Closed rando2 closed 3 years ago
Hello everyone! I went through the commit history for the nutraceuticals and pharmaceuticals section.
Our aim is to submit within the next two weeks (ideally Feb 8).
For the pharmaceuticals, I ended up having to use a bit of subjectivity in weighing contributions (how many lines of text is a figure comparable to?), so please let me know if you have any concerns. I'm attaching the commit log I used to try to get a reading on this for reference -- I believe I've removed all the nutraceuticals commits, but again, let me know if I missed something. I didn't categorize every single commit for people who had a lot -- when they are only 2-3 lines, they're typically edits. I also didn't put people on the named author list if they were just fixing typos in this section without making contributions to the ideas of the text.
Position | Person | Total Lines Modified | Wrote Text? | Other contributions | Approval |
---|---|---|---|---|---|
1 | @rando2 | ~2814~ 2346 | Yes | Project Administration, Editing | Feb 9 |
2 | @nilswellhausen | 201 | Yes | Project Administration, Visualization | Feb 10 |
3 | @soumitagh | 246 | Yes | Feb 9 | |
4 | @aadattoli | 207 | Yes | Feb 9 | |
4 | @hufengling | 191 | Yes | Feb 24 | |
5 | @byrdjb | 126 | Yes | PRs merged | |
5 | ~@likhithakolla~ | ~116~ | ~Yes~ | Feb 9 | |
5 | @ajlee21 | 107 | Yes | PR merged | |
5 | @dianerafi | 88 | Yes | Feb 9 | |
5 | @kevinsunofficial | Visualization | Feb 9 | ||
5 | @qiyanjun | Visualization | Feb 24 | ||
6 | @marouenbg | 64 | Yes | conf on email | |
6 | @Jeff-Field | 47 | Yes | PRs merged | |
6 | ~@esell17~ | ~42~ | ~Yes~ | Feb 10 | |
6 | @nafisajadavji | Supervision, Editing | Feb 9 | ||
7 | @cbrueffer | 51 | Project Administration | Feb 14 | |
7 | @RLordan | 29 | Yes | Project Administration | Feb 9 |
7 | @anskelly | Editing | Feb 9 | ||
7 | @ypar | Yes | Editing | Feb 11 | |
7 | @rbharath | Editing | Feb 9 | ||
7 | @rishirajgoel | Editing | Feb 10 | ||
7 | @jinhui2 | 11 | Yes | Feb 9 | |
9 | @SiminaB | 1037 | Project Administration, Editing | PR merged | |
10 | @agitter | 144 | Project Administration, Visualization | Feb 12 | |
11 | @cgreene | ~563~ 508 | ~Yes~ | Project Administration, Editing | Feb 9 |
Commit Log: gitlog.20.treatments.xlsx
Acknowledgements:
Note: ~Strike through~ represent changes after moving vaccines to its own manuscript
Hello @rando2 ! For the therapeutics manuscript, I think I should just be in the acknowledgements, because I contributed very little and don't know enough about the therapeutics to be able to review it intelligently. But congratulations on your progress!
We are going to need to move the vaccines section to a new paper -- even without it, we are significantly over the requested word limit (which is 12,000 words-- without vaccines, we're currently at > 16,000)! I'll go through the commits to see how this changes the author list/order and provide updates here. The good news is that I believe the rest of the paper is pretty up-to-date, so we should be able to get a draft sent out to authors for approval very soon!
In case you're interested, in the nutraceuticals section you could cite a brief commentary in JASA regarding vitamin D: https://jamanetwork.com/journals/jama/fullarticle/2775003 It is not very exciting because it ends by concluding that we don't know whether it helps or not, which is also how it begins. I have lots of days and even years which have that Ourobouros quality, but I don't know if I deserve being cited for it.
Thanks @dziakj1, we actually submitted the nutraceuticals yesterday! It's impossible to make any strong conclusions but I think @RLordan added some insight to the situation in terms of what we do know and how they work in the body, so hopefully his summary will be more helpful 🤞
People who are moving off this manuscript to the vaccines manuscript: Authors: @esell17, @likhithakolla Acknowledgements: @dziakj1 Please let me know if I missed something, but it seemed like your text was all about the vaccines!
