<div dir="ltr">Greetings paper contributors,<div><br></div><div>You will find the paper in advanced form. Here it is again: <a href="https://docs.google.com/document/d/1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM/edit?usp=sharing">https://docs.google.com/document/d/1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM/edit?usp=sharing</a></div><div><br></div><div>I believe I finished most of the necessary for submission/ I added a "Contribution to the Field Statement". You will find it at the end of the paper. I am including it here for your convenience:<br></div><div><br></div><div>Contribution to the Field Statement</div><div>Biological computational models have reuse and reproducibility issues The paper covers the problem from a wide perspective of a large group of modelers It reviews the issues and separates them into a list of difficulties that start from reproducibility, reduce credibility, and eventually hinder reuse. There are many publications that point out the scientific reproducibility crisis. However, the main contribution of this review paper is that it also provides possible insights for solutions and focuses specifically on Biological computational models and multiscale problems. Perhaps the most important artifact in the paper is that it is summarized in one table. Many details are provided, including reference to real world examples. This paper can be easily reused by a policy holder or by a modeler as a checklist to better plan research and avoid pitfalls.</div><div><br></div><div>If anyone wants to fix this text, please do this inside the paper </div><div><br></div><div>I suggest we submit this paper as a Review paper. you will find other possible article types here: <a href="https://www.frontiersin.org/journals/systems-biology#article-types">https://www.frontiersin.org/journals/systems-biology#article-types</a> </div><div><br></div><div>Here is the TODO list towards submission:</div><div><div>- Wait for John Gennari to decide if he wants to join - I asked multiple times already and hope he will join and take responsibility as an author - here is explanation what this means: <a href="https://www.frontiersin.org/about/policies-and-publication-ethics">https://www.frontiersin.org/about/policies-and-publication-ethics</a></div><div><br></div><div>- Proof read the paper - I will do this this week once more from start to finish to find errors, I will appreciate another eye - especially verifying that the references are correct after edits </div><div> </div><div>- Double check formatting to fit the Journal guidelines: <a href="https://www.frontiersin.org/about/author-guidelines">https://www.frontiersin.org/about/author-guidelines</a> </div><div><br></div><div>- Approve the version with all authors - we must do this again and get full approval - this may take a while - yet I suggest you all read <a href="https://www.frontiersin.org/about/policies-and-publication-ethics">https://www.frontiersin.org/about/policies-and-publication-ethics</a> </div><div><br></div><div>- Determine who else wants to be listed as corresponding author - currently I marked Marcell and myself, yet others may want to correspond. </div><div><br></div><div>- Split the paper into files to be uploaded to the journal web site and go over the submission checklist: <a href="https://www.frontiersin.org/journals/systems-biology/sections/data-and-model-integration#submission-checklist">https://www.frontiersin.org/journals/systems-biology/sections/data-and-model-integration#submission-checklist</a><br></div><div><br></div><div>- Upload the paper to the journal submission system<br></div></div><div><br></div><div>I will appreciate help in some stages, yet the main stage I will need our help with is the approval stage - so please stage reviewing the paper now to make sure you are ok with the text you will be signed on.</div><div><br></div><div>I expect finishing all the elements by next week and ask for your approval. Hopefully you will all find this in good form.</div><div><br></div><div> Jacob</div><div><br></div><div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, Oct 25, 2021 at 10:39 PM Jacob Barhak <<a href="mailto:jacob.barhak@gmail.com">jacob.barhak@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr">Thanks Eric, Thanks Hana, Thanks Robin, <div><br></div><div>This was just a sanity check that all text is traceable back to originators - it seems that with your statements the contributor list is complete except from John Gennari who asked to be not listed.</div><div><br></div><div>John Gennari , I ask you again publicly to review the new version and decide if you will join the author list. Many of your suggestions are in the text - in my mind its significant contribution and you should be listed as an author. I personally merged multiple fo your ideas and texts in the new version - not all due to issues I explained before, yet many were merged.</div><div><br></div><div>You are already in the acknowledgements, yet I think you should be added to the list of authors.</div><div><br></div><div>If there is a serious disagreement that forces you to avoid joining, you should raise it publicly so we can all be aware of the reason. If there is an error in the text we can correct it, if there is a slight modification that will make you happy to join, it can still be done. Yet we need to know ahead of time.</div><div><br></div><div>You already cleared us from copyright issues by making a public announcement so we can move forward, yet I still hope you will reconsider. You did contribute a lot and deserve more than acknowledgement.</div><div><br></div><div>Hopefully you will accept my appeal.</div><div><br></div><div> Jacob</div><div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, Oct 25, 2021 at 8:40 AM Thompson, Robin <<a href="mailto:Robin.N.Thompson@warwick.ac.uk" target="_blank">Robin.N.Thompson@warwick.ac.uk</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
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Hi all,
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<div>Hope everyone is well. Just a quick note to say that I fully support Eric in making any improvements he would like to the stochastic modelling section.</div>
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<div>Best wishes,</div>
<div>Robin
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Dr Robin Thompson<br>
Assistant Professor of Mathematical Epidemiology<br>
Mathematics Institute<br>
University of Warwick, UK<br>
<a href="http://www.robin-thompson.co.uk" target="_blank">www.robin-thompson.co.uk</a><br>
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<div>On 25 Oct 2021, at 12:36, Eric Forgoston <<a href="mailto:eric.forgoston@montclair.edu" target="_blank">eric.forgoston@montclair.edu</a>> wrote:</div>
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<div>Hi Jacob,<br>
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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.<br>
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<div><span>---------------------<br>
Dr. Eric Forgoston<br>
Professor of Applied Mathematics<br>
Chair, Department of </span><span><span><span>Applied Mathematics and Statistics</span></span><br>
Montclair State University<br>
Montclair, NJ 07043 USA<br>
+1 973 655-7242 <br>
<span><a href="https://eric-forgoston.github.io/" target="_blank">https://eric-forgoston.github.io/</a></span></span><br>
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<div dir="ltr" class="gmail_attr">On Mon, Oct 25, 2021 at 12:57 AM Jacob Barhak <<a href="mailto:jacob.barhak@gmail.com" target="_blank">jacob.barhak@gmail.com</a>> wrote:<br>
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<div dir="auto">Thanks James, And thanks Eric.
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<div dir="auto">James - your idea is not bad. However, there is a conflict between the two approaches to present the work. </div>
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<div dir="auto">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. </div>
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<div>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..</div>
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<div>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.</div>
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<div>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.</div>
<div><br>
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<div>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.</div>
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<div>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. </div>
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<div>We can always have a better version in the future.</div>
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<div>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. </div>
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<div>Hopefully this will calm down the conversation so we can focus on action.</div>
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<div>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?</div>
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<div> 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 . </div>
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<div>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? </div>
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<div>As you can see the concept of traceability back to origin is important to me - I ask that you help me here. </div>
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<div> Jacob</div>
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<div dir="ltr" class="gmail_attr">On Sun, Oct 24, 2021, 17:32 James Osborne <<a href="mailto:jmosborne@unimelb.edu.au" target="_blank">jmosborne@unimelb.edu.au</a>> wrote:<br>
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<div dir="ltr">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.
<div>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)<br>
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My very low effort proposal is to. </div>
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<div> * change the section title "Utility of Models" to something like "Challenges with using multiscale models <br>
* Then put the difficulties/ challenges listed in the table into subsections called things like "Challenge 1: Evaluating Model Credibility "<br>
<br>
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.
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<div>I believe it will make the papers intent clearer and easier to read.</div>
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<div>But if you're against it I rest my case and defer to your opinion.</div>
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<div>James </div>
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On Mon, Oct 25, 2021 at 8:53 AM Jacob Barhak <<a href="mailto:jacob.barhak@gmail.com" rel="noreferrer" target="_blank">jacob.barhak@gmail.com</a>> wrote:<br>
><br>
> Well James,<br>
><br>
> 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.<br>
><br>
> I hope you understand.<br>
><br>
> Jacob<br>
><br>
> On Sun, Oct 24, 2021, 03:51 James Osborne <<a href="mailto:jmosborne@unimelb.edu.au" rel="noreferrer" target="_blank">jmosborne@unimelb.edu.au</a>> wrote:<br>
>><br>
>> Jacob<br>
>><br>
>> I was just about to make some suggestions on structure which were added to the bakers dozen version version.<br>
>><br>
>> I'll make in suggest mode then you can decide of they work or not.<br>
>><br>
>> James<br>
>><br>
>> On Sun, Oct 24, 2021 at 7:44 PM Jacob Barhak <<a href="mailto:jacob.barhak@gmail.com" rel="noreferrer" target="_blank">jacob.barhak@gmail.com</a>> wrote:<br>
>>><br>
>>> Hi Eric,<br>
>>><br>
>>> You are the last one I remember who wanted to edit. Please check the manuscript<br>
>>> <a href="https://docs.google.com/document/d/1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM/edit?usp=sharing" rel="noreferrer" target="_blank">
https://docs.google.com/document/d/1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM/edit?usp=sharing</a><br>
>>><br>
>>> 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 .<br>
>>><br>
>>> 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.<br>
>>><br>
>>> 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.<br>
>>><br>
>>> The tasks left to do are:<br>
>>> - 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<br>
>>> - Finish the edits to the stochastic section - Eric - you asked for this<br>
>>> - Finish formatting to fit the Journal guidelines<br>
>>> - Add a cover letter and split the paper into sections to be uploaded to the journal web site<br>
>>> - Approve the version with all authors - we must do this again and get full approval - this may take a while<br>
>>> - Determine who else wants to be listed as corresponding author - currently I marked Marcell and myself, yet others may want to correspond. <br>
>>> - Upload the paper to the journal submission system<br>
>>><br>
>>> I hope for no obstacles and full cooperation to make the process smooth.<br>
>>><br>
>>> Jacob<br>
>>><br>
>>><br>
>>><br>
