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choderalab / openmoltools

An open set of tools for automating tasks relating to small molecules
MIT License
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Authorship #181

Open bannanc opened 8 years ago

bannanc commented 8 years ago

Hi,

@davidlmobley and I are working on a paper where we cite openmoltools. We are trying to figure out who should be included on the authors list.

Thank you! Caitlin

rmcgibbo commented 8 years ago

(Related: One easy thing is to set up the latest release with Zenodo, because that'll give you a citable DOI for the code: https://guides.github.com/activities/citable-code/)

davidlmobley commented 8 years ago

@rmcgibbo - cool, that's helpful.

To others: Relating to authorship - one thing we probably ought to also do is have a list of authors, or at least primary authors (???) in the README.md to make it more accessible. How is this normally done? I've not been involved much with "big" packages before - not that this is big yet, but there are a reasonable number of people who have contributed at least something. Do we have some sort of list of people who have contributed "a lot" and those are the main authors, and other people are acknowledged?

rmcgibbo commented 8 years ago

How is this normally done?

I have never done anything particularly formal for projects that I've participated in (github already shows the contributor graph with various visualizations), but I know cpptraj has a pretty nice list in the README of all of the authors and how they've contributed over the years.

jchodera commented 8 years ago

The code in this repo is just kind of a random grab-bag of stuff the either has been published (e.g. the ThermoML Archive Benchmark paper) or hasn't yet been published. Which parts of openmmtools are you using?

Also, do you want to be able to cite a specific version of openmmtools for which you are also releasing scripts? If so, cutting a release that is also connected to Zenodo sounds like it might be a reasonable idea.

davidlmobley commented 8 years ago

In this particular case it's a variety of things from the openeye, gromacs, amber, and packmol modules, including a number of things we wrote ourselves from scratch and others which Kyle or others had written already. We can make a first approximation of authorship by reading code/thinking about it, but I wanted to raise the larger issue of how to attribute authorship for the package as a whole, since someone citing it presumably will want to be able to list authors.

And yes, we'll want to cite a specific version which already has a version tag. I was not aware of Zenodo so I'll look into that as it'll be helpful.

On Thu, Jan 28, 2016 at 2:17 PM, John Chodera notifications@github.com wrote:

The code in this repo is just kind of a random grab-bag of stuff the either has been published (e.g. the ThermoML Archive Benchmark paper) or hasn't yet been published. Which parts of openmmtools are you using?

Also, do you want to be able to cite a specific version of openmmtools for which you are also releasing scripts? If so, cutting a release that is also connected to Zenodo sounds like it might be a reasonable idea.

— Reply to this email directly or view it on GitHub https://github.com/choderalab/openmoltools/issues/181#issuecomment-176447011 .

David Mobley dmobley@gmail.com 949-385-2436