[Vp-reproduce-subgroup] [Vp-integration-subgroup] Paper review and revision check list
Winston Garira
Winston.Garira at univen.ac.za
Tue Jan 18 00:09:19 PST 2022
I APPROVE!
Thank you.
Winston
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________________________________
From: Ruth Bowness <rb2250 at bath.ac.uk>
Sent: Tuesday, January 18, 2022 7:57:53 AM
To: Jacob Barhak <jacob.barhak at gmail.com>; Gilberto Gonzalez-Parra <gilberto.gonzalezparra at nmt.edu>
Cc: Faeder, James R <faeder at pitt.edu>; Rahuman Sheriff <sheriff at ebi.ac.uk>; vp-reproduce-subgroup at lists.simtk.org <vp-reproduce-subgroup at lists.simtk.org>; vp-integration-subgroup at lists.simtk.org <vp-integration-subgroup at lists.simtk.org>; John Gennari <gennari at uw.edu>; Ruth Bowness <rec9 at st-andrews.ac.uk>; Winston Garira <Winston.Garira at univen.ac.za>; Jonathan Karr <jonrkarr at gmail.com>
Subject: Re: [Vp-reproduce-subgroup] [Vp-integration-subgroup] Paper review and revision check list
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I approve. Many thanks!
Ruth
________________________________
From: Jacob Barhak <jacob.barhak at gmail.com>
Sent: 18 January 2022 04:48
To: Gilberto Gonzalez-Parra <gilberto.gonzalezparra at nmt.edu>
Cc: Faeder, James R <faeder at pitt.edu>; Rahuman Sheriff <sheriff at ebi.ac.uk>; vp-reproduce-subgroup at lists.simtk.org <vp-reproduce-subgroup at lists.simtk.org>; vp-integration-subgroup at lists.simtk.org <vp-integration-subgroup at lists.simtk.org>; John Gennari <gennari at uw.edu>; Ruth Bowness <rb2250 at bath.ac.uk>; Ruth Bowness <rec9 at st-andrews.ac.uk>; Winston Garira <Winston.Garira at univen.ac.za>; Jonathan Karr <jonrkarr at gmail.com>
Subject: Re: [Vp-reproduce-subgroup] [Vp-integration-subgroup] Paper review and revision check list
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Hi Ruth, Hi Jonathan, Hi Winston,
You are the last 3 authors that need approval - I apologize in advance if you sent your final approval and I did not get it. Sometimes it gets lost. Please REPLY TO ALL to this email with APPROVE, DISAPPROVE, or ABSTAIN so we can have your approval in public record and resolve this quickly.
Hopefully you can do it within a day or two - both reviewers endorsed the paper and I just sent the editor the message below.
Sheriff, your recollection is correct - Tomas Helikar did participate in our discussions. Yet the idea of sorting the challenges belongs to John Gennari who managed one of the versions. That version was not traceable, so any text taken from it, had to be validated by the authors that wrote that text. As far as I know no new contributions in the submitted version can be traced back to Tomas and he did not claim any contribution that was omitted nor raised any objection - and I did ask several times for objections by anyone. So his name is not in the list of authors, yet he is acknowledged in the paper acknowledgement section since he did participate in some meetings. If you ask me, I believe he wanted to contribute when we opened the paper for contributions, yet could not find the time.
Tomas, if I am wrong, please correct me now so we can fix this prior to finalization. .
And Sheriff, this paper is somewhat reproducible. If you trace back the versions we have public, you can find all authors listed contributing with a few exceptions. For example, John Rice contributed significant portions of the reproducibility section, yet I uploaded the text from him into the paper - so you will see my name instead of his. Also, some contributors added comments that I edited into the paper in the early days. Some authors also contributed to the activities that generated references for the paper - so their contribution was substantial. As far as I know the list of authors we have is complete except from John Gennari who made a large contribution to the paper, yet chose to abstain yet allowed us to proceed and use the text - I still hope he will rejoin, yet honor his decision if he chooses not to. He is acknowledged for his contribution - this way he gains some honor.
Hopefully the last few authors will approve as well as the editor and we can move forward.
Jacob
########## The message I send to the editor #############
Hi Shayn,
You will find a new manuscript draft in the system - I just uploaded figures in different formats in high resolution as the first reviewer requested.
I would like to add one more affiliation for one of our authors - William Waites has two affiliations - see below - I tried to update this in the system, yet the system blocks me from editing the authors list for some reason.
William Waites, Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, UK and Department of Computer and Information Sciences, University of Strathclyde, Glasgow, Scotland
I would ask to delay the manuscript until all our authors approve the final version - we have 15 of the 18 approve the manuscript - I will do my best to get the last 3 approve quickly. Once I get approval I can submit.
Thank you for processing this quickly. I wish our big group will be as fast as you.
Jacob
On Mon, Jan 17, 2022 at 6:34 PM Gilberto Gonzalez-Parra <gilberto.gonzalezparra at nmt.edu<mailto:gilberto.gonzalezparra at nmt.edu>> wrote:
The status has changed to
17 Jan 2022
Review of Review Editor 1 finalized.
13 Jan 2022
Editorial Office reminded you to respond to reviewer 1 and/or resubmit your manuscript in the discussion forum.
10 Jan 2022
Review of Review Editor 2 finalized.
So both reviewers endorsed it. BTW, approve.
***************************************************************************
Gilberto C. Gonzalez-Parra, Ph.D in Applied Mathematics.
Faculty of the Mathematics Department
New Mexico Tech, NM, USA.
****************************************************************************
On Mon, Jan 17, 2022 at 4:07 PM Faeder, James R <faeder at pitt.edu<mailto:faeder at pitt.edu>> wrote:
Approve.
Thanks Jacob and everyone else for all of your efforts on the revisions.
