[Vp-integration-subgroup] [Vp-reproduce-subgroup] Shayn Peirce-Cottler via Frontiers: Manuscript
Eric Forgoston
eric.forgoston at montclair.edu
Mon Oct 25 04:36:24 PDT 2021
Hi Jacob,
The stochastic text was written by me. Robin and William provided lots of
comments which I incorporated (James G had one comment as well), but the
text was mine.
Cheers,
Eric
---------------------
Dr. Eric Forgoston
Professor of Applied Mathematics
Chair, Department of Applied Mathematics and Statistics
Montclair State University
Montclair, NJ 07043 USA
+1 973 655-7242
https://eric-forgoston.github.io/
On Mon, Oct 25, 2021 at 12:57 AM Jacob Barhak <jacob.barhak at gmail.com>
wrote:
> Thanks James, And thanks Eric.
>
> James - your idea is not bad. However, there is a conflict between the
> two approaches to present the work.
>
> The previous approach was set by Sheriff who noticed that there is a path
> from reproducibility, through credibility, to utility to allow
> integration. And the structure followed that flow. It was not perfect, yet
> the idea was good and important - this was a major observation he
> introduced early on. We eventually focused on challenges in the utility
> section since this is where it seems we are stuck today - although many of
> the challenges are rooted before utility.
>
> John Gannari took a different approach and focused on the challenges - he
> merged some sections to get straight to the point. This is noticeable
> especially in the two credibility sections that were merged into one..
>
> I tried to follow this idea, yet his version was not something I can work
> on because it has not matured and was not traceable and lost many details
> and nuances that seem important - at least to me. Yes, there were so many
> trees that the reader may have lost the forest. When editing I was thinking
> how to make the merge - however, it was not obvious how to do it while
> maintaining the idea Sheriff introduced without a lot of work and while not
> removing other nuances. So I decided for practical reasons to keep the
> structure closer to what Sheriff asked - believe me I saw the value of
> John's approach - it was just much more work and our resources are limited.
>
> Eventually I decided that the most important thing in this work is the
> summary - basically the table and its detailed explanation in the sections
> we wrote. Think about it. What we summarized can be reused by an official
> to decide where to allocate efforts in the future - even we can reuse this
> when writing a proposal to focus on resolving issues and point to that
> summary as an explanation to why we are working on some topics. We show
> the grave reality as is and admit there are problems and suggest possible
> solutions. This is important. This is why I am pushing towards fast
> publication - if we publish fast, our findings may have more impact than if
> we continue perfecting the product towards publication.
>
> So I am not really arguing against your points, they are valid, yet in my
> mind the priority is to get the paper published so we can move on and fix
> those problems rather than discussing what is the best way to present them.
> I agree that the presentation is not perfect - yet in my mind it is more
> than good enough.
>
> This is why I am pushing and I hope I am transmitting this sense of
> urgency to the group properly. We can always continue discussions later,
> yet for now let us agree on something and make sure it gets published
> properly.
>
> We can always have a better version in the future.
>
> Please remember that this is the best I could do after working many
> consecutive hours on it. And I did add many of John's ideas in the new
> version - whatever was lost I apologize, yet I am only human and can do so
> much. I really tried hard to preserve all ideas - I hope I did well enough.
>
> Hopefully this will calm down the conversation so we can focus on action.
>
> I see Eric changed the text in the stochastic section. This concludes
> major changes other than formatting and proofs if I recall correctly.
> However, before I proceed further I would like Eric to acknowledge that
> this test was his alone and was not just copied from another version. We
> had no traceability on the other version and I know there were many
> anonymous edits. Even when Hana added some sections to the paper she ported
> Alex's changes by mistake - after a while people forget what text they
> wrote - it's normal. I want a fully traceable paper back to originators -
> it is not an unusual request in a group that declares they are interested
> in reproducibility - if we cannot trace our own edits, how ever do we think
> we can ever trace a complex mathematical model?
>
> So Eric, I ask that you publicly verify that the text you added here is
> your own and only yours and does not have contributions from an anonymous
> contributor .
>
> Also Hana, you added two more paragraphs in the units standardization
> section - can you verify that those are yours and only yours - and from
> anonymous contributors? You already verified this for the paragraphs you
> added in data definitions - can you double check the paragraphs in
> the units section and reply to all declaring this is your text alone?
>
> As you can see the concept of traceability back to origin is important to
> me - I ask that you help me here.
>
> Jacob
>
>
>
>
>
> On Sun, Oct 24, 2021, 17:32 James Osborne <jmosborne at unimelb.edu.au>
> wrote:
>
>> My main suggestion is what I did to the previous version (John Gs) bit
>> didn't make it over. Which was to have some more levels to the sections.
>> As it is they are all the same level and therefore there's no break
>> between the introduction material and the main focus of the paper (in my
>> opinion the table of difficulties or challenges and subsequent sections)
>>
>> My very low effort proposal is to.
>>
>> * change the section title "Utility of Models" to something like
>> "Challenges with using multiscale models
>> * Then put the difficulties/ challenges listed in the table into
>> subsections called things like "Challenge 1: Evaluating Model Credibility "
>>
>> This wouldn't change any content so would not mess up tracking
>> contributions or the "content" of the paper but would make it more readable
>> as the reader would have more help identifying the contribution from the
>> paper.
>>
>> I believe it will make the papers intent clearer and easier to read.
>>
>> But if you're against it I rest my case and defer to your opinion.
>>
>> James
>>
>>
>> On Mon, Oct 25, 2021 at 8:53 AM Jacob Barhak <jacob.barhak at gmail.com>
>> wrote:
>> >
>> > Well James,
>> >
>> > You should look at the new version. And please no more suggestions
>> other than proofs or pointing out errors. We really are not at that stage
>> anymore. We had many months for suggestions. It is time for finalization
>> towards what the editor asked for.
>> >
>> > I hope you understand.
>> >
>> > Jacob
>> >
>> > On Sun, Oct 24, 2021, 03:51 James Osborne <jmosborne at unimelb.edu.au>
>> wrote:
>> >>
>> >> Jacob
>> >>
>> >> I was just about to make some suggestions on structure which were
>> added to the bakers dozen version version.
>> >>
>> >> I'll make in suggest mode then you can decide of they work or not.
>> >>
>> >> James
>> >>
>> >> On Sun, Oct 24, 2021 at 7:44 PM Jacob Barhak <jacob.barhak at gmail.com>
>> wrote:
>> >>>
>> >>> Hi Eric,
>> >>>
>> >>> You are the last one I remember who wanted to edit. Please check the
>> manuscript
>> >>>
>> https://docs.google.com/document/d/1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM/edit?usp=sharing
>> >>>
>> >>> I finished editing the references and am almost ready for
>> transformation to match the guidelines. I finished addressing the editor
>> requesting for removal of bullet points everywhere but the stochastic
>> section .
>> >>>
>> >>> I ask that you do not add any more references and focus only on text
>> in the stochastic section. Handling the references took about 4 hours alone
>> and still needs inspection.
>> >>>
>> >>> However, I will appreciate help with minor proofs - I made
>> significant changes so there is a chance for typos still. Some of the
>> changes have been made after more than 12 hours of consecutive work. So
>> polish will help - yet no more major changes.
>> >>>
>> >>> The tasks left to do are:
>> >>> - Ask John Gennari to inspect the paper again - it has major
>> contributions from his version and he should join the authors list - I must
>> be ask again
>> >>> - Finish the edits to the stochastic section - Eric - you asked for
>> this
>> >>> - Finish formatting to fit the Journal guidelines
>> >>> - Add a cover letter and split the paper into sections to be uploaded
>> to the journal web site
>> >>> - Approve the version with all authors - we must do this again and
>> get full approval - this may take a while
>> >>> - Determine who else wants to be listed as corresponding author -
>> currently I marked Marcell and myself, yet others may want to correspond.
>> >>> - Upload the paper to the journal submission system
>> >>>
>> >>> I hope for no obstacles and full cooperation to make the process
>> smooth.
>> >>>
>> >>> Jacob
>> >>>
>> >>>
>> >>>
>> >>> On Sat, Oct 23, 2021 at 9:08 PM Jacob Barhak <jacob.barhak at gmail.com>
>> wrote:
>> >>>>
>> >>>> So Gilberto,
>> >>>>
>> >>>> The last approved version is the only one we can continue from -
>> this is unfortunate that there is a need to back port some modifications -
>> hence the conversation with Eric and Hana - yet to maintain traceability
>> and honor all contributors - this is necessary.
>> >>>>
>> >>>> And yes, there will be some differences - it's unavoidable. Yet I
>> pretty much merged the other traceable versions by now. If I missed
>> anything - I apologize - there is a limit to human capabilities.
>> >>>>
>> >>>> We discussed this multiple times on this list, if this is a stopper
>> for you, let me know immediately so I will stop work to resolve this issue.
>> >>>>
>> >>>> Otherwise, I will continue - I think I resolved most points except
>> from references and removal of bullets - still working on that and I will
>> have to deal with modifying conclusions at the end.
>> >>>>
>> >>>> And Gilberto, if you want to contribute time towards changing order
>> of sections and handle references to comply with the target journal
>> guidelines, please go online on the Jitsi channel.and I will show you the
>> extent of work needed. I will be here for at least 3 more hours - until
>> midnight - yet to be efficient, please join on jitsi if you want to talk
>> while I continue modifications.
>> >>>>
>> >>>> I hope I can finish most of the work except references perhaps by
>> midnight.
>> >>>>
>> >>>> Jacob
>> >>>>
>> >>>>
>> >>>>
>> >>>> On Sat, Oct 23, 2021 at 8:32 PM Gilberto Gonzalez-Parra <
>> gilberto.gonzalezparra at nmt.edu> wrote:
>> >>>>>
>> >>>>> Hi Jacob,
>> >>>>>
>> >>>>> I noticed that we are not using the last version that has many
>> modifications. Are you using the previous version that was originally
>> submitted to cureus ? and trying to incorporate the changes of the last
>> version ?
>> >>>>>
>> >>>>> I noticed that the section/challenge Barriers to model
>> implementation and real-world use was removed. I think in one of the emails
>> it says that there is no solution proposed for this. I can write some
>> general ideas for this.
>> >>>>>
>> >>>>> In the current version in the table it appears "Model application
>> and implementation barriers" just after "Missing Annotations in Models" but
>> later in the document appears just before stochastic modeling. I think we
>> should keep the same order that is in the table. The article would look
>> better organized.
>> >>>>>
>> >>>>> Best,
>> >>>>>
>> >>>>>
>> ***************************************************************************
>> >>>>> Gilberto C. Gonzalez-Parra, Ph.D in Applied Mathematics.
>> >>>>> Faculty of the Mathematics Department
>> >>>>> New Mexico Tech, NM, USA.
>> >>>>>
>> ****************************************************************************
>> >>>>>
>> >>>>>
>> >>>>> On Sat, Oct 23, 2021 at 5:38 PM Jacob Barhak <
>> jacob.barhak at gmail.com> wrote:
>> >>>>>>
>> >>>>>> Hi Eric, and also greeting for the other paper contributors
>> >>>>>>
>> >>>>>> Here is a real time update just to give an idea of current editing
>> status.
>> >>>>>>
>> >>>>>> It took almost 6 hours to get the manuscript to the point that
>> contributions from Sheriff, Alex, John Gennari, and Hana were integrated. I
>> assume Eric will add his edits later - since those are in one section, it
>> should not cause any conflict. However, Eric, please be careful when
>> editing the stochastic section. Pease look at the comments Hana and I
>> exchanged. I am also adding the chat between us so it will be easier on you:
>> >>>>>>
>> >>>>>> "
>> >>>>>> Hi Hana
>> >>>>>> Can you see the chat?
>> >>>>>> I can. There's just a lot going on around here right now, so I'm
>> not fast with typing
>> >>>>>> I put the references in the comments, can you see them?
>> >>>>>> Yes I See them - yet you will have to ensure that this is your
>> text - you see, you copied text from a document where we do not have
>> contributor history - this was the main issue - so you will have not to
>> prove this was your text and only your text - this is the problem I am
>> faced with - I have to establish tracability - in this document I know you
>> added the text - yet I cannot verify that you did not include text from
>> anonymous since I already concluded you added text from Alex - this is how
>> I stumbled on this - I apologize yet I really am serious about tracing back
>> authorship..
>> >>>>>> And thanks fro helping
>> >>>>>> If you want, you can join jitsi:
>> https://meet.jit.si/CollaborativePaperEditing and we can chat using
>> voice
>> >>>>>> I just saw your comment - it is public confirmation - this is good
>> enough thank you
>> >>>>>> The first two paragraphs are from the original paper. The third
>> paragraph is from Alex. The last two are mine. It looks like someone (other
>> than me) italicized the in vitro and in vivo and changed the verb on the
>> "Even data that are..." (I had is), but everything else is mine.
>> >>>>>> If you can modify things to the original version you added - it
>> will be better - if someone manipulated the text I want to remove it - even
>> if it is small changes
>> >>>>>> I know you're trying to get things done today, but I'll be out
>> tonight, so if anything else comes up, I probably won't get to it until the
>> morning.
>> >>>>>> Well, "are" is the correct verb there, so that should probably
>> stay. I can remove the italicization.
>> >>>>>> Do not worry - I am making good progress and may not need help
>> until I am done - I appreciate the help and the fact you are working on it
>> over the weekend - I will later also make this chat public for
>> transparency. I do believe you have contributed a lot to this paper - its
>> not the first time you are going over it - I can only thank you .
>> >>>>>> the are was my change today I believe so its not a problem - yet
>> google suggests is instead I guess is and are both acceptable with data
>> .... nevermind that.
>> >>>>>> "
>> >>>>>>
>> >>>>>> I did my best to keep all ideas and other texts intact and there
>> are many comments to mark changes - the paper became longer, yet not too
>> much and I feel it is still reasonable .
>> >>>>>>
>> >>>>>> I am now moving to the next part of complying with the requests of
>> the editor:
>> >>>>>> 1) Determine authorship
>> >>>>>> 2) Converging format to journal guidelines - this also means
>> references
>> >>>>>> 3) Detach from group - some elements already marked
>> >>>>>> 4) Revise bullet points into paragraphs
>> >>>>>>
>> >>>>>> I plan to continue editing until midnight CST with a break for
>> dinner - so if anyone has comments - please feel free to join the open
>> channel that shows the editing and influence real-time.
>> >>>>>>
>> >>>>>> Hopefully you will find the merged version in order.
>> >>>>>>
>> >>>>>> Jacob
>> >>>>>>
>> >>>>>>
>> >>>>>>
>> >>>>>>
>> >>>>>>
>> >>>>>>
>> >>>>>> On Sat, Oct 23, 2021 at 2:50 PM Jacob Barhak <
>> jacob.barhak at gmail.com> wrote:
>> >>>>>>>
>> >>>>>>> Hi Eric,
>> >>>>>>>
>> >>>>>>> You wanted to edit the stochastic section - you are welcome to do
>> it. Yet I ask no more references or deletions - I am overloaded already.
>> >>>>>>>
>> >>>>>>> The version benign edited is:
>> >>>>>>>
>> https://docs.google.com/document/d/1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM/edit
>> >>>>>>>
>> >>>>>>> You will need to login so that your edits will be traceable.
>> >>>>>>>
>> >>>>>>> You can join me while editing in:
>> >>>>>>> https://meet.jit.si/CollaborativePaperEditing
>> >>>>>>>
>> >>>>>>> I am sharing my screen there while editing.
>> >>>>>>>
>> >>>>>>> You might be able to help me with other sections as well.
>> >>>>>>>
>> >>>>>>> Jacob
>> >>>>>>>
>> >>>>>>>
>> >>>>>>> On Sat, Oct 23, 2021 at 2:44 PM Eric Forgoston <
>> eric.forgoston at montclair.edu> wrote:
>> >>>>>>>>
>> >>>>>>>> Hi Jacob,
>> >>>>>>>>
>> >>>>>>>> If you give me a link to the paper you are editing and edit
>> access to the paper I can update the stochastic section.
>> >>>>>>>>
>> >>>>>>>> Cheers,
>> >>>>>>>>
>> >>>>>>>> Eric
>> >>>>>>>> ---------------------
>> >>>>>>>> Dr. Eric Forgoston
>> >>>>>>>> Professor of Applied Mathematics
>> >>>>>>>> Chair, Department of Applied Mathematics and Statistics
>> >>>>>>>> Montclair State University
>> >>>>>>>> Montclair, NJ 07043 USA
>> >>>>>>>> +1 973 655-7242
>> >>>>>>>> https://eric-forgoston.github.io/
>> >>>>>>>>
>> >>>>>>>>
>> >>>>>>>> On Sat, Oct 23, 2021 at 1:39 PM Jacob Barhak <
>> jacob.barhak at gmail.com> wrote:
>> >>>>>>>>>
>> >>>>>>>>> Greetings Paper Contributors,
>> >>>>>>>>>
>> >>>>>>>>> The paper editing process started and you can follow it live on:
>> >>>>>>>>> https://meet.jit.si/CollaborativePaperEditing
>> >>>>>>>>>
>> >>>>>>>>> I will keep the channel open as long as I am editing so that
>> the process will be as transparent as possible.
>> >>>>>>>>>
>> >>>>>>>>> The first step would be to reconcile the differences between
>> those 4 versions traceable back to authors:
>> >>>>>>>>>
>> https://docs.google.com/document/d/1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM/edit
>> - the submitted version
>> >>>>>>>>>
>> https://docs.google.com/document/d/1VvyP3YZQdQYjj8DFKOpQ4pn_0pdDGgiT/edit
>> - first committed version
>> >>>>>>>>>
>> https://docs.google.com/document/d/1Ag4ipuybjtthxgV0YjXqYP7AwwNSYcWh/edit
>> - first committed version
>> >>>>>>>>>
>> https://drive.google.com/file/d/1U_lTHrV6STXWNT3GiCepvsLk1WdYgzN5/view -
>> its the first document posted
>> >>>>>>>>>
>> >>>>>>>>> After this step is done I will move towards adhering to those
>> instructions:
>> >>>>>>>>> https://www.frontiersin.org/about/author-guidelines
>> >>>>>>>>>
>> >>>>>>>>> I estimate I will be working till late today with very few
>> breaks and hopefully make sufficient progress.
>> >>>>>>>>>
>> >>>>>>>>> Feel free to visit and perhaps even help. If you do, please
>> raise your voice so I can hear you - I am sharing my screen and not seeing
>> the video when I edit - so you will have to let me know you are in the room.
>> >>>>>>>>>
>> >>>>>>>>> Hopefully some of you will visit.
>> >>>>>>>>>
>> >>>>>>>>> Jacob
>> >>>>>>>>>
>> >>>>>>>>> On Fri, Oct 22, 2021 at 2:52 PM Jacob Barhak <
>> jacob.barhak at gmail.com> wrote:
>> >>>>>>>>>>
>> >>>>>>>>>> Thanks Sheriff,
>> >>>>>>>>>>
>> >>>>>>>>>> With your green light I can start editing
>> >>>>>>>>>>
>> >>>>>>>>>> Eric, the base of John's version will be merged to the best
>> of my ability, yet unfortunately, it has omissions and later version based
>> on it are not traceable back to contributors, so I can only use some of
>> the base.
>> >>>>>>>>>>
>> >>>>>>>>>> If you want to repeat edits so those will be traceable it is
>> possible. Yet we cannot copy verbatim without going to details.
>> >>>>>>>>>>
>> >>>>>>>>>> To make things easier, I will open a channel over the weekend
>> during edits where anyone can join and communicate while watching the edits
>> live.
>> >>>>>>>>>>
>> >>>>>>>>>> Hopefully it will make things smoother.
>> >>>>>>>>>>
>> >>>>>>>>>> Jacob
>> >>>>>>>>>>
>> >>>>>>>>>>
>> >>>>>>>>>>
>> >>>>>>>>>>
>> >>>>>>>>>>
>> >>>>>>>>>>
>> >>>>>>>>>> On Fri, Oct 22, 2021, 13:40 Eric Forgoston <
>> eric.forgoston at montclair.edu> wrote:
>> >>>>>>>>>>>
>> >>>>>>>>>>> Dear Jacob and all,
>> >>>>>>>>>>>
>> >>>>>>>>>>> I suggest, as others have done, to use the John G. version as
>> structurally it has already cleaned up most of the issues raised by the
>> Editor, and also has many revised and improved sections. In particular, the
>> stochastic section that I worked on with others is far superior to the one
>> in the paper submitted to Frontiers.
>> >>>>>>>>>>>
>> >>>>>>>>>>> Best wishes,
>> >>>>>>>>>>>
>> >>>>>>>>>>> Eric
>> >>>>>>>>>>> ---------------------
>> >>>>>>>>>>> Dr. Eric Forgoston
>> >>>>>>>>>>> Professor of Applied Mathematics
>> >>>>>>>>>>> Chair, Department of Applied Mathematics and Statistics
>> >>>>>>>>>>> Montclair State University
>> >>>>>>>>>>> Montclair, NJ 07043 USA
>> >>>>>>>>>>> +1 973 655-7242
>> >>>>>>>>>>> https://eric-forgoston.github.io/
>> >>>>>>>>>>>
>> >>>>>>>>>>>
>> >>>>>>>>>>> On Fri, Oct 22, 2021 at 12:57 PM Rahuman Sheriff <
>> sheriff at ebi.ac.uk> wrote:
>> >>>>>>>>>>>>
>> >>>>>>>>>>>> Congratulations Marcella,
>> >>>>>>>>>>>>
>> >>>>>>>>>>>> Hi Jacob and all,
>> >>>>>>>>>>>>
>> >>>>>>>>>>>> As Tomas mentioned, John G’s version is bit more organised.
>> >>>>>>>>>>>> Although it would be nice to take that one forward, I also
>> fine with you recovering your version incorporating requested changes
>> including mine.
>> >>>>>>>>>>>> I would prefer this manuscript progresses ahead, instead of
>> another long discussion.
>> >>>>>>>>>>>> Green signal from my side.
>> >>>>>>>>>>>> Best regards
>> >>>>>>>>>>>> Sheriff
>> >>>>>>>>>>>>
>> >>>>>>>>>>>>
>> >>>>>>>>>>>> On 22 Oct 2021, at 01:49, Jacob Barhak <
>> jacob.barhak at gmail.com> wrote:
>> >>>>>>>>>>>>
>> >>>>>>>>>>>> Congratulations Marcella,
>> >>>>>>>>>>>>
>> >>>>>>>>>>>> Indeed you bring good news.
>> >>>>>>>>>>>>
>> >>>>>>>>>>>> You should not worry about the manuscript. You have done
>> plenty and we can handle if from now on, you can focus on your family.
>> >>>>>>>>>>>>
>> >>>>>>>>>>>> Jacob
>> >>>>>>>>>>>>
>> >>>>>>>>>>>> On Thu, Oct 21, 2021, 10:33 Torres, Marcella <
>> mtorres at richmond.edu> wrote:
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> This streamlined approach sounds good to me; thanks Jacob
>> for offering to coordinate edits. I think the one month deadline is a good
>> maximum, since Frontiers favors quick turnaround.
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> I don't insist on participating in the revisions, but I am
>> available to help with cleaning up grammar, typos, and so on - I noticed
>> quite a few minor issues when reviewing the document for submission.
>> However, my son was born a few days ago and I have limited time.
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> Marcella
>> >>>>>>>>>>>>> ________________________________
>> >>>>>>>>>>>>> From: Jacob Barhak <jacob.barhak at gmail.com>
>> >>>>>>>>>>>>> Sent: Wednesday, October 20, 2021 11:53:58 PM
>> >>>>>>>>>>>>> To: Alexander Kulesza <alexander.kulesza at novadiscovery.com>
>> >>>>>>>>>>>>> Cc: Hana <h.dobrovolny at tcu.edu>; James Osborne <
>> jmosborne at unimelb.edu.au>; John Rice <john.rice at noboxes.org>; Torres,
>> Marcella <mtorres at richmond.edu>; 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>; Jonathan Karr <
>> jonrkarr at gmail.com>; John Gennari <gennari at uw.edu>; Winston Garira <
>> Winston.Garira at univen.ac.za>
>> >>>>>>>>>>>>> Subject: Re: [Vp-integration-subgroup] Fwd: Shayn
>> Peirce-Cottler via Frontiers: Manuscript
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> External Email: Use caution in opening links, attachments,
>> and buying gift cards.
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> Thanks Alex, Thanks John,
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> Your contribution is appreciated and since John cleared us
>> to move forward it simplifies things. I hope he will change his mind about
>> authorship since he contributed a lot, yet I will respect his wishes -
>> perhaps after seeing the final version he will change his mind.
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> If Sheriff gives me a green light I can incorporate his
>> modifications as well. I do ask that if any of the listed authors has any
>> serious concerns and plans to not approve a modified version that addresses
>> the editors requests alone alongside those I mentioned above, to step up
>> before the work is done so we can resolve things before energy is spent.
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> If there will be no blocks I plan to start work over the
>> weekend if I see no objections by then.
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> I appreciate the offer to help with bibliography, from
>> experience I know it is perhaps the most time consuming. However, since we
>> have many links and specialized publications in our list - I am not sure if
>> any tool can make it easier - the last time I had to do a lot of manual
>> work to fit a specific format and find all missing links and also fix some
>> errors - no tool would have helped me then. This time I think it will be a
>> bit easier. Yet I ask for no more references to be added - I also want to
>> add more references, yet I am stopping myself. We can always expand the
>> work in another future version if we have new findings.
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> Again note that I will only try to address the requests of
>> the editor at this point without trying to perfect anything beyond what I
>> wrote above and I want to keep things as traceable as possible. Once I am
>> done,we will see if we can approve this manuscript for publication.
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> Unless any blockers appear, if anyone wants to actively
>> participate in the editing over the weekend, please let me know so we can
>> communicate better.
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> Jacob
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> On Tue, Oct 19, 2021 at 2:02 AM Alexander Kulesza <
>> alexander.kulesza at novadiscovery.com> wrote:
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> Dear Jacob,
>> >>>>>>>>>>>>> thanks for forwarding and you suggestions, which seems more
>> than reasonable.
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> My contributions from May 19th, May31st and June 2nd are in
>> https://docs.google.com/document/d/1VvyP3YZQdQYjj8DFKOpQ4pn_0pdDGgiT/edit?usp=sharing&ouid=113860487708206439519&rtpof=true&sd=true
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> The other document
>> https://docs.google.com/document/d/1esZvWWVBvpwvuFUi3C3161lthZkEBFyMRrwwozitBi4/edit?usp=sharing
>> I created initially to suggest my edits without editing the core version
>> can be disregarded as I have tranferred all of them into the main document,
>> cited above.
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> If we were on Latex, I could offer to create the
>> bibliography but unfortunately we lack a bibliography manager integrated in
>> Word/GDoc. If we were to work with Mendeley and someone could create a
>> group for this paper that has a shared library I could offer to transfer
>> citations from the paper into that database too.
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> Please let me know.
>> >>>>>>>>>>>>> A
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> On Tue, 19 Oct 2021 at 05:51, Jacob Barhak <
>> jacob.barhak at gmail.com> wrote:
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> Greetings white paper contributors,
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> Below is the response from the editor to my request and my
>> thank you.
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> The editor grants us the extension by rejecting the paper
>> and allowing time to come up with a better version. There is no time limit
>> now, yet I want to get her a revised version within a month.
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> The requests are simple and easy to satisfy - and I know
>> there are many of you who want more revisions, yet I suggest we reduce them
>> to only what is manageable and necessary. Otherwise we will never get this
>> paper published despite its importance.
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> The most time consuming effort would be adhering to the
>> journal format as defined here:
>> >>>>>>>>>>>>> https://www.frontiersin.org/about/author-guidelines
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> I think the most time consuming task would be dealing with
>> the references - otherwise the format guidelines seem reasonable.
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> We can also add some revisions we started working on.
>> However, I will personally insist on :
>> >>>>>>>>>>>>> 1. traceability - currently there is no traceability in the
>> revised version in the summer
>> >>>>>>>>>>>>> 2. non deletion - do not delete any content unless you
>> wrote it originally or unless you announced it beforehand to the group and
>> got no objections within a few days
>> >>>>>>>>>>>>> 3. Avoid Adding more material that is not in the existing
>> versions we had - especially references - we don't have time for that and
>> that is not what the editor asked us anyway.
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> I will also ask for fast responses from all contributors.
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> To be practical, I marked the submitted version and opened
>> the document to those who requested editing rights in the past. If you
>> want editing rights, let me know - however, the edits should be minimal and
>> focus on areas you edited in the past and be aware that if your edits will
>> not get approved by everyone, we will revert to the old version we all
>> accepted. The submitted version was marked so we can always get back to it.
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> If you want editing rights, let me know and I will respond
>> within a day - I cannot promise to be fatter than that these days.
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> Alex, John, Sheriff, you had other versions you created, I
>> want to merge some of your changes to the manuscript in this version - here
>> are my suggestions:
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> - Sheriff, I will soften the language as you requested -
>> this was your main request in the past, yet I will go over your list of
>> changes and see what I else can be done without reinventing the paper
>> >>>>>>>>>>>>> - John - I will 1) merge the credibility sections , 2)
>> delete the history related to the working group since it matches with what
>> was requested, and 3) move the model validation barrier section away from
>> the table since we did not suggest a solution there. Hopefully this will
>> make the paper more appealing to you and you will be willing to add your
>> name to the list
>> >>>>>>>>>>>>> - Alex, your changes were made on May 16, 2021 and shared
>> in a way I can see the differences and trace them back to you - I will try
>> to add your references and see if I can incorporate your text changes as
>> much as I can.
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> If the 3 of you are ok with me migrating your changes, I
>> can start the work to save time. Yet I want your ok first.
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> I know Eric and Hana were working on some sections and feel
>> strongly about those - specifically the stochastic modeling part - I am
>> open to your changes, please suggest what you feel strongly about..
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> I recall Johnathan Karr wanted to make some changes, please
>> let me know if there is anything you feel strongly about - he had a lot of
>> text in the paper ..
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> If I forgot anyone who had major requests, please remind
>> me. .
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> I am trying to avoid a never ending revisioning cycle. So I
>> am asking you to trust me and centralize the work in hope I get a better
>> version by the end of the week..
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> Hopefully most of you will be ok with that.
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> Jacob
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> ---------- Forwarded message ---------
>> >>>>>>>>>>>>> From: Jacob Barhak <jacob.barhak at gmail.com>
>> >>>>>>>>>>>>> Date: Mon, Oct 18, 2021 at 9:34 PM
>> >>>>>>>>>>>>> Subject: Re: Shayn Peirce-Cottler via Frontiers: Manuscript
>> >>>>>>>>>>>>> To: Peirce-Cottler, Shayn (smp6p) <smp6p at virginia.edu>
>> >>>>>>>>>>>>> Cc: Shayn Peirce-Cottler (Via FrontiersIn) <
>> shayn at virginia.edu>,systemsbiology.editorial.office at frontiersin.org <
>> systemsbiology.editorial.office at frontiersin.org>, Vodovotz, Yoram <
>> vodovotzy at upmc.edu>
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> Thanks Shayn,
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> You will get a revised manuscript targeted at your journal
>> and get back to you with a more polished version and satisfies your
>> requests.
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> It will also allow us to incorporate newer versions of the
>> text that answer some of your requests. We really wish to publish it fast,
>> yet we need more time for the approval process. So your solution seems
>> correct - I hope you hear back from us within a month or so.
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> Many thanks for the rapid responses.
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> Jacob
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> --
>> >>>>>>>>>>>>> Jacob Barhak Ph.D.
>> >>>>>>>>>>>>> Sole Proprietor, Software Developer, and Computational
>> Disease Modeler
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> Jacob Barhak Analytics
>> >>>>>>>>>>>>> 701 Brazos St
>> >>>>>>>>>>>>> Suite 548
>> >>>>>>>>>>>>> Austin TX, 78701
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> Email: jacob.barhak at gmail.com
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> https://sites.google.com/view/jacob-barhak/home
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> On Mon, Oct 18, 2021 at 7:43 PM Peirce-Cottler, Shayn
>> (smp6p) <smp6p at virginia.edu> wrote:
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> Hi Jacob,
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> Thank you for your detailed reply. I agree that the issues
>> can be addressed as you have described below, and that you may need more
>> time to do so. Hence, I am going to officially reject this first submission
>> to remove any imposed deadlines, and I certainly encourage you to make the
>> updates listed below, and submit a new manuscript at your earliest
>> convenience.
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> Please let me know if you have any questions, and thanks
>> again for considering this journal! I think the topic fits very nicely with
>> the scope of the journal, and it is certainly an important topic to our
>> multi-scale modeling community!
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> -Shayn
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> Shayn Peirce-Cottler, Ph.D.
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> Professor of Biomedical Engineering
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> Harrison Distinguished Teaching Professor
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> BME Graduate Program Director
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> University of Virginia
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> Charlottesville, VA
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> From: Jacob Barhak <jacob.barhak at gmail.com>
>> >>>>>>>>>>>>> Date: Monday, October 18, 2021 at 1:57 AM
>> >>>>>>>>>>>>> To: Peirce-Cottler Shayn <shayn at virginia.edu>
>> >>>>>>>>>>>>> Cc: "systemsbiology.editorial.office at frontiersin.org" <
>> systemsbiology.editorial.office at frontiersin.org>, "Vodovotz, Yoram" <
>> vodovotzy at upmc.edu>
>> >>>>>>>>>>>>> Subject: Re: Shayn Peirce-Cottler via Frontiers: Manuscript
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> Hi Shayn,
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> Thanks for returning the response quickly. To you comments.
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> 1. This is the list of authors that agreed to submit this
>> manuscript for review - I collected their approvals for this version
>> personally.
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> Jonathan Karr, Icahn Institute for Data Science and Genomic
>> Technology and Department of Genetics and Genomic Sciences, Icahn School of
>> Medicine at Mount Sinai USA
>> >>>>>>>>>>>>> Rahuman Sheriff, The European Bioinformatics Institute
>> (EMBL-EBI), UK
>> >>>>>>>>>>>>> James Osborne, School of Mathematics and Statistics,
>> University of Melbourne, Australia
>> >>>>>>>>>>>>> Gilberto Gonzalez Parra, Mathematics Department, New Mexico
>> Tech, USA
>> >>>>>>>>>>>>> Eric Forgoston, Department of Applied Mathematics and
>> Statistics, Montclair State University, USA
>> >>>>>>>>>>>>> Ruth Bowness, Department of Mathematical Sciences,
>> University of Bath, UK
>> >>>>>>>>>>>>> Yaling Liu, Department of Mechanical Engineering and
>> Mechanics , Department of Bioengineering, Lehigh University, USA
>> >>>>>>>>>>>>> Robin Thompson, Mathematics Institute & The Zeeman
>> Institute for Systems Biology and Infectious Disease Epidemiology Research,
>> University of Warwick, UK
>> >>>>>>>>>>>>> Winston Garira - Department Of Mathematics And Applied
>> Mathematics , Modelling Health and Environmental Linkages Research Group.
>> University of Venda, South Africa
>> >>>>>>>>>>>>> Jacob Barhak - Barhak, Jacob, USA
>> >>>>>>>>>>>>> John Rice - Independent Retired Working Group Volunteer, USA
>> >>>>>>>>>>>>> Marcella Torres, School of Arts and Sciences, University of
>> Richmond, USA
>> >>>>>>>>>>>>> Hana M. Dobrovolny , Department of Physics & Astronomy,
>> Texas Christian University, Fort Worth, USA
>> >>>>>>>>>>>>> Tingting Tang, Department of Mathematics and Statistics in
>> San Diego State University (SDSU) and SDSU Imperial Valley, USA
>> >>>>>>>>>>>>> William Waites, Centre for Mathematical Modelling of
>> Infectious Diseases, London School of Hygiene and Tropical Medicine, UK
>> >>>>>>>>>>>>> James Glazier, Biocomplexity Institute, Indiana University,
>> Bloomington, USA
>> >>>>>>>>>>>>> James R. Faeder, Department of Computational and Systems
>> Biology, University of Pittsburgh, Pittsburgh, USA
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> If there is a mismatch of authors in the submission, it can
>> be easily corrected - we kept the paper traceable when we constructed it so
>> we can point to exact texts contributed by each contributor through their
>> google account and versions kept in google docs with few exceptions where I
>> personally added text their wrote and have email conversations supporting
>> that . I personally collected all those contributions in google docs when
>> I assembled the version you see and made sure it is agreed upon by the
>> contributors. It is important to note that There was one contributor that
>> asked for more revisions and did not approve this manuscript, yet allowed
>> submitting the text without association to it to avoid delays. The entire
>> conversation was documented publicly in our mailing list and we got consent
>> from this contributor to continue and use the text - You can find the
>> conversation here:
>> https://lists.simtk.org/pipermail/vp-reproduce-subgroup/2021-March/000019.html
>> - so there are no copyright issues and the name of the author is not
>> included in the list above at their request. Those included in the list
>> have contributed and approved. If needed, we will correct the list in the
>> journal to match this list. Please note that we kept the entire process as
>> transparent as possible so there will be no issues. If there are any
>> concerns of authorship, I will be happy to dig into the history and pull
>> out details.
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> 2. The reason the manuscript was submitted in this form is
>> to get confirmation on initial fit and to get some initial feedback. We
>> were interested in fast review to get the information quickly out - Also
>> note that we did not intend this to be a final version - we already have
>> some modifications in the work that we would like to introduce where more
>> people contributed , yet we have not reached agreement on those so we
>> cannot formally publish them - however, we did reach agreement on
>> submitting this version for review so the editor can focus us on what is
>> important to change to get published with a 3rd Party - enough of us agreed
>> in a vote that your Journal seems is a suitable 3rd party and hence the
>> submission. We will be happy to spend the time to convert the manuscript to
>> the desired format if you find the content suitable for the journal. So far
>> your requests are reasonable and I will convey them to the group through
>> our mailing list.
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> 3. Please note that after the list of authors there is a
>> disclaimer : "The opinion of the contributors do not reflect the opinions
>> of the entire working group". Initially this paper started as an activity
>> requested by the working group leads. However, by no means it represents
>> all opinions. The introduction in this version of the paper captures some
>> of this history of how the manuscript was created and modified. However, we
>> have other versions of the manuscript in work where this history is deleted
>> - If you prefer, we can easily create a version that detaches from the
>> working group to eliminate all concerns - this is a relatively easy fix.
>> However, whatever fix we do, we will have to approve with all contributors.
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> 4 The revisions can be done in reasonable time. However,
>> the process of collecting approval for all contributors to legally approve
>> the revised manuscript will take more than 14 days. All contributors must
>> approve a manuscript for publication. With this number of authors we will
>> probably not make it in the time you mentioned - only the approval process
>> for collecting all approvals took alone about 3 weeks to approve this
>> version you see. Hopefully you will understand this and extend this time
>> period beyond 14 days.
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> In summary:
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> Making the fixes you asked for towards publication is easy
>> - yet getting the approval from so many people may take us more time than
>> what you provide. If it is possible to get an extension, it will be
>> appreciated.
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> I will add this conversation to our mailing list so we can
>> start the process of revising the manuscript. However, if after this email
>> you have more issues with this paper, Please advise on the best course of
>> action you see fit so we can adjust accordingly.
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> Hopefully we can address your concerns in time to publish
>> the manuscript in a timely manner.
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> Jacob
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> --
>> >>>>>>>>>>>>> Jacob Barhak Ph.D.
>> >>>>>>>>>>>>> Sole Proprietor, Software Developer, and Computational
>> Disease Modeler
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> Jacob Barhak Analytics
>> >>>>>>>>>>>>> 701 Brazos St
>> >>>>>>>>>>>>> Suite 548
>> >>>>>>>>>>>>> Austin TX, 78701
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> Email: jacob.barhak at gmail.com
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> https://sites.google.com/view/jacob-barhak/home
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> On Sun, Oct 17, 2021 at 9:56 AM Shayn Peirce-Cottler (Via
>> FrontiersIn) <noreply at frontiersin.org> wrote:
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> Dear Jacob,
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> Thank you for your manuscript submission. I cannot send it
>> out for review in its current form because I have a few concerns, but if
>> you can address the following issues, I will certainly reconsider a revised
>> manuscript if the following are adequately addressed:
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> 1. The author list that is on the first page differs from
>> the author list that was provided at the time of submission.
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> 2. The manuscript needs to be submitted using the official
>> Frontiers template.
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> 3. The manuscript states that it represents the views of a
>> number of special interest and working groups, and the authors should
>> provide assurances that they have the authority and approval to speak on
>> behalf of the working groups that are listed.
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> 4. There are places throughout the manuscript, and most
>> frequently in the second half, where information is provided as bulleted
>> talking points without context. Those sections should be revised into
>> paragraphs of text or summarized in a table (or figure).
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> If you wish to submit a revised manuscript, the journal
>> provides a 14-day time window for you to do so. Please let me know if you
>> have any questions.
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> Thank you,
>> >>>>>>>>>>>>> Shayn
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> ---------------------------------
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> Manuscript title: Model Integration in Computational
>> Biology: The Role of Reproducibility, Credibility and Utility
>> >>>>>>>>>>>>> Manuscript ID: 793932
>> >>>>>>>>>>>>> Authors: Marcella Torres, Jacob Barhak, Ruth Bowness, Hana
>> Maria Dobrovolny, James Faeder, Eric Forgoston, Winston Garira, Yaling Liu,
>> James Osborne, Gilberto Gonzalez Parra, John Rice, Rahuman Sheriff,
>> Tingting Tang, Robin Thompson, William Waites
>> >>>>>>>>>>>>> Date submitted: 12 Oct 2021
>> >>>>>>>>>>>>> Edited by: Shayn Peirce-Cottler
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> Research Topic: Insights in Systems Biology: Multiscale
>> Mechanistic Modeling 2021
>> >>>>>>>>>>>>> Review forum direct access link:
>> https://review.frontiersin.org/review/793932/0/0
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> _______________________________________________
>> >>>>>>>>>>>>> Vp-integration-subgroup mailing list
>> >>>>>>>>>>>>> Vp-integration-subgroup at lists.simtk.org
>> >>>>>>>>>>>>>
>> https://lists.simtk.org/mailman/listinfo/vp-integration-subgroup
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> --
>> >>>>>>>>>>>>> Alexander Kulesza
>> >>>>>>>>>>>>> Team leader
>> >>>>>>>>>>>>> Modeling & simulation / Biomodeling
>> >>>>>>>>>>>>> alexander.kulesza at novadiscovery.com
>> >>>>>>>>>>>>> +33 7 82 92 44 62
>> >>>>>>>>>>>>> nova
>> >>>>>>>>>>>>> DISCOVERY
>> >>>>>>>>>>>>> www.novadiscovery.com
>> >>>>>>>>>>>>> 1 Place Verrazzano, 69009 Lyon
>> >>>>>>>>>>>>> +33 9 72 53 13 01
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> This message is intended only for the personal and
>> confidential use of the designated recipient(s) named above. If you are not
>> the intended recipient of this message you are hereby notified that any
>> review, dissemination, distribution or copying of this message is strictly
>> prohibited. Email transmission cannot be guaranteed to be secure or
>> error-free. Therefore, we do not represent that this information is
>> complete or accurate and it should not be relied upon as such. All
>> information is subject to change without notice.
>> >>>>>>>>>>>>
>> >>>>>>>>>>>> _______________________________________________
>> >>>>>>>>>>>> Vp-integration-subgroup mailing list
>> >>>>>>>>>>>> Vp-integration-subgroup at lists.simtk.org
>> >>>>>>>>>>>>
>> https://lists.simtk.org/mailman/listinfo/vp-integration-subgroup
>> >>>>>>>>>>>>
>> >>>>>>>>>>>>
>> >>>>>>>>>>>> _______________________________________________
>> >>>>>>>>>>>> Vp-reproduce-subgroup mailing list
>> >>>>>>>>>>>> Vp-reproduce-subgroup at lists.simtk.org
>> >>>>>>>>>>>>
>> https://lists.simtk.org/mailman/listinfo/vp-reproduce-subgroup
>> >>>>>>
>> >>>>>> _______________________________________________
>> >>>>>> Vp-reproduce-subgroup mailing list
>> >>>>>> Vp-reproduce-subgroup at lists.simtk.org
>> >>>>>> https://lists.simtk.org/mailman/listinfo/vp-reproduce-subgroup
>>
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