Author approval for resubmission

[jeromekelleher]

We have updated the manuscript and written responses to the reviewers points. I think everything has been resolved barring a few minor points (#228, #219). Therefore we are basically ready to resubmit, which I would like to do on Friday.

Authors: can you please confirm below that you are happy for this to be resubmitted?

Here are the documents:

• Diff from the original submission: review-diff.pdf
• Response to reviewers: response-to-reviewers.pdf
• Full manuscript:paper.pdf

Unfortunately we have still not been able to contact @ivan-krukov so we cannot include him in the author list. Please see the updated Acknowledgements.

If you would like to make any changes, please either go ahead and make a PR directly, or open an issue to discuss.

@agladstein @andrewkern @apragsdale @awohns @benjeffery @castedo @cdquinto @daniel-goldstein @DomNelson @eldonb @fbaumdicker @gbinux @GertjanBisschop @grahamgower @gregorgorjanc @gtsambos @hugovk @hyanwong @ivan-krukov @JereKoskela @jeromekelleher @jgallowa07 @KLohse @mmatschiner @molpopgen @mufernando @nspope @petrelharp @saunack @sgravel @shajoezhu @TPPSellinger @winni2k

[jeromekelleher]

ps. Exact wording of references to the appendices is likely to change and we convert to GENETICS style, so let's not worry too much about that.

[hyanwong]

Yes, please resubmit. Thanks for all your work on this @jeromekelleher (and everyone else!)

[mmatschiner]

Excellent work, thanks to all and primarily @jeromekelleher ! Feel free to resubmit.

[JereKoskela]

Looks great to me. Thanks everyone!

[molpopgen]

Approve.

[bguo068]

Looks great! Thanks for the hard work.

[mufernando]

LGTM! Great work, y'all!

[apragsdale]

Thanks for the hard work, Jerome and all! Approved.

[grahamgower]

LGTM too!

[cdquinto]

Looks good to me! Thank you all for your hard work!

El mié, 24 nov 2021 a las 11:25, Aaron Ragsdale @.***>) escribió:

Thanks for the hard work, Jerome and all! Approved.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/tskit-dev/msprime-1.0-paper/issues/229#issuecomment-978081685, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADFCAQ6HE7C2KREBIMF3OGLUNUNYRANCNFSM5IWHXFNQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

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[nspope]

Looks good, thanks!

[hugovk]

Thank you! I'm happy for this to be resubmitted.

[castedo]

:+1: grande

to Jerome and re-submission.

[GertjanBisschop]

Approved. And thank you!

[KLohse]

Approved! Thanks for all the hard work Jerome (et al.)

On Wed, 24 Nov 2021 at 20:31, Gertjan Bisschop @.***> wrote:

Approved. And thank you!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/tskit-dev/msprime-1.0-paper/issues/229#issuecomment-978199841, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEDTOV2KUGXOAPBQXWOKZNLUNVDSBANCNFSM5IWHXFNQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

[fbaumdicker]

Approve.

[awohns]

Looks great! Thanks!

[andrewkern]

approved! just submitted a PR but feel free to ignore

[shajoezhu]

Approved! Many thanks @Jerome Kelleher @.***> !

On Wed, Nov 24, 2021 at 10:32 PM Andrew Kern @.***> wrote:

approved! just submitted a PR but feel free to ignore

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/tskit-dev/msprime-1.0-paper/issues/229#issuecomment-978360636, or unsubscribe https://github.com/notifications/unsubscribe-auth/AA4FP7KXVKKXTGA3CLDA3HLUNVRZDANCNFSM5IWHXFNQ .

[TPPSellinger]

I didn't find anything to change. Seems fine to resubmit. Thanks Jerome (and to all the other authors).

[saunack]

looks even more polished than earlier. approved from my end.

[gregorgorjanc]

LGTM! Thanks @jeromekelleher !

[eldonb]

I opened an issue with some very small comments; otherwise looks great, thanks @jeromekelleher and everyone

[daniel-goldstein]

Looks great, thank you Jerome and all for the incredible work!

[agladstein]

Looks good!

[jeromekelleher]

Sorry USA-folks, I didn't realise I'd stupidly set the deadline to coincide with Thanksgiving. I'll ask for a few more days extension, I'm sure there'll be no problem.

[benjeffery]

LGTM!

[gtsambos]

all good by me

On Thu, Nov 25, 2021 at 1:40 AM Jerome Kelleher @.***> wrote:

We have updated the manuscript and written responses to the reviewers points. I think everything has been resolved barring a few minor points (

228 https://github.com/tskit-dev/msprime-1.0-paper/issues/228, #219

https://github.com/tskit-dev/msprime-1.0-paper/issues/219). Therefore we are basically ready to resubmit, which I would like to do on Friday.

Authors: can you please confirm below that you are happy for this to be resubmitted?

Here are the documents:

• Diff from the original submission: review-diff.pdf https://github.com/tskit-dev/msprime-1.0-paper/files/7596463/review-diff.pdf
• Response to reviewers: response-to-reviewers.pdf https://github.com/tskit-dev/msprime-1.0-paper/files/7596470/response-to-reviewers.pdf
• Full manuscript: paper.pdf https://github.com/tskit-dev/msprime-1.0-paper/files/7596471/paper.pdf

Unfortunately we have still not been able to contact @ivan-krukov https://github.com/ivan-krukov so we cannot include him in the author list. Please see the updated Acknowledgements.

If you would like to make any changes, please either go ahead and make a PR directly, or open an issue to discuss.

@agladstein https://github.com/agladstein @andrewkern https://github.com/andrewkern @apragsdale https://github.com/apragsdale @awohns https://github.com/awohns @benjeffery https://github.com/benjeffery @castedo https://github.com/castedo @cdquinto https://github.com/cdquinto @daniel-goldstein https://github.com/daniel-goldstein @DomNelson https://github.com/DomNelson @eldonb https://github.com/eldonb @fbaumdicker https://github.com/fbaumdicker @gbinux https://github.com/gbinux @GertjanBisschop https://github.com/GertjanBisschop @grahamgower https://github.com/grahamgower @gregorgorjanc https://github.com/gregorgorjanc @gtsambos https://github.com/gtsambos @hugovk https://github.com/hugovk @hyanwong https://github.com/hyanwong @ivan-krukov https://github.com/ivan-krukov @JereKoskela https://github.com/JereKoskela @jeromekelleher https://github.com/jeromekelleher @jgallowa07 https://github.com/jgallowa07 @KLohse https://github.com/KLohse @mmatschiner https://github.com/mmatschiner @molpopgen https://github.com/molpopgen @mufernando https://github.com/mufernando @nspope https://github.com/nspope @petrelharp https://github.com/petrelharp @saunack https://github.com/saunack @sgravel https://github.com/sgravel @shajoezhu https://github.com/shajoezhu @TPPSellinger https://github.com/TPPSellinger @winni2k https://github.com/winni2k

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/tskit-dev/msprime-1.0-paper/issues/229, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEHOXQU2NXTFAZACKWEBCUTUNT2PJANCNFSM5IWHXFNQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

-- PhD Student Melbourne Integrative Genomics and School of Mathematics and Statistics University of Melbourne https://gtsambos.github.io/

[sgravel]

Looks great! Happy to have you submit when you are ready.

[jeromekelleher]

(Note: I've updated the links above in the description with the current version of documents, which I hope are more-or-less final.)

[petrelharp]

Approve! (belatedly.) Looks great! (I would be inclined to add a note to the bit about coalescent simulations saying that "However, the tools we present here are useful (in conjunction with other tools) for simulating genomes under selection." But everyone's signed off, so let's add that in the final round.)

[jgallowa07]

Approve!

[jeromekelleher]

Thanks all, looks like we just have @winni2k and @DomNelson holding out. I'll try contacting them in other ways.

[DomNelson]

Approved!

[winni2k]

Approved :)

[jeromekelleher]

Thanks all, it's been resubmitted :crossed_fingers: