 um 13:43 schrieb Richard Gowers notifications@github.com:

I'd be interested in this. I'm going to try and get coverage higher (and find any easy bugs)

— You are receiving this because you were assigned. Reply to this email directly, view it on GitHub, or mute the thread.

orbeckst commented 6 years ago

@pslacerda @jandom @kain88-de @dotsdl @whitead @richardjgowers @ianmkenney @AndySomogyi @PicoCentauri @mohebifar – thank you for contributing to GromacsWrapper. I'd like to write a short Journal of Open Source Software paper. If you are interested in being an author on this mini-paper then please reply on this issue.

At a minimum, you will need to read the draft of the paper, make corrections if necessary, and ok it. I would also expect willingness in helping to respond to referees' requests for revisions.

I will create a repo for the paper and invite everyone who wants to be an author. Anyone who does not want to be an author will be acknowledged in the acknowledgements (unless they do not want to be mentioned at all).

The top of this issue has links to JOSS and the author instructions.

— @orbeckst

Oliver Beckstein, DPhil * @orbeckst https://becksteinlab.physics.asu.edu/

Associate Professor of Physics Arizona State University Center for Biological Physics and Department of Physics Tempe, AZ 85287-1504 USA

Department of Physics: https://physics.asu.edu/content/oliver-beckstein Center for Biological Physics: https://cbp.asu.edu/content/oliver-beckstein

AndySomogyi commented 6 years ago

Hi Oliver.

I not sure I’ve contributed a huge amount, but I’d very much like to help in writing and editing a paper. Let me know what you’d like me to do.

Sent from my iPhone

On Aug 16, 2018, at 9:39 PM, Oliver Beckstein notifications@github.com wrote:

@pslacerda @jandom @kain88-de @dotsdl @whitead @richardjgowers @ianmkenney @AndySomogyi @PicoCentauri @mohebifar – thank you for contributing to GromacsWrapper. I'd like to write a short Journal of Open Source Software paper. If you are interested in being an author on this mini-paper then please reply on this issue.

At a minimum, you will need to read the draft of the paper, make corrections if necessary, and ok it. I would also expect willingness in helping to respond to referees' requests for revisions.

I will create a repo for the paper and invite everyone who wants to be an author. Anyone who does not want to be an author will be acknowledged in the acknowledgements (unless they do not want to be mentioned at all).

The top of this issue has links to JOSS and the author instructions.

— @orbeckst

Oliver Beckstein, DPhil * @orbeckst https://becksteinlab.physics.asu.edu/

Associate Professor of Physics Arizona State University Center for Biological Physics and Department of Physics Tempe, AZ 85287-1504 USA

Department of Physics: https://physics.asu.edu/content/oliver-beckstein Center for Biological Physics: https://cbp.asu.edu/content/oliver-beckstein

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

PicoCentauri commented 6 years ago

Following @AndySomogyi I would also be happy if I can contribute anything to the paper!

pslacerda commented 6 years ago

Of course I want!

I'm had almost forgot about MD but in the last months I did some modelling and I very want to do more (and submit the JOSS paper).

If you have Telegram would be nice to chat there (I can create a group) and my email is the one I sign the commits.

orbeckst commented 6 years ago

If you have Telegram would be nice to chat there (I can create a group) and my email is the one I sign the commits.

I think we can just use the issue tracker for discussion, then everything is in one place. Use this thread for general discussion, open new issues for anything specific and reference #147 in the new issues in order to link them back to this master issue.

orbeckst commented 6 years ago

I opened PR #158 with a stub for the paper. Please add your author meta data. I assume that you can leave anything empty that you do not want to provide.

orbeckst commented 6 years ago

Anyone else who wants to be an author on the paper should just announce it in this thread – there's no cut-off until it is submitted.

jandom commented 6 years ago

Yup, i'm on board!

ianmkenney commented 6 years ago

I'll contribute to the paper

orbeckst commented 6 years ago

@pslacerda was concerned about the suitability of a "thin wrapper" for JOSS. I stated my opinion https://github.com/Becksteinlab/GromacsWrapper/issues/159#issuecomment-414742062 but will repeat it here as it fits better in this thread:

But first I'm worried about the acceptance criteria of JOSS for binding libraries.

I don't think that is a worry. The library enabled us to create other packages such as https://github.com/Becksteinlab/MDPOW that has been used in three papers at least. It also contains new code (e.g., in gromacs/setup.py). It is useful for constructing workflows (e.g. in https://github.com/Becksteinlab/mdworks). Only recently has there been made a serious attempt at a Gromacs Python API https://github.com/kassonlab/gmxapi , which looks great but still requires changes in the Gromacs sources. We will certainly cite gmxapi but also point out that the GromacsWrapper approach works with different versions of Gromacs, which allows version-independent scripts.

whitead commented 6 years ago

Hi, I'd be happy to help to the article and be listed as a co-author for my small contribution to the repo. I will get the requested info next week. Thanks again to all the contributors for making this useful package!

Regarding acceptance criteria, I also agree that this should pass the criteria. I've needed to cite this tool in my own work and it really enables workflows impossible with Gromacs alone, especially for high-throughput simulations and complex multi-step simulations. It also wows students in my class when we can do MD in a jupyter notebook.

dotsdl commented 6 years ago

I have limited bandwidth at the moment, but I'd be happy to contribute to the paper as much as I can. I want to function in a supporting role in building the draft, and am happy to take direction to help distribute the load.

AndySomogyi commented 6 years ago

Am I reading this correctly that the paper should only about 1000 words?

I'm going to give the other papers there a read, and post some thoughts on how to best describe GromacsWrapper in only 1000 words.

orbeckst commented 6 years ago

Am I reading this correctly that the paper should only about 1000 words?

Yes!

The reviewers will also look at documentation, try to install it, try to run a simple tutorial (that's why #159 is important), look if we have CI with tests, etc.

The review will happen on the issue tracker. If you find some of the JOSS papers under review then you'll see what typical reviewer comments are.

mohebifar commented 6 years ago

I changed only a few lines of the code, and I don't really know much about the whole library's code. I also haven't even used Gromacs for over a year now. However, I would still love to help as much as I can.

I think I can proofread the drafts, but I don't believe it's fair to be listed as a co-author for such a tiny contribution!

orbeckst commented 6 years ago

I don't believe it's fair to be listed as a co-author for such a tiny contribution!

@mohebifar , my opinion for software papers is that anyone who makes a valuable contribution (i.e., something that gets merged) should be recognized and should have a shot at authorship. If you don't want the additional responsibilities (see top of the issue https://github.com/Becksteinlab/GromacsWrapper/issues/147#issue-349054806) – and some people don't! – or if you don't want to be listed as an author then that's totally fine and we would like to acknowledge you. Either way, you should have the choice. Just let me know how to proceed:

  1. author or
  2. acknowledgements or
  3. no mention at all?

(EDIT: proof-reading is always welcome, no matter what you choose, thank you)

mohebifar commented 6 years ago

Thanks @orbeckst! I definitely want to be an author!

Is there a specific deadline for submission? I have got my master's thesis back from reviewers this week, so there is a little bit of work there that hopefully I will get done by the end of this week. I think I will be able to start working on the JOSS paper next week or a week after that.

orbeckst commented 5 years ago

Sorry everyone, been occupied with other things. No firm promises on when this JOSS paper is going to happen, but will happen eventually (preferrably in 2019).