Best regards,
Jim
From: Rahuman Sheriff <sheriff at ebi.ac.uk<mailto:sheriff at ebi.ac.uk>>
Date: Monday, January 17, 2022 at 5:02 PM
To: Jacob Barhak <jacob.barhak at gmail.com<mailto:jacob.barhak at gmail.com>>
Cc: vp-reproduce-subgroup at lists.simtk.org<mailto:vp-reproduce-subgroup at lists.simtk.org> <vp-reproduce-subgroup at lists.simtk.org<mailto:vp-reproduce-subgroup at lists.simtk.org>>, vp-integration-subgroup at lists.simtk.org<mailto:vp-integration-subgroup at lists.simtk.org> <vp-integration-subgroup at lists.simtk.org<mailto:vp-integration-subgroup at lists.simtk.org>>, John Gennari <gennari at uw.edu<mailto:gennari at uw.edu>>, Faeder, James R <faeder at pitt.edu<mailto:faeder at pitt.edu>>, Alexander Kulesza <alexander.kulesza at novadiscovery.com<mailto:alexander.kulesza at novadiscovery.com>>
Subject: Re: [Vp-reproduce-subgroup] [Vp-integration-subgroup] Paper review and revision check list
Dear Jacob,
Please find the Figure 1 attached.
It is not clear to me whether the manuscript has been accepted. If the reviewer1’s response is overdue, we need to wait. If the review1 doesn’t respond at all, the editor might assign the manuscript to another reviewer.
Irrespective of that I approve.
On a different note, if I remember correctly, Tomas Helikar also contributed to the ordering of the table which is used in the figure. probably he mad other contributions too in John Gennari’s version.
Best regards
Sheriff
On 14 Jan 2022, at 13:19, Alexander Kulesza <alexander.kulesza at novadiscovery.com<mailto:alexander.kulesza at novadiscovery.com>> wrote:
Dear Jacob, dear all,
APPROVE
Attached, Figure 2 in HR in different formats.
Best
Alexander
On Fri, 14 Jan 2022 at 07:38, Jacob Barhak <jacob.barhak at gmail.com<mailto:jacob.barhak at gmail.com>> wrote:
Thanks Marcella,
In that case, it seems we have no reviewer objection and hopefully the editor will be positive as well . To speed up the process we need the following::
1. Sheriff - please send a high resolution image for Figure 1
2. Alex - Please send a high resolution image for Figure 2
3. Everyone please review the manuscript and Reply to all in this email with one word - either APPROVE, DISAPPROVE, ABSTAIN
Where:
APPROVE means you are ok with the version we reached - please note that we do have some new elements there and your approval means you understand what it means - please read the paper well and understand the nuances of approval.
DISAPPROVE- means that you no longer agree with the version we reached and we need to discuss the paper more and withdraw it - if you have some serious objection, it is the last chance to get the paper back to the drawing board
ABSTAIN - You have no objection for the paper being published, yet you want your name withdrawn
Also, if anyone else has any objections for this paper being published, please raise them now so we can discuss them.
I call again to John Gennarri to join us as an author - he did substantial work and many of his contributions are in the final version - including the order in figure 2. I can trace back many of his contributions and I think he should get credit for it - hopefully my last call will be accepted and he will rejoin.
William - I did not forget your second affiliation - I just could not change it in the system - I will write to the editor about that when we get the final acceptance notice.
I look forward to seeing your final decisions - hopefully it will be fast this time.
Jacob
On Thu, Jan 13, 2022 at 8:50 PM Torres, Marcella <mtorres at richmond.edu<mailto:mtorres at richmond.edu>> wrote:
Sorry, I was not clear enough: no response is required for Reviewer 2, as they have endorsed the manuscript. A response to Reviewer 1 is overdue, however; see the email below.
Frontiers in Systems Biology Editorial Office has sent you a message. Please click 'Reply' to send a direct response
This is to remind you that your response to the reviewer 1 is overdue in the interactive review forum of your manuscript 822606 under consideration for publication in Frontiers in Systems Biology, section Multiscale Mechanistic Modeling.
To access the review forum, click:
http://www.frontiersin.org/Review/EnterReviewForum.aspx?activationno=5f3876ba-0de4-47c1-8dff-1c2bcb5c6b11&retab=1<https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Flinks.email.frontiersin.org%2Fls%2Fclick%3Fupn%3D99YMbkkQ8WNJiHLectmHSn5XnTmYe57aPeiziTpYNtyfClFbQqFlwPq2nUMZBzQ7srQvkLkPbc-2F-2BZbZ-2BczlOsMnoBdURYE7vBE6wrLrCJR4-2BCXMD-2FyylaGS-2FaxCSwEXxntm7RnNdDdmDL5k3W2WQo0ie3jVFLbWE6g0wuBJBzfQ-3DOLrv_B-2Fy9jbSVGoT8qhSwbw0AFtm6DlDsGMQJjIadnFC13-2FJyATqJzBD73VYfuDTc-2F-2BJaS4kVj6eazmIcCMUijXaF7cwmpIPfXo62oyUmieGoN2C1Y5Or-2Fqw1mDFet-2FbgSMXcJvyRgL8VJvJK-2Bw-2BULW-2FawzD0QPdwLV1hkLM4-2F9kG-2BJqcbrOIV4DgfEtFEs9z2qt9wTumRZRHdyMGfQyetT9cia1k0sDolZ7ukB5Ik6E4DTmj3yHv4voIEhFHR5lhm-2Bbs&data=04%7C01%7CWinston.Garira%40univen.ac.za%7Ce905d707905f4301190c08d9da477a53%7Cf38ba9d8554c48a2ae4213b1e7f3c797%7C0%7C0%7C637780823036368924%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=JSMGALmcqJzlr7wqzodxKo6bOzT4bbcGt%2B1Vv6wf4do%3D&reserved=0>
Should you require a deadline extension for your resubmission, please do let us know by selecting "Request Extension" in the review forum, if you have not done so already. We encourage you to submit your revised manuscript with tracked changes to facilitate the review.