I updated the table above to reflect other changes (i.e., I separated Casey & my commits for the two different manuscripts)
Hi everyone! I am still working on checking all the therapeutics are roughly up-to-date and that we don't say anything super outdated (e.g., #837). I'm hoping to finish this tomorrow and then send the docx out to all authors.
If anyone is open to reviewing PRs tomorrow (or to updating your favorite drug!) this would be hugely helpful -- please let me know if you don't mind being tagged! I'm happy to review for anyone who has anything they want changed!
Thank you all so much!
The build is going out to co-authors over email momentarily. I'm leaving this comment here in case people want to use emojis to indicate that they're comfortable submitting the manuscript in its current state!
Good luck!!👍
On Tue, Feb 9, 2021 at 5:23 PM HM Rando notifications@github.com wrote:
The build is going out to co-authors over email momentarily. I'm leaving this comment here in case people want to use emojis to indicate that they're comfortable submitting the manuscript in its current state!
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Looks good👍
Yes, good luck!
good luck!!
On Fri, Jan 29, 2021, 4:34 PM HM Rando notifications@github.com wrote:
Hello everyone! I went through the commit history for the nutraceuticals and pharmaceuticals section.
Our aim is to submit within the next two weeks (ideally Feb 8).
- As far as I can tell, @RLordan https://github.com/RLordan wrote the nutraceuticals section almost entirely on his own, so that author list is very short <#m_3988177908201061300_749> -- please let me know ASAP if you think you were skipped over!
- Is anyone willing to draft a section explaining the adenovirus-vectored vaccines? Or evaluating the status of the ones that are known to be in development/being administered?
- Is anyone willing to review my mRNA vaccine PRs? I'm trying to get them up-to-date today.
For the pharmaceuticals, I ended up having to use a bit of subjectivity in weighing contributions (how many lines of text is a figure comparable to?), so please let me know if you have any concerns. I'm attaching the commit log I used to try to get a reading on this for reference -- I believe I've removed all the nutraceuticals commits, but again, let me know if I missed something. I didn't categorize every single commit for people who had a lot -- when they are only 2-3 lines, they're typically edits. I also didn't put people on the author list if they were just fixing typos in this section without making contributions to the ideas of the text. Position Person Total Lines Modified Wrote Text? Other contributions 1 @rando2 https://github.com/rando2 2814 Yes Project Administration 2 @nilswellhausen https://github.com/nilswellhausen 201 Yes Project Administration, Visualization 3 @soumitagh https://github.com/soumitagh 246 Yes 4 @aadattoli https://github.com/aadattoli 207 Yes 4 @hufengling https://github.com/hufengling 191 Yes 5 @byrdjb https://github.com/byrdjb 126 Yes 5 @likhithakolla https://github.com/likhithakolla 116 Yes 5 @ajlee21 https://github.com/ajlee21 107 Yes 5 @dianerafi https://github.com/dianerafi 88 Yes PA 5 @kevinsunofficial https://github.com/kevinsunofficial Visualization 5 @qiyanjun https://github.com/qiyanjun Visualization 6 @marouenbg https://github.com/marouenbg 64 Yes 6 @Jeff-Field https://github.com/Jeff-Field 47 Yes 6 @esell17 https://github.com/esell17 42 Yes 6 @nafisajadavji https://github.com/nafisajadavji Supervision, Editing 7 @cbrueffer https://github.com/cbrueffer 51 PA 7 @RLordan https://github.com/RLordan 29 Yes 7 @anskelly https://github.com/anskelly Editing 7 @ypar https://github.com/ypar Yes Editing 8 @jinhui2 https://github.com/jinhui2 11 Yes 9 @dziakj1 https://github.com/dziakj1 2 Yes 10 @SiminaB https://github.com/SiminaB 1037 Project Administration, Editing 11 @agitter https://github.com/agitter 144 Project Administration, Visualization 12 @cgreene https://github.com/cgreene 563 Yes Project Administration, Editing
Commit Log: gitlog.20.treatments.xlsx https://github.com/greenelab/covid19-review/files/5896353/gitlog.20.treatments.xlsx
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Looks good to me! 🌈
On Tue, Feb 9, 2021 at 5:58 PM soumitagh notifications@github.com wrote:
good luck!!