>>> On Sat, Oct 23, 2021 at 9:08 PM Jacob Barhak <<a href="mailto:jacob.barhak@gmail.com" rel="noreferrer" target="_blank">jacob.barhak@gmail.com</a>> wrote:<br>
>>>><br>
>>>> So Gilberto,<br>
>>>><br>
>>>> 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.<br>
>>>><br>
>>>> 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.<br>
>>>><br>
>>>> 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.<br>
>>>><br>
>>>> 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.<br>
>>>><br>
>>>> 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.<br>
>>>><br>
>>>> I hope I can finish most of the work except references perhaps by midnight.<br>
>>>><br>
>>>> Jacob<br>
>>>><br>
>>>><br>
>>>><br>
>>>> On Sat, Oct 23, 2021 at 8:32 PM Gilberto Gonzalez-Parra <<a href="mailto:gilberto.gonzalezparra@nmt.edu" rel="noreferrer" target="_blank">gilberto.gonzalezparra@nmt.edu</a>> wrote:<br>
>>>>><br>
>>>>> Hi Jacob,<br>
>>>>><br>
>>>>> 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 ?<br>
>>>>><br>
>>>>> 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.<br>
>>>>><br>
>>>>> 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.<br>
>>>>><br>
>>>>> Best,<br>
>>>>><br>
>>>>> ***************************************************************************<br>
>>>>> Gilberto C. Gonzalez-Parra, Ph.D in Applied Mathematics.<br>
>>>>> Faculty of the Mathematics Department<br>
>>>>> New Mexico Tech, NM, USA.<br>
>>>>> ****************************************************************************<br>
>>>>><br>
>>>>><br>
>>>>> On Sat, Oct 23, 2021 at 5:38 PM Jacob Barhak <<a href="mailto:jacob.barhak@gmail.com" rel="noreferrer" target="_blank">jacob.barhak@gmail.com</a>> wrote:<br>
>>>>>><br>
>>>>>> Hi Eric, and also greeting for the other paper contributors<br>
>>>>>><br>
>>>>>> Here is a real time update just to give an idea of current editing status.<br>
>>>>>><br>
>>>>>> 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:<br>
>>>>>><br>
>>>>>> "<br>
>>>>>> Hi Hana<br>
>>>>>> Can you see the chat?<br>
>>>>>> I can. There's just a lot going on around here right now, so I'm not fast with typing<br>
>>>>>> I put the references in the comments, can you see them?<br>
>>>>>> 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..<br>
>>>>>> And thanks fro helping<br>
>>>>>> If you want, you can join jitsi: <a href="https://meet.jit.si/CollaborativePaperEditing" rel="noreferrer" target="_blank">
https://meet.jit.si/CollaborativePaperEditing</a> and we can chat using voice<br>
>>>>>> I just saw your comment - it is public confirmation - this is good enough thank you<br>
>>>>>> 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.<br>
>>>>>> 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<br>
>>>>>> 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.<br>
>>>>>> Well, "are" is the correct verb there, so that should probably stay. I can remove the italicization.<br>
>>>>>> 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 .<br>
>>>>>> 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.<br>
>>>>>> "<br>
>>>>>><br>
>>>>>> 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 .<br>
>>>>>><br>
>>>>>> I am now moving to the next part of complying with the requests of the editor:<br>
>>>>>> 1) Determine authorship<br>
>>>>>> 2) Converging format to journal guidelines - this also means references<br>
>>>>>> 3) Detach from group - some elements already marked<br>
>>>>>> 4) Revise bullet points into paragraphs<br>
>>>>>><br>
>>>>>> 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.<br>
>>>>>><br>
>>>>>> Hopefully you will find the merged version in order.<br>
>>>>>><br>
>>>>>> Jacob<br>
>>>>>><br>
>>>>>><br>
>>>>>><br>
>>>>>><br>
>>>>>><br>
>>>>>><br>
>>>>>> On Sat, Oct 23, 2021 at 2:50 PM Jacob Barhak <<a href="mailto:jacob.barhak@gmail.com" rel="noreferrer" target="_blank">jacob.barhak@gmail.com</a>> wrote:<br>
>>>>>>><br>
>>>>>>> Hi Eric,<br>
>>>>>>><br>
>>>>>>> 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.<br>
>>>>>>><br>
>>>>>>> The version benign edited is:<br>
>>>>>>> <a href="https://docs.google.com/document/d/1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM/edit" rel="noreferrer" target="_blank">
https://docs.google.com/document/d/1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM/edit</a><br>
>>>>>>><br>
>>>>>>> You will need to login so that your edits will be traceable.<br>
>>>>>>><br>
>>>>>>> You can join me while editing in:<br>
>>>>>>> <a href="https://meet.jit.si/CollaborativePaperEditing" rel="noreferrer" target="_blank">
https://meet.jit.si/CollaborativePaperEditing</a><br>
>>>>>>><br>
>>>>>>> I am sharing my screen there while editing.<br>
>>>>>>><br>
>>>>>>> You might be able to help me with other sections as well.<br>
>>>>>>><br>
>>>>>>> Jacob<br>
>>>>>>><br>
>>>>>>><br>
>>>>>>> On Sat, Oct 23, 2021 at 2:44 PM Eric Forgoston <<a href="mailto:eric.forgoston@montclair.edu" rel="noreferrer" target="_blank">eric.forgoston@montclair.edu</a>> wrote:<br>
>>>>>>>><br>
>>>>>>>> Hi Jacob,<br>
>>>>>>>><br>
>>>>>>>> If you give me a link to the paper you are editing and edit access to the paper I can update the stochastic section.<br>
>>>>>>>><br>
>>>>>>>> Cheers,<br>
>>>>>>>><br>
>>>>>>>> Eric<br>
>>>>>>>> ---------------------<br>
>>>>>>>> Dr. Eric Forgoston<br>
>>>>>>>> Professor of Applied Mathematics<br>
>>>>>>>> Chair, Department of Applied Mathematics and Statistics<br>
>>>>>>>> Montclair State University<br>
>>>>>>>> Montclair, NJ 07043 USA<br>
>>>>>>>> +1 973 655-7242<br>
>>>>>>>> <a href="https://eric-forgoston.github.io/" rel="noreferrer" target="_blank">
https://eric-forgoston.github.io/</a><br>
>>>>>>>><br>
>>>>>>>><br>
>>>>>>>> On Sat, Oct 23, 2021 at 1:39 PM Jacob Barhak <<a href="mailto:jacob.barhak@gmail.com" rel="noreferrer" target="_blank">jacob.barhak@gmail.com</a>> wrote:<br>
>>>>>>>>><br>
>>>>>>>>> Greetings Paper Contributors,<br>
>>>>>>>>><br>
>>>>>>>>> The paper editing process started and you can follow it live on:<br>
>>>>>>>>> <a href="https://meet.jit.si/CollaborativePaperEditing" rel="noreferrer" target="_blank">
https://meet.jit.si/CollaborativePaperEditing</a><br>
>>>>>>>>><br>
>>>>>>>>> I will keep the channel open as long as I am editing so that the process will be as transparent as possible.<br>
>>>>>>>>><br>
>>>>>>>>> The first step would be to reconcile the differences between those 4 versions traceable back to authors:<br>
>>>>>>>>> <a href="https://docs.google.com/document/d/1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM/edit" rel="noreferrer" target="_blank">
https://docs.google.com/document/d/1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM/edit</a> - the submitted version<br>
>>>>>>>>> <a href="https://docs.google.com/document/d/1VvyP3YZQdQYjj8DFKOpQ4pn_0pdDGgiT/edit" rel="noreferrer" target="_blank">
https://docs.google.com/document/d/1VvyP3YZQdQYjj8DFKOpQ4pn_0pdDGgiT/edit</a> - first committed version<br>
>>>>>>>>> <a href="https://docs.google.com/document/d/1Ag4ipuybjtthxgV0YjXqYP7AwwNSYcWh/edit" rel="noreferrer" target="_blank">
https://docs.google.com/document/d/1Ag4ipuybjtthxgV0YjXqYP7AwwNSYcWh/edit</a> - first committed version<br>
>>>>>>>>> <a href="https://drive.google.com/file/d/1U_lTHrV6STXWNT3GiCepvsLk1WdYgzN5/view" rel="noreferrer" target="_blank">
https://drive.google.com/file/d/1U_lTHrV6STXWNT3GiCepvsLk1WdYgzN5/view</a> - its the first document posted<br>
>>>>>>>>><br>
>>>>>>>>> After this step is done I will move towards adhering to those instructions:<br>
>>>>>>>>> <a href="https://www.frontiersin.org/about/author-guidelines" rel="noreferrer" target="_blank">
https://www.frontiersin.org/about/author-guidelines</a><br>
>>>>>>>>><br>
>>>>>>>>> I estimate I will be working till late today with very few breaks and hopefully make sufficient progress.<br>
>>>>>>>>><br>
>>>>>>>>> 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.<br>
>>>>>>>>><br>
>>>>>>>>> Hopefully some of you will visit.<br>
>>>>>>>>><br>
>>>>>>>>> Jacob<br>
>>>>>>>>><br>
>>>>>>>>> On Fri, Oct 22, 2021 at 2:52 PM Jacob Barhak <<a href="mailto:jacob.barhak@gmail.com" rel="noreferrer" target="_blank">jacob.barhak@gmail.com</a>> wrote:<br>
>>>>>>>>>><br>
>>>>>>>>>> Thanks Sheriff, <br>
>>>>>>>>>><br>
>>>>>>>>>> With your green light I can start editing<br>
>>>>>>>>>><br>
>>>>>>>>>> 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.<br>
>>>>>>>>>><br>
>>>>>>>>>> If you want to repeat edits so those will be traceable it is possible. Yet we cannot copy verbatim without going to details.<br>
>>>>>>>>>><br>
>>>>>>>>>> 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. <br>
>>>>>>>>>><br>
>>>>>>>>>> Hopefully it will make things smoother.<br>
>>>>>>>>>><br>
>>>>>>>>>> Jacob<br>
>>>>>>>>>><br>
>>>>>>>>>><br>
>>>>>>>>>><br>
>>>>>>>>>><br>
>>>>>>>>>><br>
>>>>>>>>>><br>
>>>>>>>>>> On Fri, Oct 22, 2021, 13:40 Eric Forgoston <<a href="mailto:eric.forgoston@montclair.edu" rel="noreferrer" target="_blank">eric.forgoston@montclair.edu</a>> wrote:<br>
>>>>>>>>>>><br>
>>>>>>>>>>> Dear Jacob and all,<br>
>>>>>>>>>>><br>
>>>>>>>>>>> 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.<br>
>>>>>>>>>>><br>
>>>>>>>>>>> Best wishes,<br>
>>>>>>>>>>><br>
>>>>>>>>>>> Eric<br>
>>>>>>>>>>> ---------------------<br>
>>>>>>>>>>> Dr. Eric Forgoston<br>
>>>>>>>>>>> Professor of Applied Mathematics<br>
>>>>>>>>>>> Chair, Department of Applied Mathematics and Statistics<br>
>>>>>>>>>>> Montclair State University<br>
>>>>>>>>>>> Montclair, NJ 07043 USA<br>
>>>>>>>>>>> +1 973 655-7242<br>
>>>>>>>>>>> <a href="https://eric-forgoston.github.io/" rel="noreferrer" target="_blank">
https://eric-forgoston.github.io/</a><br>
>>>>>>>>>>><br>
>>>>>>>>>>><br>
>>>>>>>>>>> On Fri, Oct 22, 2021 at 12:57 PM Rahuman Sheriff <<a href="mailto:sheriff@ebi.ac.uk" rel="noreferrer" target="_blank">sheriff@ebi.ac.uk</a>> wrote:<br>
>>>>>>>>>>>><br>
>>>>>>>>>>>> Congratulations Marcella,<br>
>>>>>>>>>>>><br>
>>>>>>>>>>>> Hi Jacob and all,<br>
>>>>>>>>>>>><br>
>>>>>>>>>>>> As Tomas mentioned, John G’s version is bit more organised. <br>
>>>>>>>>>>>> Although it would be nice to take that one forward, I also fine with you recovering your version incorporating requested changes including mine.<br>
>>>>>>>>>>>> I would prefer this manuscript progresses ahead, instead of another long discussion. <br>
>>>>>>>>>>>> Green signal from my side.<br>
>>>>>>>>>>>> Best regards<br>
>>>>>>>>>>>> Sheriff<br>
>>>>>>>>>>>><br>
>>>>>>>>>>>><br>
>>>>>>>>>>>> On 22 Oct 2021, at 01:49, Jacob Barhak <<a href="mailto:jacob.barhak@gmail.com" rel="noreferrer" target="_blank">jacob.barhak@gmail.com</a>> wrote:<br>
>>>>>>>>>>>><br>
>>>>>>>>>>>> Congratulations Marcella,<br>
>>>>>>>>>>>><br>
>>>>>>>>>>>> Indeed you bring good news.<br>
>>>>>>>>>>>><br>
>>>>>>>>>>>> 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.<br>
>>>>>>>>>>>><br>
>>>>>>>>>>>> Jacob<br>
>>>>>>>>>>>><br>
>>>>>>>>>>>> On Thu, Oct 21, 2021, 10:33 Torres, Marcella <<a href="mailto:mtorres@richmond.edu" rel="noreferrer" target="_blank">mtorres@richmond.edu</a>> wrote:<br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> 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.<br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> 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.<br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> Marcella<br>
>>>>>>>>>>>>> ________________________________<br>
>>>>>>>>>>>>> From: Jacob Barhak <<a href="mailto:jacob.barhak@gmail.com" rel="noreferrer" target="_blank">jacob.barhak@gmail.com</a>><br>
>>>>>>>>>>>>> Sent: Wednesday, October 20, 2021 11:53:58 PM<br>
>>>>>>>>>>>>> To: Alexander Kulesza <<a href="mailto:alexander.kulesza@novadiscovery.com" rel="noreferrer" target="_blank">alexander.kulesza@novadiscovery.com</a>><br>
>>>>>>>>>>>>> Cc: Hana <<a href="mailto:h.dobrovolny@tcu.edu" rel="noreferrer" target="_blank">h.dobrovolny@tcu.edu</a>>; James Osborne <<a href="mailto:jmosborne@unimelb.edu.au" rel="noreferrer" target="_blank">jmosborne@unimelb.edu.au</a>>;
John Rice <<a href="mailto:john.rice@noboxes.org" rel="noreferrer" target="_blank">john.rice@noboxes.org</a>>; Torres, Marcella <<a href="mailto:mtorres@richmond.edu" rel="noreferrer" target="_blank">mtorres@richmond.edu</a>>;
<a href="mailto:vp-reproduce-subgroup@lists.simtk.org" rel="noreferrer" target="_blank">
vp-reproduce-subgroup@lists.simtk.org</a> <<a href="mailto:vp-reproduce-subgroup@lists.simtk.org" rel="noreferrer" target="_blank">vp-reproduce-subgroup@lists.simtk.org</a>>;
<a href="mailto:vp-integration-subgroup@lists.simtk.org" rel="noreferrer" target="_blank">
vp-integration-subgroup@lists.simtk.org</a> <<a href="mailto:vp-integration-subgroup@lists.simtk.org" rel="noreferrer" target="_blank">vp-integration-subgroup@lists.simtk.org</a>>; Jonathan Karr <<a href="mailto:jonrkarr@gmail.com" rel="noreferrer" target="_blank">jonrkarr@gmail.com</a>>;
John Gennari <<a href="mailto:gennari@uw.edu" rel="noreferrer" target="_blank">gennari@uw.edu</a>>; Winston Garira <<a href="mailto:Winston.Garira@univen.ac.za" rel="noreferrer" target="_blank">Winston.Garira@univen.ac.za</a>><br>
>>>>>>>>>>>>> Subject: Re: [Vp-integration-subgroup] Fwd: Shayn Peirce-Cottler via Frontiers: Manuscript<br>
>>>>>>>>>>>>> <br>
>>>>>>>>>>>>> External Email: Use caution in opening links, attachments, and buying gift cards.<br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> Thanks Alex, Thanks John,<br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> 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.<br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> 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.<br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> If there will be no blocks I plan to start work over the weekend if I see no objections by then.<br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> 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.<br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> 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.<br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> 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.<br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> Jacob<br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> On Tue, Oct 19, 2021 at 2:02 AM Alexander Kulesza <<a href="mailto:alexander.kulesza@novadiscovery.com" rel="noreferrer" target="_blank">alexander.kulesza@novadiscovery.com</a>> wrote:<br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> Dear Jacob,<br>
>>>>>>>>>>>>> thanks for forwarding and you suggestions, which seems more than reasonable.<br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> My contributions from May 19th, May31st and June 2nd are in <a href="https://docs.google.com/document/d/1VvyP3YZQdQYjj8DFKOpQ4pn_0pdDGgiT/edit?usp=sharing&ouid=113860487708206439519&rtpof=true&sd=true" rel="noreferrer" target="_blank">
https://docs.google.com/document/d/1VvyP3YZQdQYjj8DFKOpQ4pn_0pdDGgiT/edit?usp=sharing&ouid=113860487708206439519&rtpof=true&sd=true</a><br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> The other document <a href="https://docs.google.com/document/d/1esZvWWVBvpwvuFUi3C3161lthZkEBFyMRrwwozitBi4/edit?usp=sharing" rel="noreferrer" target="_blank">
https://docs.google.com/document/d/1esZvWWVBvpwvuFUi3C3161lthZkEBFyMRrwwozitBi4/edit?usp=sharing</a> 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.<br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> 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.<br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> Please let me know.<br>
>>>>>>>>>>>>> A<br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> On Tue, 19 Oct 2021 at 05:51, Jacob Barhak <<a href="mailto:jacob.barhak@gmail.com" rel="noreferrer" target="_blank">jacob.barhak@gmail.com</a>> wrote:<br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> Greetings white paper contributors,<br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> Below is the response from the editor to my request and my thank you.<br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> 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.<br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> 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.<br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> The most time consuming effort would be adhering to the journal format as defined here:<br>
>>>>>>>>>>>>> <a href="https://www.frontiersin.org/about/author-guidelines" rel="noreferrer" target="_blank">
https://www.frontiersin.org/about/author-guidelines</a><br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> I think the most time consuming task would be dealing with the references - otherwise the format guidelines seem reasonable.<br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> We can also add some revisions we started working on. However, I will personally insist on :<br>
>>>>>>>>>>>>> 1. traceability - currently there is no traceability in the revised version in the summer<br>
>>>>>>>>>>>>> 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<br>
>>>>>>>>>>>>> 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.<br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> I will also ask for fast responses from all contributors.<br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> 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.<br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> 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.<br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> 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:<br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> - 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<br>
>>>>>>>>>>>>> - 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 <br>
>>>>>>>>>>>>> - 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.<br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> 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.<br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> 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..<br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> 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 ..<br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> If I forgot anyone who had major requests, please remind me. .<br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> 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..<br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> Hopefully most of you will be ok with that.<br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> Jacob<br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> ---------- Forwarded message ---------<br>
>>>>>>>>>>>>> From: Jacob Barhak <<a href="mailto:jacob.barhak@gmail.com" rel="noreferrer" target="_blank">jacob.barhak@gmail.com</a>><br>
>>>>>>>>>>>>> Date: Mon, Oct 18, 2021 at 9:34 PM<br>
>>>>>>>>>>>>> Subject: Re: Shayn Peirce-Cottler via Frontiers: Manuscript<br>
>>>>>>>>>>>>> To: Peirce-Cottler, Shayn (smp6p) <<a href="mailto:smp6p@virginia.edu" rel="noreferrer" target="_blank">smp6p@virginia.edu</a>><br>
>>>>>>>>>>>>> Cc: Shayn Peirce-Cottler (Via FrontiersIn) <<a href="mailto:shayn@virginia.edu" rel="noreferrer" target="_blank">shayn@virginia.edu</a>>,<a href="mailto:systemsbiology.editorial.office@frontiersin.org" rel="noreferrer" target="_blank">systemsbiology.editorial.office@frontiersin.org</a>
<<a href="mailto:systemsbiology.editorial.office@frontiersin.org" rel="noreferrer" target="_blank">systemsbiology.editorial.office@frontiersin.org</a>>, Vodovotz, Yoram <<a href="mailto:vodovotzy@upmc.edu" rel="noreferrer" target="_blank">vodovotzy@upmc.edu</a>><br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> Thanks Shayn,<br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> You will get a revised manuscript targeted at your journal and get back to you with a more polished version and satisfies your requests.<br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> 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.<br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> Many thanks for the rapid responses.<br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> Jacob<br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> --<br>
>>>>>>>>>>>>> Jacob Barhak Ph.D.<br>
>>>>>>>>>>>>> Sole Proprietor, Software Developer, and Computational Disease Modeler<br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> Jacob Barhak Analytics<br>
>>>>>>>>>>>>> 701 Brazos St<br>
>>>>>>>>>>>>> Suite 548<br>
>>>>>>>>>>>>> Austin TX, 78701<br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> Email: <a href="mailto:jacob.barhak@gmail.com" rel="noreferrer" target="_blank">
jacob.barhak@gmail.com</a><br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> <a href="https://sites.google.com/view/jacob-barhak/home" rel="noreferrer" target="_blank">
https://sites.google.com/view/jacob-barhak/home</a><br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> On Mon, Oct 18, 2021 at 7:43 PM Peirce-Cottler, Shayn (smp6p) <<a href="mailto:smp6p@virginia.edu" rel="noreferrer" target="_blank">smp6p@virginia.edu</a>> wrote:<br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> Hi Jacob,<br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> <br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> 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. <br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> <br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> 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!<br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> <br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> -Shayn<br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> <br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> <br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> Shayn Peirce-Cottler, Ph.D.<br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> Professor of Biomedical Engineering<br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> Harrison Distinguished Teaching Professor<br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> BME Graduate Program Director<br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> University of Virginia<br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> Charlottesville, VA<br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> <br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> From: Jacob Barhak <<a href="mailto:jacob.barhak@gmail.com" rel="noreferrer" target="_blank">jacob.barhak@gmail.com</a>><br>
>>>>>>>>>>>>> Date: Monday, October 18, 2021 at 1:57 AM<br>
>>>>>>>>>>>>> To: Peirce-Cottler Shayn <<a href="mailto:shayn@virginia.edu" rel="noreferrer" target="_blank">shayn@virginia.edu</a>><br>
>>>>>>>>>>>>> Cc: "<a href="mailto:systemsbiology.editorial.office@frontiersin.org" rel="noreferrer" target="_blank">systemsbiology.editorial.office@frontiersin.org</a>" <<a href="mailto:systemsbiology.editorial.office@frontiersin.org" rel="noreferrer" target="_blank">systemsbiology.editorial.office@frontiersin.org</a>>,
"Vodovotz, Yoram" <<a href="mailto:vodovotzy@upmc.edu" rel="noreferrer" target="_blank">vodovotzy@upmc.edu</a>><br>
>>>>>>>>>>>>> Subject: Re: Shayn Peirce-Cottler via Frontiers: Manuscript<br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> <br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> Hi Shayn,<br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> <br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> Thanks for returning the response quickly. To you comments.<br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> <br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> 1. This is the list of authors that agreed to submit this manuscript for review - I collected their approvals for this version personally.<br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> <br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> 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<br>
>>>>>>>>>>>>> Rahuman Sheriff, The European Bioinformatics Institute (EMBL-EBI), UK<br>
>>>>>>>>>>>>> James Osborne, School of Mathematics and Statistics, University of Melbourne, Australia<br>
>>>>>>>>>>>>> Gilberto Gonzalez Parra, Mathematics Department, New Mexico Tech, USA<br>
>>>>>>>>>>>>> Eric Forgoston, Department of Applied Mathematics and Statistics, Montclair State University, USA<br>
>>>>>>>>>>>>> Ruth Bowness, Department of Mathematical Sciences, University of Bath, UK<br>
>>>>>>>>>>>>> Yaling Liu, Department of Mechanical Engineering and Mechanics , Department of Bioengineering, Lehigh University, USA<br>
>>>>>>>>>>>>> Robin Thompson, Mathematics Institute & The Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research, University of Warwick, UK<br>
>>>>>>>>>>>>> Winston Garira - Department Of Mathematics And Applied Mathematics , Modelling Health and Environmental Linkages Research Group. University of Venda, South Africa<br>
>>>>>>>>>>>>> Jacob Barhak - Barhak, Jacob, USA<br>
>>>>>>>>>>>>> John Rice - Independent Retired Working Group Volunteer, USA<br>
>>>>>>>>>>>>> Marcella Torres, School of Arts and Sciences, University of Richmond, USA<br>
>>>>>>>>>>>>> Hana M. Dobrovolny , Department of Physics & Astronomy, Texas Christian University, Fort Worth, USA<br>
>>>>>>>>>>>>> Tingting Tang, Department of Mathematics and Statistics in San Diego State University (SDSU) and SDSU Imperial Valley, USA<br>
>>>>>>>>>>>>> William Waites, Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, UK<br>
>>>>>>>>>>>>> James Glazier, Biocomplexity Institute, Indiana University, Bloomington, USA<br>
>>>>>>>>>>>>> James R. Faeder, Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, USA<br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> <br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> 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:
<a href="https://lists.simtk.org/pipermail/vp-reproduce-subgroup/2021-March/000019.html" rel="noreferrer" target="_blank">
https://lists.simtk.org/pipermail/vp-reproduce-subgroup/2021-March/000019.html</a> - 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.<br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> <br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> <br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> 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.<br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> <br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> 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.<br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> <br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> 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.<br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> <br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> In summary:<br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> 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.<br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> <br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> 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.<br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> <br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> Hopefully we can address your concerns in time to publish the manuscript in a timely manner.<br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> <br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> Jacob<br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> <br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> --<br>
>>>>>>>>>>>>> Jacob Barhak Ph.D.<br>
>>>>>>>>>>>>> Sole Proprietor, Software Developer, and Computational Disease Modeler<br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> Jacob Barhak Analytics<br>
>>>>>>>>>>>>> 701 Brazos St<br>
>>>>>>>>>>>>> Suite 548<br>
>>>>>>>>>>>>> Austin TX, 78701<br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> Email: <a href="mailto:jacob.barhak@gmail.com" rel="noreferrer" target="_blank">
jacob.barhak@gmail.com</a><br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> <a href="https://sites.google.com/view/jacob-barhak/home" rel="noreferrer" target="_blank">
https://sites.google.com/view/jacob-barhak/home</a><br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> <br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> <br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> On Sun, Oct 17, 2021 at 9:56 AM Shayn Peirce-Cottler (Via FrontiersIn) <<a href="mailto:noreply@frontiersin.org" rel="noreferrer" target="_blank">noreply@frontiersin.org</a>> wrote:<br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> Dear Jacob,<br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> 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:<br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> 1. The author list that is on the first page differs from the author list that was provided at the time of submission.<br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> 2. The manuscript needs to be submitted using the official Frontiers template.<br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> 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.<br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> 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).<br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> 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.<br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> Thank you,<br>
>>>>>>>>>>>>> Shayn<br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> ---------------------------------<br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> Manuscript title: Model Integration in Computational Biology: The Role of Reproducibility, Credibility and Utility<br>
>>>>>>>>>>>>> Manuscript ID: 793932<br>
>>>>>>>>>>>>> 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<br>
>>>>>>>>>>>>> Date submitted: 12 Oct 2021<br>
>>>>>>>>>>>>> Edited by: Shayn Peirce-Cottler<br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> Research Topic: Insights in Systems Biology: Multiscale Mechanistic Modeling 2021<br>
>>>>>>>>>>>>> Review forum direct access link: <a href="https://review.frontiersin.org/review/793932/0/0" rel="noreferrer" target="_blank">
https://review.frontiersin.org/review/793932/0/0</a><br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> _______________________________________________<br>
>>>>>>>>>>>>> Vp-integration-subgroup mailing list<br>
>>>>>>>>>>>>> <a href="mailto:Vp-integration-subgroup@lists.simtk.org" rel="noreferrer" target="_blank">
Vp-integration-subgroup@lists.simtk.org</a><br>
>>>>>>>>>>>>> <a href="https://lists.simtk.org/mailman/listinfo/vp-integration-subgroup" rel="noreferrer" target="_blank">
https://lists.simtk.org/mailman/listinfo/vp-integration-subgroup</a><br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> --<br>
>>>>>>>>>>>>> Alexander Kulesza<br>
>>>>>>>>>>>>> Team leader<br>
>>>>>>>>>>>>> Modeling & simulation / Biomodeling<br>
>>>>>>>>>>>>> <a href="mailto:alexander.kulesza@novadiscovery.com" rel="noreferrer" target="_blank">
alexander.kulesza@novadiscovery.com</a><br>
>>>>>>>>>>>>> +33 7 82 92 44 62<br>
>>>>>>>>>>>>> nova<br>
>>>>>>>>>>>>> DISCOVERY<br>
>>>>>>>>>>>>> <a href="http://www.novadiscovery.com/" rel="noreferrer" target="_blank">
www.novadiscovery.com</a><br>
>>>>>>>>>>>>> 1 Place Verrazzano, 69009 Lyon<br>
>>>>>>>>>>>>> +33 9 72 53 13 01<br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>> 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.<br>
>>>>>>>>>>>><br>
>>>>>>>>>>>> _______________________________________________<br>
>>>>>>>>>>>> Vp-integration-subgroup mailing list<br>
>>>>>>>>>>>> <a href="mailto:Vp-integration-subgroup@lists.simtk.org" rel="noreferrer" target="_blank">
Vp-integration-subgroup@lists.simtk.org</a><br>
>>>>>>>>>>>> <a href="https://lists.simtk.org/mailman/listinfo/vp-integration-subgroup" rel="noreferrer" target="_blank">
https://lists.simtk.org/mailman/listinfo/vp-integration-subgroup</a><br>
>>>>>>>>>>>><br>
>>>>>>>>>>>><br>
>>>>>>>>>>>> _______________________________________________<br>
>>>>>>>>>>>> Vp-reproduce-subgroup mailing list<br>
>>>>>>>>>>>> <a href="mailto:Vp-reproduce-subgroup@lists.simtk.org" rel="noreferrer" target="_blank">
Vp-reproduce-subgroup@lists.simtk.org</a><br>
>>>>>>>>>>>> <a href="https://lists.simtk.org/mailman/listinfo/vp-reproduce-subgroup" rel="noreferrer" target="_blank">
https://lists.simtk.org/mailman/listinfo/vp-reproduce-subgroup</a><br>
>>>>>><br>
>>>>>> _______________________________________________<br>
>>>>>> Vp-reproduce-subgroup mailing list<br>
>>>>>> <a href="mailto:Vp-reproduce-subgroup@lists.simtk.org" rel="noreferrer" target="_blank">
Vp-reproduce-subgroup@lists.simtk.org</a><br>
>>>>>> <a href="https://lists.simtk.org/mailman/listinfo/vp-reproduce-subgroup" rel="noreferrer" target="_blank">
https://lists.simtk.org/mailman/listinfo/vp-reproduce-subgroup</a></div>
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