We look forward to receiving your revised manuscript. For any issues, please immediately contact the Associate Editor as well as the Editorial Office.
Best regards,
Your Frontiers in Systems Biology team
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________________________________
From: Jacob Barhak <jacob.barhak at gmail.com<mailto:jacob.barhak at gmail.com>>
Sent: Thursday, January 13, 2022 8:14 PM
To: Torres, Marcella <mtorres at richmond.edu<mailto:mtorres at richmond.edu>>
Cc: Rahuman Sheriff <sheriff at ebi.ac.uk<mailto:sheriff at ebi.ac.uk>>; vp-reproduce-subgroup at lists.simtk.org<mailto:vp-reproduce-subgroup at lists.simtk.org> <vp-reproduce-subgroup at lists.simtk.org<mailto:vp-reproduce-subgroup at lists.simtk.org>>; vp-integration-subgroup at lists.simtk.org<mailto:vp-integration-subgroup at lists.simtk.org> <vp-integration-subgroup at lists.simtk.org<mailto:vp-integration-subgroup at lists.simtk.org>>; John Gennari <gennari at uw.edu<mailto:gennari at uw.edu>>; Faeder, James R <faeder at pitt.edu<mailto:faeder at pitt.edu>>
Subject: Re: [Vp-reproduce-subgroup] [Vp-integration-subgroup] Paper review and revision check list
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Thanks Marcella, Thanks Gilberto,
Since the second reviewer did not respond, I think we have more time - we did respond in time however.
The figures were provided by Alex and Sheriff - they seem pretty good resolution to me, yet if we want increased resolution, they will have to generate those again from the same software that generated thm originally - Basically the images have to be at least 300 dpi and export it as pdf and extract it as tiff or eps - not jpg.
Section 2.2.2 in the instruction provides information about the image quality:
https://www.frontiersin.org/about/author-guidelines<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.frontiersin.org%2Fabout%2Fauthor-guidelines&data=04%7C01%7CWinston.Garira%40univen.ac.za%7Ce905d707905f4301190c08d9da477a53%7Cf38ba9d8554c48a2ae4213b1e7f3c797%7C0%7C0%7C637780823036368924%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=%2BsG%2F%2FjiC3IvJdSbwVKG%2FWlOdYMufQ2JI0ebuJH55Lm8%3D&reserved=0>
Hopefully we can have those ready.
However, I do ask that all authors be ready to approve the paper assuming the other reviewer will be positive - we worked on thai for a year and there were many discussions - before this paper gets published I want all authors to be good with the final outcome. We will do this formally like we did before - yet I want everyone to be ready to avoid any delays. Hopefully it will take us less than 3 weeks this time.
Jacob
On Thu, Jan 13, 2022 at 1:05 PM Torres, Marcella <mtorres at richmond.edu<mailto:mtorres at richmond.edu>> wrote:
Hi again all,
On the 7th I shared comments from Reviewer 1 that we are now late responding to. Is it possible to provide high resolution figures, or no (see below)?
Reviewer 2 has endorsed the manuscript.
<image.png>
Reviewer 1 comment:
Reviewer 1 | 07 Jan 2022 | 14:36
#3
I would like to thank the authors for having fully addressed my comments. I'm satisfied about the quality the manuscript has been reached in this latest version. Finally, I would only suggest the authors to provide an high quality resolution of both new figures. Thank you.
Marcella Torres, Ph.D.
Director of Mathematical Studies
University of Richmond
Jepson Hall Room 212
221 Richmond Way
Richmond, VA 23173
(804) 289-8081
Pronouns: she/her
________________________________
From: Vp-reproduce-subgroup <vp-reproduce-subgroup-bounces at lists.simtk.org<mailto:vp-reproduce-subgroup-bounces at lists.simtk.org>> on behalf of Rahuman Sheriff <sheriff at ebi.ac.uk<mailto:sheriff at ebi.ac.uk>>
Sent: Monday, January 10, 2022 3:09 PM
To: Jacob Barhak <jacob.barhak at gmail.com<mailto:jacob.barhak at gmail.com>>
Cc: vp-reproduce-subgroup at lists.simtk.org<mailto:vp-reproduce-subgroup at lists.simtk.org> <vp-reproduce-subgroup at lists.simtk.org<mailto:vp-reproduce-subgroup at lists.simtk.org>>; vp-integration-subgroup at lists.simtk.org<mailto:vp-integration-subgroup at lists.simtk.org> <vp-integration-subgroup at lists.simtk.org<mailto:vp-integration-subgroup at lists.simtk.org>>; John Gennari <gennari at uw.edu<mailto:gennari at uw.edu>>; Faeder, James R <faeder at pitt.edu<mailto:faeder at pitt.edu>>
Subject: Re: [Vp-reproduce-subgroup] [Vp-integration-subgroup] Paper review and revision check list
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Thanks Jakob for submitting the revision and others for the support. Thanks William for editing my response.
Best
Sheriff
On 7 Jan 2022, at 04:52, Jacob Barhak <jacob.barhak at gmail.com<mailto:jacob.barhak at gmail.com>> wrote:
Thanks Hana, Thanks William, and thanks to Gilberto, Alex, and Sheriff,
With your help and some effort, the revised paper was resubmitted in time - just now.
William, please keep on reminding me about your second affiliation - I kept a comment as a reminder to do this - the submission system did not allow making any changes in Author information - not sure why - if this gets accepted we should ask the editor to add your affiliation manually.
I urge all other authors to look at the changes we made and our response. We will have to approve the manuscript with everyone before it gets published - hopefully we will convince the reviewers this review round.
Jacob
On Thu, Jan 6, 2022 at 3:51 PM Dobrovolny, Hana <h.dobrovolny at tcu.edu<mailto:h.dobrovolny at tcu.edu>> wrote:
I've read through the paper and fixed a few grammar mistakes.