On Fri, Jan 29, 2021, 4:34 PM HM Rando notifications@github.com wrote:
Hello everyone! I went through the commit history for the nutraceuticals and pharmaceuticals section.
Our aim is to submit within the next two weeks (ideally Feb 8).
- As far as I can tell, @RLordan https://github.com/RLordan wrote the nutraceuticals section almost entirely on his own, so that author list is very short <#m_3988177908201061300_749> -- please let me know ASAP if you think you were skipped over!
- Is anyone willing to draft a section explaining the adenovirus-vectored vaccines? Or evaluating the status of the ones that are known to be in development/being administered?
- Is anyone willing to review my mRNA vaccine PRs? I'm trying to get them up-to-date today.
For the pharmaceuticals, I ended up having to use a bit of subjectivity in weighing contributions (how many lines of text is a figure comparable to?), so please let me know if you have any concerns. I'm attaching the commit log I used to try to get a reading on this for reference -- I believe I've removed all the nutraceuticals commits, but again, let me know if I missed something. I didn't categorize every single commit for people who had a lot -- when they are only 2-3 lines, they're typically edits. I also didn't put people on the author list if they were just fixing typos in this section without making contributions to the ideas of the text. Position Person Total Lines Modified Wrote Text? Other contributions 1 @rando2 https://github.com/rando2 2814 Yes Project Administration 2 @nilswellhausen https://github.com/nilswellhausen 201 Yes Project Administration, Visualization 3 @soumitagh https://github.com/soumitagh 246 Yes 4 @aadattoli https://github.com/aadattoli 207 Yes 4 @hufengling https://github.com/hufengling 191 Yes 5 @byrdjb https://github.com/byrdjb 126 Yes 5 @likhithakolla https://github.com/likhithakolla 116 Yes 5 @ajlee21 https://github.com/ajlee21 107 Yes 5 @dianerafi https://github.com/dianerafi 88 Yes PA 5 @kevinsunofficial https://github.com/kevinsunofficial Visualization 5 @qiyanjun https://github.com/qiyanjun Visualization 6 @marouenbg https://github.com/marouenbg 64 Yes 6 @Jeff-Field https://github.com/Jeff-Field 47 Yes 6 @esell17 https://github.com/esell17 42 Yes 6 @nafisajadavji https://github.com/nafisajadavji Supervision, Editing 7 @cbrueffer https://github.com/cbrueffer 51 PA 7 @RLordan https://github.com/RLordan 29 Yes 7 @anskelly https://github.com/anskelly Editing 7 @ypar https://github.com/ypar Yes Editing 8 @jinhui2 https://github.com/jinhui2 11 Yes 9 @dziakj1 https://github.com/dziakj1 2 Yes 10 @SiminaB https://github.com/SiminaB 1037 Project Administration, Editing 11 @agitter https://github.com/agitter 144 Project Administration, Visualization 12 @cgreene https://github.com/cgreene 563 Yes Project Administration, Editing
Commit Log: gitlog.20.treatments.xlsx < https://github.com/greenelab/covid19-review/files/5896353/gitlog.20.treatments.xlsx
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Looks good! 👍
Super! Well done everyone! 👍
Looks good! 👍
Get Outlook for iOShttps://aka.ms/o0ukef
From: Ronan Lordan notifications@github.com Sent: Tuesday, February 9, 2021 6:30:43 PM To: greenelab/covid19-review covid19-review@noreply.github.com Cc: Wang, Jinhui jinhui2@pennmedicine.upenn.edu; Mention mention@noreply.github.com Subject: [External] Re: [greenelab/covid19-review] Steps for Therapeutics Manuscript Submission (#738)
Super! Well done everyone! 👍
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Wonderful! 🥇
Wonderful, Good luck!
On 29 Jan 2021, at 16:34, HM Rando notifications@github.com wrote:
Hello everyone! I went through the commit history for the nutraceuticals and pharmaceuticals section.
Our aim is to submit within the next two weeks (ideally Feb 8).
