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popsim-consortium / adding-species-manuscript

manuscript materials for the adding species paper
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create list of authors #32

Closed andrewkern closed 2 years ago

andrewkern commented 2 years ago

Here is the current proposal for author list (TODO: determine order within sections; currently alphabetical). Criteria for inclusion (esp in the middle section of authors) is low - contribution of a species, or improvement of the documentation, or addition of a demographic model, or QC'ing a species, all count. I'll be emailing people to check if they want to be on here (and, encouraging people to QC an un-QC'ed species if they'd like), but we're all happy with including the whole list:

and then

and then

and then

and then

lauterbur commented 2 years ago

Workshop helpers (those not yet included on the author list):

Hackathon attendees (those who put a species on sign up sheet, need to confirm they participated)

gregorgorjanc commented 2 years ago

Ignacio Echevarria @iechevarriaz started the BosTau implementation, but had to move on, so I took it over.

https://github.com/popsim-consortium/stdpopsim/pull/558

jeromekelleher commented 2 years ago

Looks good to me @lauterbur. One person who seems to be missing is @grahamgower - he was one the helpers in the Europe time zone.

petrelharp commented 2 years ago

Checking some other places: we've got all the contributors to the workshops repo. Looking back at meeting notes, names I see on this discussion not listed above are Reed Cartwright, lots of Jeff Adrion.

I've looked through all the contributors to the stdpopsim repo for docs and things not analysis2-related since the first paper (july 2020); here's everyone not already listed above. I think everyone here goes in or could go in if they finish off whatever it is they were working on - I will go through and check for dangling bits.

There is however an important question here: some of these people are here because they have added demographic models, not new species - should they go on this paper, or on the analysis2 paper? (Or, something else?)

There's also hyanwong and awohns who put in a few very minor (but useful!) fixups; not sure whether to add them? And, three or four people with like 1 to 5-line fixups, like ragreenburg, that I'm leaving out.

apragsdale commented 2 years ago

I do not think I should be an author on this paper, as it's not something I've focused on.

petrelharp commented 2 years ago

And, and looking at the issues, some more to add:

petrelharp commented 2 years ago

I do not think I should be an author on this paper, as it's not something I've focused on.

Up to you, but that's not our authorship model here, I think? You've made enough contributions that you should definitely be an author on some stdpopsim paper; we might discuss whether that's this paper or not. And, remember that if it's not something you've focused on then you'll be one of a bunch of middle authors? What do you think?

ShyamieG commented 2 years ago

I also should not be included on this paper - I was not able to contribute the species I had planned to, unfortunately. I do hope to be able to come back to this in the future, though.

manolofperez commented 2 years ago

Hi Peter,

Thanks for the email. I also don't feel that I have done enough to deserve autorship on this paper. Though I have added one species, I was not able to contribute further.

The workshop was really useful by the way, I learned a lot. I hope I can manage to come back to contribute to this great community.

Em ter., 26 de abr. de 2022 15:49, Shyamalika Gopalan < @.***> escreveu:

I also should not be included on this paper - I was not able to contribute the species I had planned to, unfortunately. I do hope to be able to come back to this in the future, though.

— Reply to this email directly, view it on GitHub https://github.com/popsim-consortium/adding-species-manuscript/issues/32#issuecomment-1110136814, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABBXHUSDJCU23PXPMEUW6PLVHA3EFANCNFSM5T6ALQYA . You are receiving this because you were mentioned.Message ID: @.*** com>

petrelharp commented 2 years ago 
Thanks for the email. I also don't feel that I have done enough to deserve
autorship on this paper. Though I have added one species, I was not able to
contribute further.

Ah-ha - I think that adding one species is definitely enough for inclusion! (We're not saying "all authors contributed equally", remember!) But, clearly we need some discussion about authorship exepectations, which we can have at next weeks' meeting.

mufernando commented 2 years ago

I haven't contributed to the species part, so I do not want to be included as an author.

percyfal commented 2 years ago

I don't think I should be in this paper either although I did initiate the addition of one species during the workshop. However, the species was not suggested by me, nor did I complete the task. To echo some previous sentiments, the workshop was really great and I hope there will be another opportunity further ahead to contribute more.

fbaumdicker commented 2 years ago

I would be happy to be considered as a co-author for this manuscript. However, there are some small tests missing to support gene conversion, which I should be able to finish within this week. I am using the potential authorship as an incentive to get this done as soon as possible. However, if you feel that this is not the right time or place to include the GC stuff to stdpopsim, I would understand.

petrelharp commented 2 years ago

Great, let's get it in here @fbaumdicker!

agladstein commented 2 years ago

I'm happy to be a coauthor. What is the timeline here? I'm trying to find time to review the manuscript.

lauterbur commented 2 years ago

Great, @agladstein ! @gphocs-dev (Ilan) and @dschride are taking a close look this week and we anticipate some substantial changes, but we're hoping to get this pushed through pretty quickly after that. If you can find time next week that would probably work well.

petrelharp commented 2 years ago

As discussed at today's meeting, I'm going to make a proposed ordering, with the following categories:

  1. elise
  2. central organizers/movers on the junior side
  3. middle junior people
  4. middle senior people
  5. central organizers/writers on the senior side
  6. ilan

If you've got concerns about the framework (or the details), please let us know.

petrelharp commented 2 years ago

OK, updated! I'm not a fan of the "junior/senior" division, and I think that (3) and (4) ought to be merged, really.

petrelharp commented 2 years ago

I'm not finding emails for these people - if anyone knows, let me know (via email or slack): @iechevarriaz @platipo

gregorgorjanc commented 2 years ago

Ignacio Echevarría @.***>

With regards, Gregor

On Tue, May 3 2022 at 9:52 pm, Peter Ralph @.***> wrote:

I'm not finding emails for these people - if anyone knows, let me know (via email or slack): @iechevarriaz https://github.com/iechevarriaz @platipo https://github.com/platipo

— Reply to this email directly, view it on GitHub https://github.com/popsim-consortium/adding-species-manuscript/issues/32#issuecomment-1116448061, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAFRGSQTW37QWBBCKRQIVVDVIFYVNANCNFSM5T6ALQYA . You are receiving this because you were mentioned.Message ID: @.*** com>

reedacartwright commented 2 years ago

I'm glad to be a coauthor.

reedacartwright commented 2 years ago

One advantage of having large author lists for community projects like this is that there are certain NIH and NSF grants available for scientific networks, and these author lists can be used to demonstrate the effectiveness of the network already.

hyanwong commented 2 years ago

I'm happy to be a coauthor (although as Peter says, I've only made a few tweaks here and there, I imagine I might carry on contributing improvements in the future).

aays commented 2 years ago

Happy to be a co-author - very glad to be included! I'm looking forward to using stdpopsim for C. reinhardtii simulations in the future.

gtsambos commented 2 years ago

Hiya! Thanks for including me as an author -- I don't feel I have contributed much since the workshops last year, but I haven't kept on top of the authorship criteria. My affiliation is the same -- School of Mathematics and Statistics, University of Melbourne, Australia -- but if an email address is also required, it would be best to update it to g.tsambos@gmail.com as I will be finishing up here soon

lauterbur commented 2 years ago

@gtsambos You did a lot for the workshops, and those were a big part of this, so you made a big contribution!

petrelharp commented 2 years ago

Current status: Screenshot from 2022-05-10 09-35-47

xin-huang commented 2 years ago

My affiliation is

1 Department of Evolutionary Anthropology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria. 2 Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Austria.

attrna commented 2 years ago

Thank you! @petrelharp, my major affiliation is the Institute of Ecology and Evolution, University of Oregon, Eugene, OR

reedacartwright commented 2 years ago

@petrelharp Can you update my affiliation to School of Life Sciences and The Biodesign Institute, Arizona State University, Tempe, AZ USA Thanks.

petrelharp commented 2 years ago

I'm accumulating changes over at #43, btw.

saurabhbelsare commented 2 years ago

Hi Peter, My affiliation is Institute of Ecology and Evolution, University of Oregon, Eugene, OR

agladstein commented 2 years ago

My affiliation is correct

noscode commented 2 years ago

Hello everyone! Sorry for long silence, moving issues. I am very excited about the paper. My affiliation during the QC was Computer Technologies Laboratory, ITMO University. However, giving the recent circumstances if there are some problems with this affiliation feel free to delete it. If some affiliation is still required then it could be "independent researcher" or something like that.

gtsambos commented 2 years ago

Hiya! Thanks for including me as an author -- I don't feel I have contributed much since the workshops last year, but I haven't kept on top of the authorship criteria. My affiliation is the same -- School of Mathematics and Statistics, University of Melbourne, Australia -- but if an email address is also required, it would be best to update it to @.*** as I will be finishing up here soon.

On Thu, 5 May 2022, 2:22 am Ahmed Hasan, @.***> wrote:

Happy to be a co-author - very glad to be included! I'm looking forward to using stdpopsim for C. reinhardtii simulations in the future.

— Reply to this email directly, view it on GitHub https://github.com/popsim-consortium/adding-species-manuscript/issues/32#issuecomment-1117552296, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEHOXQRGG2C7KVUAIN3P7UTVIKP4LANCNFSM5T6ALQYA . You are receiving this because you were mentioned.Message ID: @.*** com>

manolofperez commented 2 years ago

Hello,

In that case I would be more than happy to agree with my inclusion. I will face it as an incentive to be more active in the stdpopsim community.

Therefore, I can definitely help with QCing and with anything else you need.

Em ter., 3 de mai. de 2022 às 15:25, Peter Ralph @.***> escreveu:

OK, updated! I'm not a fan of the "junior/senior" division, and I think that (3) and (4) ought to be merged, really.

— Reply to this email directly, view it on GitHub https://github.com/popsim-consortium/adding-species-manuscript/issues/32#issuecomment-1116419915, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABBXHUQTATKO5N5OGPDX53TVIFVRRANCNFSM5T6ALQYA . You are receiving this because you were mentioned.Message ID: @.*** com>

--

*MANOLO PEREZ*PhD in Evolutionary Genetics - UFSCar CV http://buscatextual.cnpq.br/buscatextual/visualizacv.do?id=S8394347 | Website https://sites.google.com/site/manolofperez/ Skype: manolofperez +55 15997597570

petrelharp commented 2 years ago

You're on there already, @manolofperez! Current status: Screenshot from 2022-10-11 06-44-59

manolofperez commented 2 years ago

Thanks @petrelharp