Hana
*******************************************************
Dr. Hana Dobrovolny
Associate Professor of Biophysics
Texas Christian University
TCU Box 298840
Fort Worth, TX 76129
phone: (817) 257-6379 fax: (817) 257-7742
email: h.dobrovolny at tcu.edu<mailto:h.dobrovolny at tcu.edu>
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________________________________
From: Vp-integration-subgroup <vp-integration-subgroup-bounces at lists.simtk.org<mailto:vp-integration-subgroup-bounces at lists.simtk.org>> on behalf of Jacob Barhak <jacob.barhak at gmail.com<mailto:jacob.barhak at gmail.com>>
Sent: January 5, 2022 11:48 PM
To: William Waites; James Glazier
Cc: vp-reproduce-subgroup at lists.simtk.org<mailto:vp-reproduce-subgroup at lists.simtk.org>; vp-integration-subgroup at lists.simtk.org<mailto:vp-integration-subgroup at lists.simtk.org>; John Gennari; Faeder, James R
Subject: Re: [Vp-integration-subgroup] [Vp-reproduce-subgroup] Paper review and revision check list
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Greetings paper contributors,
Gilberto has addressed the final point and added text in the paper and review, thus concluding our response.
I went over the paper from start to finish again and cleaned it up.
There are two last comments in the paper addressed to William Waites and James Glazier - if you can quickly check those, it would help.
If someone else wants to read the paper once more, please do this today - otherwise I will convert the paper and our response to reviewers and submit it to the Journal portal.
If anyone has any objections, now is the time to raise them so we can withdraw rather than submit.
Here is the link to the revised paper:
https://docs.google.com/document/d/1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM/edit?usp=sharing<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fdocs.google.com%2Fdocument%2Fd%2F1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM%2Fedit%3Fusp%3Dsharing__%3B!!K6Z8K8YTIA!Qmy11SwUfgLnvEtA_Yy8DDA-OCSuTnTFPcnArqqv3zx410koRSJz-doddC0hvK3OmJ8%24&data=04%7C01%7CWinston.Garira%40univen.ac.za%7Ce905d707905f4301190c08d9da477a53%7Cf38ba9d8554c48a2ae4213b1e7f3c797%7C0%7C0%7C637780823036368924%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=PoFOhzAK3pEKiW%2FX6ByEKYp73FLvnTIymhTEWvPjbHo%3D&reserved=0>
Here is the link to response for reviewers:
https://docs.google.com/document/d/1bO1CDbMMlyyweYayP9rGohPIfgvIhfe14sFchtJMJ-s/edit?usp=sharing<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fdocs.google.com%2Fdocument%2Fd%2F1bO1CDbMMlyyweYayP9rGohPIfgvIhfe14sFchtJMJ-s%2Fedit%3Fusp%3Dsharing__%3B!!K6Z8K8YTIA!Qmy11SwUfgLnvEtA_Yy8DDA-OCSuTnTFPcnArqqv3zx410koRSJz-doddC0haRkeB0o%24&data=04%7C01%7CWinston.Garira%40univen.ac.za%7Ce905d707905f4301190c08d9da477a53%7Cf38ba9d8554c48a2ae4213b1e7f3c797%7C0%7C0%7C637780823036368924%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=h0HPOc5XUCGG0%2FQKqTmRTOT4LOumAf7j6n1c9ZOzTmo%3D&reserved=0>
Hopefully there will be no objections and can submit this tomorrow.
Jacob
On Tue, Jan 4, 2022 at 11:30 PM Jacob Barhak <jacob.barhak at gmail.com<mailto:jacob.barhak at gmail.com>> wrote:
Hi Alex, Hi William, Hi Gilberto, and all other contributors.
Alex, William and Gilberto are mentioned since we are the most active contributors.
We have 2 days to finish edits.
William - I attempted to add your suggestions to the paper regarding issue 11. You are free to revise further.
Gilberto - I merged some of your texts, yet it seems you are the only one I saw interested in resolving issue 12 where the reviewer asks to remove the "Model Application and Implementation Barriers" section. Please suggest your corrections as soon as possible. If you cannot do this by tomorrow I will do my best to add a response based on your idea. Yet I really hope you can do this before me.
Please finalize any edits you have - and if anyone has any objection to the text, please raise it within one day since after tomorrow I will start closing down all issues.
I would ask for a volunteer that will go over the paper once more after its finalized and check for typos and grammar - we do not want the paper to return again due to this issue. Time is tight, so please volunteer fast.
Hopefully we can get it done in time.
Jacob
On Tue, Jan 4, 2022 at 7:25 AM Alexander Kulesza <alexander.kulesza at novadiscovery.com<mailto:alexander.kulesza at novadiscovery.com>> wrote:
Dear Jacob, dear all,
thanks for endorsing my figure. I'll gladly add this. Please find enclosed the .png.
What you say makes sense and I agree that exaggerating changes is not speeding up approval. Please still consider it as a tool to perform "major" change (ordering of sections is a major change of a paper in my opinion) without changing too much the sections as such. But I agree that this could be tried out should the reviewers insist.
I therefore reverted the table change (disconnecting ist from Figure 1) and suggest the following Figure caption:
"Figure 2: Sketch of difficulties persistent that impede reproducibility, credibility, utility and integration of models, especially in computational biology. An assignment of these difficulties to the four different concepts interpreting them as hurdles is attempted. We would like to point out that this sequential assessment model indicated in the graph is only one of the possibilities a modeler would assess the suitability of available models. In the rest of the paper we therefore address each difficulty separately. "
With that sentence we can discuss the difficulties in any order.
Best
Alexander
On Tue, 4 Jan 2022 at 13:24, Jacob Barhak <jacob.barhak at gmail.com<mailto:jacob.barhak at gmail.com>> wrote:
Yes Alex,
Your image is much better than mine, please use it instead in the paper and send a link to the image itself in an acceptable image format so I can upload it to the submission system later on.
As for changing the table and order, I am not sure. Although it may be possible. We need to think about it. Yet we really are crunched in time, so I am leaning to say no.
First, because some of the difficulties span more than one category, for example unit standardization affects integration as well as reproducibility, only it appears first at reproducibility, therefore it was placed there in the figure.
Second, if you look at the text there are some transition sentences among sections, that connect them, so swapping those around may just mess things. I am not sure it if will also mess up acronym definitions on the first appearance as well, so shuffling order is not something's I would do unless necessary. And it was not requested by reviewers anyway.
I am also trying to minimize changes and focus only on what was requested rather than change a lot more. Otherwise we may never finish changing things since each one of the 18 of us will have a one last item they MUST have corrected. I personally did not add some recent publications I had, although I added one publication James asked to add in the previous approval round and corrected one that Sheriff mentioned. Yet I really want to avoid opening the paper to significant changes.
If you start opening corrections beyond what was requested, this will drag on forever since we do have a large list of contributors and each one of us will generate a new idea. So please focus on what was asked unless absolutely necessary.
So I suggest not changing the table, and changing only the figure and keeping order intact. I hope I am projecting the sense of urgency - we had the paper lying around for a couple of weeks during the holiday without much progress, I ask not to escalate things just because a deadline is looming.
If you have extra time on your hands in the next couple of days, I suggest you focus on addressing the last two points in the response that we have not resolved yet. I know Gilberto wanted to fix one of them, yet you are welcome to do it. Those are things requested by the review
Hopefully my arguments make sense.
Jacob
On Tue, Jan 4, 2022, 06:45 Alexander Kulesza <alexander.kulesza at novadiscovery.com<mailto:alexander.kulesza at novadiscovery.com>> wrote:
Dear all,
I have thought about the additional Figure requested by the reviewer. Jacob your Figure nicely shows the assignment of the difficulties we detail in our central table with the 4 big concepts.
I feel however that the text-heavy figure is a lot o redundancy with the rest of the elements (existing figure & table). Therefore I wanted to throw another suggestion forward (inspired by systematic reviews narrowing down eligible studies/data).
@all please notice that the assignment I would do is a bit different to what is currently done in the paper. The order of sections would have to be altered. Not sure if that is acceptable.
<image.png>
The table with Difficulties (hurdles) and solutions would then be
Difficulty
Potential Solutions
Reproducibility
Models are written in different languages
Common transport specifications such as SBML or CellML, and proper documentation and annotation
Models are hard to locate
Archive web sites such as: BioModels, SimTK, IMAGWiki, and the future modeleXchange
Lack of common platforms for executing models and simulations
Platforms such as BioSimulators, and runBioSimulations
Unit standardization
Standardization efforts, and machine learning solutions such as ClinicalUnitMapping.com<https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fclinicalunitmapping.com%2F&data=04%7C01%7CWinston.Garira%40univen.ac.za%7Ce905d707905f4301190c08d9da477a53%7Cf38ba9d8554c48a2ae4213b1e7f3c797%7C0%7C0%7C637780823036368924%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=ctmyqlzzJKJ%2F41ZusRl2q4fJYWbJ6%2FuPzv%2BDs40dqZs%3D&reserved=0>
Credibility
Models have built-in barriers to Evaluating model credibility
Better modeling practices, documentation, and tests.
Data availability and measurement definitions
Models that merge human interpretation, and newer measurement devices
Missing annotations in models
Adoption of policies such as those COMBINE suggests
Utility
Models are not consistently licensed to allow for reuse
Abandoning some old school open source licenses and promoting licenses that release to public domain
Different scales and modeling paradigms
Standardization effort and centralization tools
Stochastic modeling difficulties
Development of tools that guarantee repeatability and standards to address stochastic simulations
Integration
Model application and implementation barriers
Education of modelers, users, and the public
Modeling requires adaptation towards integration
Tools for composing models such as SBML-Comp, and SemGen
Following this assignment.
Please let me know what you think. I have added this suggestion in track changes mode to the revision draft.
Best
Alexander
On Mon, 3 Jan 2022 at 07:27, Jacob Barhak <jacob.barhak at gmail.com<mailto:jacob.barhak at gmail.com>> wrote:
Thanks Alex,
You did great by adding the new material that the reviewers actually asked for. This is great - I found myself adding the new FDA document to find out that you already added it - I just voice read it ona long drive and figured it fits well - it seems you were faster - great.
I merged your edits and I am ok with adding your response to the reviewers - I only had an issue with one example paragraph that you deleted - I left it with a comment - please check if it is possible to keep this example somewhere in the text.
I will assemble a letter that includes all those responses point by point and will try to use your text almost verbatim if possible. You really bring important knowledge with you.
It seems most points have been answered to some level - even a figure was created - although I wish I was a better artist.
I will try to assemble the response letter for everyone within the next few days. And unless there will be objections I will try to pass it by reviewers with a new version. If the new version is accepted, we will do a final approval round before publication.
Many thanks to all those who contributed.
Jacob
On Sun, Jan 2, 2022 at 7:27 AM Alexander Kulesza <alexander.kulesza at novadiscovery.com<mailto:alexander.kulesza at novadiscovery.com>> wrote:
Dear all,
Happy new year to everyone. I hope that you are all well and safe and have spent a nice holiday season.
I have tried to address
Reviewer 2
Moreover, when the authors mention ASME V&V40 procedure, it could be useful to spend few words about the model credibility pipeline drawn for predictive models in biomedicine, such as the one suggested in "Credibility of in Silico Trial Technologies-A Theoretical Framing", Viceconti, M., Juarez, M.A., Curreli, C., ...Russo, G., Pappalardo, F., IEEE Journal of Biomedical and Health Informatics, 2020, 24(1), pp. 4–13, 8884189.
For this specific aspect, the authors should talk about "specific question of interest" and not "specific purpose" in the paragraph called "Credibility of Models" to follow in such a way a standardised language.
I have worked on the followng document in "track changes" mode:
https://docs.google.com/document/d/1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM/edit<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fdocs.google.com%2Fdocument%2Fd%2F1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM%2Fedit__%3B!!K6Z8K8YTIA!Qmy11SwUfgLnvEtA_Yy8DDA-OCSuTnTFPcnArqqv3zx410koRSJz-doddC0hrtFQ-XI%24&data=04%7C01%7CWinston.Garira%40univen.ac.za%7Ce905d707905f4301190c08d9da477a53%7Cf38ba9d8554c48a2ae4213b1e7f3c797%7C0%7C0%7C637780823036368924%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=mseGpx%2Fs%2BDeFvZSJ6m4S%2BpZCA4zZ6k3%2BMsibt91pbNg%3D&reserved=0>
Actually, I ended up in changing rather drastically the section. I think that all ideas and all text is conserved, but I would very much like to encourage you to read, comment and challenge this revision. Please tell me if that goes to far. No problem to revert to an earlier version if necessary.
I suggest the following formulation in the rebuttal letter:
When trying to better describe the "credibility pipeline" (CoU definition, verification, validation, uncertainty quantification, e.g. as described in Viceconti et al. 2019) or others, we noticed that the section about credibility could be restructured in order to put the reader (not necessarily familiar with regulatory assessment of models) in the position to follow the argumentation.
We now roughly follow the following flow of writing:
- Every model needs a purpose and credibility is tied to that purpose as well as repeatability and reproducibility
- Credibility is essential for models that have impact on regulated areas or people's lives which is why regulatory authorities issue guidance
- The probably most advanced guidance ASME V&V40 suggests a risk-based approach and pipeline to establish credibility of a model. It is overarching and widely applicable
- Regulators and modelers work together (for example in frame of the model informed drug development program MIDD) in order to better understand, better apply and better uptake different kinds of models in regulatory applications
- More work is needed to harmonize, stay up to date and to be more inclusive
We hope that with the rather extensive change of the wording and additional passages as well as citations (see below) we could address the concern of reviewer 2 (and the general remarks of reviewer 1).
" In 2018 the American Society of Mechanical Engineers (ASME) issued an important guidance ASME V&V 40 (ASME, 2018) of how to assess credibility of computational models of medical devices through verification and validation (V&V). The guideline is centered around the definition of the context of use (CoU) of the model which is formulated based on the questions of interest the model will answer. The CoU is then analyzed in terms of the “model risk” - being the influence the model exerts on a decision and the potential consequences these decisions might incur. Commensurate with this model risk the modeler suggests establish the credibility goals, perform verification validation and uncertainty quantification actions and then assess the outcome of this exercise in order to allow judging the acceptability of the model CoU. Key to this guidance is its overarching nature which also allows adoption in other (e.g. drug development) fields irrespective of the model type (Kuemmel 2020, Viceconti 2019)."
We also feel that it is essential to underline the cross-discipline viewpoint of the ASME V&V40 which is further elaborated by the cited paper by formalizing the verification, validation and uncertainty quantification VVUQ pipeline across model types.
We therefore have added the following statement
" In the paper by (Viceconti 2019) the verification, validation and uncertainty quantification (VVUQ) pipeline is streamlined to different types of models. It is, perhaps, the closest to score credibility across model types from mechanistic physics driven models to machine learning models. However, it is still short of including very recent developments such as ensemble models, although it touches upon the topic."
We additionally strengthened our argumentation by citing additional literature
Bai, JPF, Earp, JC, Florian, J, et al. Quantitative systems pharmacology: Landscape analysis of regulatory submissions to the US Food and Drug Administration. CPT Pharmacometrics Syst Pharmacol. 2021; 10: 1479– 1484. doi.org<https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fdoi.org%2F&data=04%7C01%7CWinston.Garira%40univen.ac.za%7Ce905d707905f4301190c08d9da477a53%7Cf38ba9d8554c48a2ae4213b1e7f3c797%7C0%7C0%7C637780823036368924%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=NnEHJ7f3YFOuD%2FvDv4BoJA1Qu1QSaIaW1YEZ%2BajyDK0%3D&reserved=0>:10.1002/psp4.12709
FDA (2021b). Assessing the Credibility of Computational Modeling and Simulation in Medical Device Submissions. FDA
Available at: https://www.fda.gov/regulatory-information/search-fda-guidance-documents/assessing-credibility-computational-modeling-and-simulation-medical-device-submissions<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fwww.fda.gov%2Fregulatory-information%2Fsearch-fda-guidance-documents%2Fassessing-credibility-computational-modeling-and-simulation-medical-device-submissions__%3B!!K6Z8K8YTIA!Qmy11SwUfgLnvEtA_Yy8DDA-OCSuTnTFPcnArqqv3zx410koRSJz-doddC0harP7IHc%24&data=04%7C01%7CWinston.Garira%40univen.ac.za%7Ce905d707905f4301190c08d9da477a53%7Cf38ba9d8554c48a2ae4213b1e7f3c797%7C0%7C0%7C637780823036525180%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=kzgGEch2DZXOsiGGFqhDAeNEjb3zrAynsOcfF0X%2FSYg%3D&reserved=0> [Accessed January 2, 2022]
Galluppi, G.R., Brar, S., Caro, L., Chen, Y., Frey, N., Grimm, H.P., Rudd, D.J., Li, C.-C., Magee, M., Mukherjee, A., Nagao, L., Purohit, V.S., Roy, A., Salem, A.H., Sinha, V., Suleiman, A.A., Taskar, K.S., Upreti, V.V., Weber, B. and Cook, J. (2021), Industrial Perspective on the Benefits Realized >From the FDA’s Model-Informed Drug Development Paired Meeting Pilot Program. Clin Pharmacol Ther, 110: 1172-1175. doi:10.1002/cpt.2265
Kuemmel, C., Yang, Y., Zhang, X., Florian, J., Zhu, H., Tegenge, M., Huang, S.-M., Wang, Y., Morrison, T. and Zineh, I. (2020), Consideration of a Credibility Assessment Framework in Model-Informed Drug Development: Potential Application to Physiologically-Based Pharmacokinetic Modeling and Simulation. CPT Pharmacometrics Syst. Pharmacol., 9: 21-28. doi.org<https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fdoi.org%2F&data=04%7C01%7CWinston.Garira%40univen.ac.za%7Ce905d707905f4301190c08d9da477a53%7Cf38ba9d8554c48a2ae4213b1e7f3c797%7C0%7C0%7C637780823036525180%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=Fn7pJ5EAgXXyqFcPBl1NljHVQDpwyfshvjb5NwUtwBM%3D&reserved=0>:10.1002/psp4.12479
Musuamba, FT, Skottheim Rusten, I, Lesage, R, et al. Scientific and regulatory evaluation of mechanistic in silico drug and disease models in drug development: Building model credibility. CPT Pharmacometrics Syst Pharmacol. 2021; 10: 804– 825. doi:10.1002/psp4.12669
Viceconti M, Emili L, Afshari P, et al. Possible Contexts of Use for In Silico Trials Methodologies: A Consensus-Based Review. IEEE J Biomed Health Inform. 2021;25(10):3977-3982. doi:10.1109/JBHI.2021.3090469
All the best
Alexander
On Sun, 19 Dec 2021 at 03:10, Jacob Barhak <jacob.barhak at gmail.com<mailto:jacob.barhak at gmail.com>> wrote:
Greetings to the paper contributors,
You may have seen my other message where I posted the reviews to our paper. I am sending those again below to start a new thread discussing possible revisions.
Here is a checklist for revisions required:
1. We should discuss the references that reviewer 1 raised and add them as reference
2. Reviewer 1 asked for more discussion around V&V40 - I believe Alex added the text there originally - Alex do you think you can address the request of the reviewer?
3. Reviewer 1 asked to focus on COVID-19 at the title - I am not sure we wish to limit our scope since many of our ideas are applicable far beyond COVID-19 - I leave it up for discussion in the group on how to address this request by the reviewer
4. Reviewer 1 asked for additional graphics - I am unsure how to address this beyond ur current diagram - ideas will help
5. We need to check the "Contribution to the field" section for grammar and spelling - if someone can contribute more elegant text - now is the time - I looked over it now and found no issues - yet I may have missed something - this section may have been missed since it was added last and perhaps vetted less than other sections. Also Reviewer 2 asked for grammar corrections, so it is worthwhile proof reading the paper as a whole.
6. Reviewer 2 asks for major rewrite to emphasize why the problems are there - I think we should explain that the core of the paper is the table and perhaps emphasize it in the paper beyond what the current text - we also should reply to the reviewer and explain that the paper is composed of contributions from a large group and we made an effort to include every voice in the choir - each of those voices is important and needs to be preserved - hopefully it will convince the reviewer that change we will add will be sufficient
7. Reviewer 2 asks to revise the introduction - I believe some changes are possible - yet the introduction includes contributions from many authors - at least 10 - and I fear losing something important someone contributed - if someone has an idea on how to address this reviewer without a painful transformation, please reply to this message.
8. Reviewer 2 wants additional discussion around the "reproducibility crisis" section and asks a valid question about expectations we should address - "“Computational biomedical modeling… was expected to be less affected by the reproducibility crisis.” Is this true, and why would it be so? " - My answer to the reviewer is that unlike biological processes that have random nature and experiments would not repeat if repeated, while computer software should be deterministic and it should be repeatable if designed well. Unfortunately we are not experiencing this promise - yet I believe the reviewer wants more discussion beyond this section so I am happy to discuss this.
9. Reviewer 2- writes: "Models are Hard to Locate: Are the authors suggesting that entire simulation workflows, from model construction to analysis, should be publicly available? At what point does one consider intellectual property? Do the authors advocate for such extensive publishing for all models, or only ones that are intended to be widely re-used? - those are important points we need to discuss - we need to better explain the difficulties we are having when creating models and the reviewer is absolutely correct about expanding the discussion to IP - I suggest we create a thread for this discussion and reference it - I suggest it we merged with the licensing issue that I will address later - there is a strong connection there - the reviewer was very observant and sees the bigger problem. However,we need to eventually distill our discussion to recommendations that will inline.
10. Reviewer 2 asks that we fix the unit standardization section - I believe Hana and myself were the largest contributors there - Hana - I will start a discussion on that topic in a separate email where we can publicly discuss how to fix this - others will be welcome to contribute.
11. Reviewer 2 asks that we better handle the section on Data availability and measurement definitions: in think we need to emphasize solutions and separate it from issues that may not be solvable. Ideas are welcome.
12. Reviewer 2 asks good questions with regards to licensing following our text- I personally have good answers to the reviewer and William and I had some discussion on the topic in this list I suggest we expand this discussion in a separate thread - hopefully William and perhaps others will join the discussion. This discussion should also address the IP issues raised by the reviewer for the "models are hard to locate section."
13. Reviewer 2 asks to handle the Model Application and Implementation Barriers section. We should decide what to do there, the section may need expansion since the ideas there are solid, yet the section is short so perhaps enhancing it makes better sense. I am open to suggestions.
Those are the items I located and my suggestions. It seems we need attention from Alex, Hana, myself and william. However, anyone on the list is welcome to participate and suggest changes.
I will start the discussion threads on specific topics. Hopefully we can get it done quickly.
Jacob
-
########### Original Reviews #############
There are 2 reviews - both require major changes. I am copying the relevant text below. If more appear, I will let you know, yet I only got this message today although the reviews are dated a few days ago.
Reviewer 1:
Recommendation for the Editor: Substantial revision is required
Please list your revision requests for the authors and provide your detailed comments, including highlighting limitations and strengths of the review. If you have additional comments based on Q2 and Q3 you can add them as well.
Karr and co-authors made an interesting and exaustive point about the reproducibility crisis that leads to inability to reuse and integrate models, especially about COVID-19 disease.
Within the manuscript some typos and missing information are present.
I'd suggest the authors to revise the entire manuscript especially in terms of the state of the art, revising and updating the most relevant examples of computational models dealing with COVID-19 and in general about some semi-standardised proposals about the pipeline to follow for the verification and validation of model credibility. In particular, the authors failed to mention and cite some major results on in silico modeling about COVID-19 up to now. See for example:
a."In silico trial to test COVID-19 candidate vaccines: a case study with UISS platform", Russo, G., Pennisi, M., Fichera, E., ...Viceconti, M., Pappalardo, F., BMC Bioinformatics, 2020, 21, 527.
b. Russo G, Di Salvatore V, Sgroi G, Parasiliti Palumbo GA, Reche PA, Pappalardo F. "A multi-step and multi-scale bioinformatic protocol to investigate potential SARS-CoV-2 vaccine targets" [published online ahead of print, 2021 Oct 5]. Brief Bioinform. 2021;bbab403. doi:10.1093/bib/bbab403.
Moreover, when the authors mention ASME V&V40 procedure, it could be useful to spend few words about the model credibility pipeline drawn for predictive models in biomedicine, such as the one suggested in "Credibility of in Silico Trial Technologies-A Theoretical Framing", Viceconti, M., Juarez, M.A., Curreli, C., ...Russo, G., Pappalardo, F., IEEE Journal of Biomedical and Health Informatics, 2020, 24(1), pp. 4–13, 8884189.
For this specific aspect, the authors should talk about "specific question of interest" and not "specific purpose" in the paragraph called "Credibility of Models" to follow in such a way a standardised language.
Moreover, the authors should refer to COVID-19 also in the title, with a specific mention about the fact that the main topic of model integration in computational biology will be discussed inside the COVID-19 context.
Furthermore, for the model key concepts such as Reusability-Extensibility-Extractability-Portability the authors should described and outlined through a graphical sketch or visual representation that summarises these key point.
The authors should also fix some grammar and writing typos present in the "Contribution to the field" section.
a. Is the quality of the figures and tables satisfactory?
- No
b. Does the reference list cover the relevant literature adequately and in an unbiased manner?
- No
c. Does this manuscript refer only to published data? (unpublished or original data is not allowed for this article type)
- Yes
d. Does the review include a balanced, comprehensive, and critical view of the research area?
- Yes
Reviewer 2
Please list your revision requests for the authors and provide your detailed comments, including highlighting limitations and strengths of the review. If you have additional comments based on Q2 and Q3 you can add them as well.
The article often reads as a stream-of-consciousness account of the discussions that took place but lacks a clear thesis or recommendations. It is not clear what, if anything, the authors are advocating for. It is not always clear why the issues being discussed are problematic, or that they can be reasonably addressed. Some of the issues raised are indeed important and should be discussed, but the paper lacks focus and does not tell a cohesive story. I believe this manuscript requires a major re-write to be suitable for publication. The authors should consider narrowing the scope of the discussion and focusing on a cohesive set of recommendations or open questions. More specifically, I make a few suggestions below:
Major comments
1. The introduction is long and repeats itself (e.g., “much less is known about how viral infections spread throughout the body…” is repeated verbatim). It is not clear from the introduction what the main goal of the paper is or why the “reproducibility crisis” is truly a crisis. Why is the discussion of composition and black/white box models relevant to the introduction? Further, this section is subtitled “the promise of modeling”, which does not seem to match the content.
2. The Reproducibility Crisis: “Computational biomedical modeling… was expected to be less affected by the reproducibility crisis.” Is this true, and why would it be so? One would think that more complex models would suffer more from a lack of reproducibility. It may be helpful to define what exactly the “reproducibility crisis” refers to.
3. Models are Hard to Locate: Are the authors suggesting that entire simulation workflows, from model construction to analysis, should be publicly available? At what point does one consider intellectual property? Do the authors advocate for such extensive publishing for all models, or only ones that are intended to be widely re-used?
4. Unit standardization: The conversion from PFU or TCID50 to individual virions is likely to differ across viruses – are the authors focused on COVID here? Are the authors advocating for a standard conversion factor? It is not clear what the purpose of this discussion is. As the authors mention, different scales require different units. Even at a single scale, different models may require different units for numerical reasons. It is not clear what the authors are advocating for here.
5. Data availability and measurement definitions: This section seems to outline limitations of available data, but again makes no recommendations or proposed solution to any of the issues raised. Is this the intention? Most of the issues raised here reflect limitations of experimental science or data privacy, which likely cannot be meaningfully addressed by the modeling community.
6. Models are Not Consistently Licensed…: Are the authors implying here that all modeling work should be published with no rights reserved? Is it reasonable to expect modelers to make their work freely usable by others for profit? Is it reasonable for institutions to allow this? How much does this really contribute to reproducibility and utility?
7. Model Application and Implementation Barriers: This section seems unnecessary and out of place.
8. There are grammar and punctuation errors scattered throughout; please edit carefully.
a. Is the quality of the figures and tables satisfactory?
- Not Applicable
b. Does the reference list cover the relevant literature adequately and in an unbiased manner?
- Yes
c. Does this manuscript refer only to published data? (unpublished or original data is not allowed for this article type)
- Yes
d. Does the review include a balanced, comprehensive, and critical view of the research area?
No answer given.
========
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+33 7 82 92 44 62
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