As far as I can tell, @RLordan https://github.com/RLordan wrote the nutraceuticals section almost entirely on his own, so that author list is very short <x-msg://4/#749> -- please let me know ASAP if you think you were skipped over! Is anyone willing to draft a section explaining the adenovirus-vectored vaccines? Or evaluating the status of the ones that are known to be in development/being administered? Is anyone willing to review my mRNA vaccine PRs? I'm trying to get them up-to-date today. For the pharmaceuticals, I ended up having to use a bit of subjectivity in weighing contributions (how many lines of text is a figure comparable to?), so please let me know if you have any concerns. I'm attaching the commit log I used to try to get a reading on this for reference -- I believe I've removed all the nutraceuticals commits, but again, let me know if I missed something. I didn't categorize every single commit for people who had a lot -- when they are only 2-3 lines, they're typically edits. I also didn't put people on the author list if they were just fixing typos in this section without making contributions to the ideas of the text.
Position Person Total Lines Modified Wrote Text? Other contributions 1 @rando2 https://github.com/rando2 2814 Yes Project Administration 2 @nilswellhausen https://github.com/nilswellhausen 201 Yes Project Administration, Visualization 3 @soumitagh https://github.com/soumitagh 246 Yes
4 @aadattoli https://github.com/aadattoli 207 Yes
4 @hufengling https://github.com/hufengling 191 Yes
5 @byrdjb https://github.com/byrdjb 126 Yes
5 @likhithakolla https://github.com/likhithakolla 116 Yes
5 @ajlee21 https://github.com/ajlee21 107 Yes
5 @dianerafi https://github.com/dianerafi 88 Yes PA 5 @kevinsunofficial https://github.com/kevinsunofficial Visualization 5 @qiyanjun https://github.com/qiyanjun Visualization 6 @marouenbg https://github.com/marouenbg 64 Yes
6 @Jeff-Field https://github.com/Jeff-Field 47 Yes
6 @esell17 https://github.com/esell17 42 Yes
6 @nafisajadavji https://github.com/nafisajadavji Supervision, Editing 7 @cbrueffer https://github.com/cbrueffer 51 PA 7 @RLordan https://github.com/RLordan 29 Yes
7 @anskelly https://github.com/anskelly Editing 7 @ypar https://github.com/ypar Yes Editing 8 @jinhui2 https://github.com/jinhui2 11 Yes
9 @dziakj1 https://github.com/dziakj1 2 Yes 10 @SiminaB https://github.com/SiminaB 1037 Project Administration, Editing 11 @agitter https://github.com/agitter 144 Project Administration, Visualization 12 @cgreene https://github.com/cgreene 563 Yes Project Administration, Editing Commit Log: gitlog.20.treatments.xlsx https://github.com/greenelab/covid19-review/files/5896353/gitlog.20.treatments.xlsx — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/greenelab/covid19-review/issues/738#issuecomment-770062493, or unsubscribe https://github.com/notifications/unsubscribe-auth/AO5U4LSIL6PWK4HDFWMYWIDS4MSXLANCNFSM4VADGVXA.
:) good luck!
On Tue, Feb 9, 2021 at 7:19 PM aadattoli notifications@github.com wrote:
Wonderful, Good luck!
On 29 Jan 2021, at 16:34, HM Rando notifications@github.com wrote:
Hello everyone! I went through the commit history for the nutraceuticals and pharmaceuticals section.
Our aim is to submit within the next two weeks (ideally Feb 8).
As far as I can tell, @RLordan https://github.com/RLordan wrote the nutraceuticals section almost entirely on his own, so that author list is very short <x-msg://4/#749> -- please let me know ASAP if you think you were skipped over! Is anyone willing to draft a section explaining the adenovirus-vectored vaccines? Or evaluating the status of the ones that are known to be in development/being administered? Is anyone willing to review my mRNA vaccine PRs? I'm trying to get them up-to-date today. For the pharmaceuticals, I ended up having to use a bit of subjectivity in weighing contributions (how many lines of text is a figure comparable to?), so please let me know if you have any concerns. I'm attaching the commit log I used to try to get a reading on this for reference -- I believe I've removed all the nutraceuticals commits, but again, let me know if I missed something. I didn't categorize every single commit for people who had a lot -- when they are only 2-3 lines, they're typically edits. I also didn't put people on the author list if they were just fixing typos in this section without making contributions to the ideas of the text.
Position Person Total Lines Modified Wrote Text? Other contributions 1 @rando2 https://github.com/rando2 2814 Yes Project Administration 2 @nilswellhausen https://github.com/nilswellhausen 201 Yes Project Administration, Visualization 3 @soumitagh https://github.com/soumitagh 246 Yes 4 @aadattoli https://github.com/aadattoli 207 Yes 4 @hufengling https://github.com/hufengling 191 Yes 5 @byrdjb https://github.com/byrdjb 126 Yes 5 @likhithakolla https://github.com/likhithakolla 116 Yes 5 @ajlee21 https://github.com/ajlee21 107 Yes 5 @dianerafi https://github.com/dianerafi 88 Yes PA 5 @kevinsunofficial https://github.com/kevinsunofficial Visualization 5 @qiyanjun https://github.com/qiyanjun Visualization 6 @marouenbg https://github.com/marouenbg 64 Yes 6 @Jeff-Field https://github.com/Jeff-Field 47 Yes 6 @esell17 https://github.com/esell17 42 Yes 6 @nafisajadavji https://github.com/nafisajadavji Supervision, Editing 7 @cbrueffer https://github.com/cbrueffer 51 PA 7 @RLordan https://github.com/RLordan 29 Yes 7 @anskelly https://github.com/anskelly Editing 7 @ypar https://github.com/ypar Yes Editing 8 @jinhui2 https://github.com/jinhui2 11 Yes 9 @dziakj1 https://github.com/dziakj1 2 Yes 10 @SiminaB https://github.com/SiminaB 1037 Project Administration, Editing 11 @agitter https://github.com/agitter 144 Project Administration, Visualization 12 @cgreene https://github.com/cgreene 563 Yes Project Administration, Editing Commit Log: gitlog.20.treatments.xlsx < https://github.com/greenelab/covid19-review/files/5896353/gitlog.20.treatments.xlsx
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Nice work! Thanks for all your hard work! Good luck!
Looks great! 🎉
Sent from my iPhone
On Feb 9, 2021, at 9:10 PM, Nafisa Jadavji notifications@github.com wrote:
Nice work! Thanks for all your hard work! Good luck!
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Looking good!
@nilswellhausen I just realized -- did you still want to make updates to the neutralizing antibodies? I have not done a check on where that literature has gone!
I would love to but I dont want to stall the progress either. I am pretty swamped this week so it would certainly take a while to properly update this section. Another option is to wait what the reviewers would like to see included and then edit.
Would it help if we add a date to the neutralizing antibodies section to give readers and reviewers of sense of when this was written? Including "As of MONTH, 2020..." could clarify that this hasn't been updated to reflect the latest literature.
@cbrueffer just to check, do you need more time to approve this or are you OK with it being submitted sometime this week? I know I've been pinging you on about 3 different manuscripts this week!
No, all good @rando2! Sorry, should have stated that explicitly.
Wonderful. Looks good!
On Feb 10, 2021, at 05:51, Elizabeth (Ellie) Sell notifications@github.com wrote:
Looks great! 🎉
Sent from my iPhone
On Feb 9, 2021, at 9:10 PM, Nafisa Jadavji notifications@github.com wrote:
Nice work! Thanks for all your hard work! Good luck!
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Two notes pre-submission:
Thanks!
From: HM Rando notifications@github.com Sent: Wednesday, February 24, 2021 12:03 PM To: greenelab/covid19-review covid19-review@noreply.github.com Cc: Byrd, James (J. "Brian") jbbyrd@med.umich.edu; Mention mention@noreply.github.com Subject: Re: [greenelab/covid19-review] Steps for Therapeutics Manuscript Submission (#738)
External Email - Use Caution
Two notes pre-submission:
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Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
Hey all, I'm getting ready to send the new version of the manuscript out by email (hopefully tomorrow). I just wanted to make a note that based on the line edits made during revisions, I think it would make sense to bump @cbrueffer @RLordan up one spot each in the author list. @ajlee21 your line edits put you in group 4 but it seems like you were already there! See #977
Just an update that an email with the new draft went out yesterday! If you have any questions or didn't receive it, please just let me know!
I'm hoping to hear from everyone either with approval or edits (or a timeline for when you will be able to provide edits) by the end of next week -- let me know if this is an issue for you though, I know summer is hectic!
Person | Approval Status |
---|---|
@nilswellhausen | ✅ pending merge of #986 |
@RLordan | Aug 2 ✅ |
@cbrueffer | ✅ pending merge of #997 |
@aadattoli | Aug 10 ✅ |
@Jeff-Field | ✅ pending merge of #987 and #986 |
@rbharath | Aug 2 ✅ |
@ajlee21 | Aug 2 ✅ |
@hufengling | |
@nafisajadavji | Aug 5 ✅ |
@jinhui2 | Aug 2 ✅ |
@dianerafi | Aug 15 ✅ |
@anskelly | Aug 2 ✅ |
@marouenbg | Aug 4 ✅ |
@soumitagh | Aug 3 ✅ |
@byrdjb | ✅ |
@ypar | |
@qiyanjun | Aug 3 ✅ |
@kevinsunofficial | Aug 3 ✅ |
@rishirajgoel | |
@rando2 | Aug 2 ✅ |
@SiminaB | ✅ |
@agitter | ✅ |
@cgreene | Aug 3 ✅ |
Note: some people on this thread wrote vaccines topics, and those will be going out separately -- I'm aiming for sending that email out in 2-3 weeks.
Approve! 👍
I edited the life cycle/therapeutics figure. Besides that, I approve.
Approve! Thanks.
From: nilswellhausen @.> Sent: Tuesday, August 3, 2021 10:06 AM To: greenelab/covid19-review @.> Cc: Wang, Jinhui @.>; Mention @.> Subject: [External] Re: [greenelab/covid19-review] Steps for Therapeutics Manuscript Submission (#738)
I edited the life cycle/therapeutics figure. Besides that, I approve.
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I'm not really involved in this one but I approve.
If you haven't already, you might optionally want to cite or link to this living guideline that I read about this morning: https://www.who.int/publications/i/item/WHO-2019-nCoV-therapeutics-2021.2
Approve. Thanks
Sent from my iPhone
On Aug 3, 2021, at 10:33, John J. Dziak @.***> wrote:
If you haven't already, you might optionally want to cite or link to this living guideline that I read about this morning: https://www.who.int/publications/i/item/WHO-2019-nCoV-therapeutics-2021.2
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Approve. Thank you.
On Tue, Aug 3, 2021 at 1:03 PM qiyanjun @.***> wrote:
Approve. Thanks
Sent from my iPhone
On Aug 3, 2021, at 10:33, John J. Dziak @.***> wrote:
If you haven't already, you might optionally want to cite or link to this living guideline that I read about this morning:
https://www.who.int/publications/i/item/WHO-2019-nCoV-therapeutics-2021.2
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android.
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Soumita Ghosh University of Pensylvania
Approve. Thank you so much!
Looks good to me. I approve! Thank you
Approve! Nice work!
Nafisa M. Jadavji, Ph.D. www.jadavjilab.com
On Tue, Aug 3, 2021 at 12:21 PM Alexandra Lee @.***> wrote:
Looks good to me. I approve! Thank you
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approve. thanks
On 5 Aug 2021, at 23:42, Nafisa Jadavji @.***> wrote:
Approve! Nice work!
Nafisa M. Jadavji, Ph.D. www.jadavjilab.com
On Tue, Aug 3, 2021 at 12:21 PM Alexandra Lee @.***> wrote:
Looks good to me. I approve! Thank you
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/greenelab/covid19-review/issues/738#issuecomment-892101501, or unsubscribe https://github.com/notifications/unsubscribe-auth/AO6TZUFWAGNA3D2EZ56KATTT3A6ULANCNFSM4VADGVXA . 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&utm_campaign=notification-email .
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Approved, pending https://github.com/greenelab/covid19-review/pull/997. Thanks everyone!
I approve and can help review the remaining therapeutics pull requests.
Here's what we need to do for this hefty manuscript! PR reviews or people willing to take a stab at opening PRs very, very welcome! I will update with PRs as they have numbers -- please consider reviewing!
Most Critical: