[Vp-integration-subgroup] [Vp-reproduce-subgroup] White paper revision

[Jonathan Karr]

Hi everyone,

I think Frontiers is fine. I think the key thing is to edit the paper (for
focus and readability by a broader audience) before it is submitted to any
journal.

Regards
Jonathan

On Mon, Aug 9, 2021 at 10:31 AM Jacob Barhak <jacob.barhak at gmail.com> wrote:

> Well Marcella,
>
> If there is no objection raised or an alternative resolution with more
> support appears,  then I see no reason not to proceed. So I think we just
> need to give enough time for original contributors to raise an objection or
> propose an alternatives that will gain more support. In the past we used a
> week for such processes,  I guess that if we wait until next weekend and no
> objection is raised to the venue or an alternative with more support
> appears we can proceed. We currently have 5 original contributors
> supporting your suggested venue and one contributor than joined later in
> the revisions.
>
>
> Note that in submission you should use the original version we reached
> consensus for submission, yet note that that we plan to revise the work and
> add more contributors. You can point to revisions we started.
>
> Lets wait until next week and hope no one objects so we can proceed
> quickly.
>
>          Jacob
>
>
> On Mon, Aug 9, 2021, 08:52 Torres, Marcella <mtorres at richmond.edu> wrote:
>
>> Once enough contributors agree, the process for submission is that I’ll
>> confirm interest (I just got an email requesting for this  this morning),
>> let them know that we intend to submit 1 manuscript and what the proposed
>> title of the manuscript is. Once that initial information is submitted,
>> then I will be “emailed information about next steps”. Of course, at any
>> point we can also contact the editorial office, but would it be helpful to
>> get a sense of the process first and then ask for clarification as needed?
>> At what point will we have enough responses from contributors to begin?
>>
>>
>>
>> Best,
>>
>> Marcella
>>
>>
>>
>> *From: *Vp-reproduce-subgroup <
>> vp-reproduce-subgroup-bounces at lists.simtk.org> on behalf of John Rice <
>> john.rice at noboxes.org>
>> *Date: *Sunday, August 8, 2021 at 7:23 PM
>> *To: *Yaling Liu <yal310 at lehigh.edu>
>> *Cc: *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>, Faeder, James R <
>> faeder at pitt.edu>, Winston Garira <Winston.Garira at univen.ac.za>
>> *Subject: *Re: [Vp-reproduce-subgroup] [Vp-integration-subgroup] White
>> paper revision
>>
>> *External Email:* Use caution in opening links, attachments, and buying
>> gift cards.
>>
>>
>>
>> Me too
>>
>> Typed with two thumbs on my iPhone.  (757) 318-0671
>>
>>
>>
>> “Upon this gifted age, in its dark hour,
>>
>> Rains from the sky a meteoric shower
>>
>> Of facts . . . they lie unquestioned, uncombined.
>>
>> Wisdom enough to leech us of our ill
>>
>> Is daily spun; but there exists no loom
>>
>> To weave it into fabric.”
>>
>>
>>
>> –Edna St. Vincent Millay,
>>
>>
>>
>>
>>
>>
>> On Aug 8, 2021, at 19:09, Yaling Liu <yal310 at lehigh.edu> wrote:
>>
>> 
>>
>> I am fine with the suggested new venue and willing to revise further.
>> We don't need to wait for everyone to reply here - this email chain is way
>> too long and guess a lot of people were busy and ignored them.
>>
>>
>>
>> Thanks.
>>
>>
>>
>> Yaling
>>
>>
>>
>> On Sun, Aug 8, 2021 at 4:57 PM Jacob Barhak <jacob.barhak at gmail.com>
>> wrote:
>>
>> Thanks Hana,
>>
>>
>>
>> The revised version is far from ready to being submitted anywhere. There
>> is just too much to do there to put it in shape for submission.
>>
>>
>>
>> We do want to advance in making revisions,  yet the attempt here is to
>> accelerate the process by asking a 3rd publishing party to provide proper
>> review for what is actually needed for publication, so you may want to save
>> your efforts until after we get feedback - they will be more effective then
>> when we have feedback.
>>
>>
>>
>> However, we do need enough support and no objections to proceed to engage
>> with the new venue suggested.
>>
>>
>>
>> We have currently 3 of the 17 of the original contributors and 1 who
>> joined later that approves of a new venue. Hopefully others will follow so
>> we can proceed quickly.
>>
>>
>>
>> Thank you for the reply.
>>
>>
>>
>>           Jacob
>>
>>
>>
>>
>>
>> On Sat, Aug 7, 2021, 23:46 Dobrovolny, Hana <h.dobrovolny at tcu.edu> wrote:
>>
>> I'm fine with the suggested venue. I'll double check the sections I was
>> heading sometime this week, but I think all suggestions were incorporated
>> last time I checked.
>>
>> Hana
>>
>>
>>
>> *******************************************************
>> Dr. Hana Dobrovolny
>> Associate Professor of Biophysics
>> Texas Christian University
>> TCU Box 298840
>> Fort Worth, TX 76129
>>
>> phone: (817) 257-6379 fax: (817) 257-7742
>> email: h.dobrovolny at tcu.edu
>> *******************************************************
>>
>>
>> ------------------------------
>>
>> *From:* Vp-reproduce-subgroup <
>> vp-reproduce-subgroup-bounces at lists.simtk.org> on behalf of Jacob Barhak
>> <jacob.barhak at gmail.com>
>> *Sent:* August 7, 2021 11:18 AM
>> *To:* Torres, Marcella
>> *Cc:* vp-reproduce-subgroup at lists.simtk.org;
>> vp-integration-subgroup at lists.simtk.org; Jonathan Karr; John Gennari;
>> Winston Garira; Faeder, James R
>> *Subject:* Re: [Vp-reproduce-subgroup] [Vp-integration-subgroup] White
>> paper revision
>>
>>
>>
>> *[EXTERNAL EMAIL WARNING]* DO NOT CLICK LINKS or open attachments unless
>> you recognize the sender and know the content is safe.
>>
>> And to all white paper contributors,
>>
>>
>>
>> You are getting this message to raise it to the top of your mailboxes.
>>
>>
>>
>> Hopefully enough of you will look at this during the weekend to comment
>> on the best way to move forward while considering the new offer from
>> Marcella.
>>
>>
>>
>> The faster we move,  the better.
>>
>>
>>
>>           Jacob
>>
>>
>>
>>
>>
>>
>>
>> On Tue, Aug 3, 2021, 01:03 Jacob Barhak <jacob.barhak at gmail.com> wrote:
>>
>> Thanks Marcella,
>>
>>
>>
>> Your suggestion may be the solution here.
>>
>>
>>
>> From what I see,  this venue is a good fit. Yet we need to learn the
>> opinion of the other contributors.
>>
>>
>>
>> If we collect enough support and no contributor objects, we can approach
>> the editor and ask if the paper will receive proper review to guide
>> revisions.
>>
>>
>>
>> I look forward for more responses.
>>
>>
>>
>>           Jacob
>>
>>
>>
>>
>>
>> On Mon, Aug 2, 2021, 11:57 Torres, Marcella <mtorres at richmond.edu> wrote:
>>
>> Hi all and Jacob,
>>
>>
>>
>> I’m interested in getting it circulated, and want to propose Frontiers in
>> Systems Biology as a possible venue – I just joined the editorial board and
>> received notice of a focused issue that includes challenges in multiscale
>> modeling:
>> https://www.frontiersin.org/research-topics/24484/insights-in-systems-biology-multiscale-mechanistic-modeling-2021?utm_source=F-RTM&utm_medium=CFP_E1&utm_campaign=PRD_CFP_T1_RT-TITLE#
>> <https://urldefense.com/v3/__https:/www.frontiersin.org/research-topics/24484/insights-in-systems-biology-multiscale-mechanistic-modeling-2021?utm_source=F-RTM&utm_medium=CFP_E1&utm_campaign=PRD_CFP_T1_RT-TITLE*__;Iw!!K6Z8K8YTIA!VdlFMCuGyTWxTFwAHTufvXzSxbtUQ9ckyDlofvqR1sm1Q-6-HD2vdZtc_2WFepwnGQ8$>
>> .
>>
>>
>>
>> The journal is new, and I don’t remember it being proposed previously.
>>
>>
>>
>> I am also willing to prioritize revision and submission and apologize for
>> not participating more over the summer.
>>
>>
>>
>> Best,
>>
>> Marcella
>>
>>
>>
>> *From: *Vp-reproduce-subgroup <
>> vp-reproduce-subgroup-bounces at lists.simtk.org> on behalf of Jacob Barhak
>> <jacob.barhak at gmail.com>
>> *Date: *Monday, August 2, 2021 at 11:45 AM
>> *To: *Alexander Kulesza <alexander.kulesza at novadiscovery.com>
>> *Cc: *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>, Faeder, James R <
>> faeder at pitt.edu>, Winston Garira <Winston.Garira at univen.ac.za>
>> *Subject: *Re: [Vp-reproduce-subgroup] [Vp-integration-subgroup] White
>> paper revision
>>
>> *External Email:* Use caution in opening links, attachments, and buying
>> gift cards.
>>
>>
>>
>> Hi Alex,
>>
>>
>>
>> Thanks for your response first - it is the first public response.
>>
>>
>>
>> However, I was hoping for a discussion rather than a poll. We already
>> made a vote and the direction it took us all ended up badly so far - there
>> is no activity for a few months now. Perhaps a discussion is in order
>> before making more decisions.
>>
>>
>>
>> And Alex, time is something you manage to achieve certain goals with
>> certain priorities.
>>
>>
>>
>> The real question is if circulating this paper is on a high priority list
>> for any of the contributors?
>>
>>
>>
>> Some contributors publicly declared they have little time, yet we were
>> still able to push though in the past. What has changed?
>>
>>
>>
>> Perhaps a discussion will reveal those things.
>>
>>
>>
>>                     Jacob
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> On Mon, Aug 2, 2021 at 2:00 AM Alexander Kulesza <
>> alexander.kulesza at novadiscovery.com> wrote:
>>
>> Dear all, Dear Jacob,
>>
>>
>>
>> I hope that I speak for many others from this group wishing that the
>> ideas presented in that paper do get circulated; optimally in form of a
>> reviewed paper.
>>
>>
>>
>> I think that the time of the year impedes many of us (including myself)
>> to spend the time needed to edit the sections.
>>
>> I have created the following poll
>> https://doodle.com/poll/ydpgvgi594ubi82d?utm_source=poll&utm_medium=link
>> <https://urldefense.com/v3/__https:/doodle.com/poll/ydpgvgi594ubi82d?utm_source=poll&utm_medium=link__;!!K6Z8K8YTIA!VdlFMCuGyTWxTFwAHTufvXzSxbtUQ9ckyDlofvqR1sm1Q-6-HD2vdZtc_2WFaV6WX1c$>
>> which intends to get agreement or disgreement of the group for the
>> different optuions that exist.
>>
>>
>>
>> Please let me know what you think.
>>
>> Alexander
>>
>>
>>
>>
>>
>>
>>
>> On Thu, 29 Jul 2021 at 16:54, Jacob Barhak <jacob.barhak at gmail.com>
>> wrote:
>>
>> Greetings contributors,
>>
>>
>>
>> Two of the contributors approach me about this message privately.
>> However, there were many more who participated and no one responded
>> publicly in 2 weeks.
>>
>>
>>
>> Do you not want this paper be circulated?
>>
>>
>>
>> I am asking those questions publicly since this deserves a public
>> discussion.
>>
>>
>>
>> Hopefully this reminder will stir up the group.
>>
>>
>>
>>             Jacob
>>
>>
>>
>> On Wed, Jul 14, 2021 at 4:46 PM Jacob Barhak <jacob.barhak at gmail.com>
>> wrote:
>>
>> Hi Gilberto,
>>
>>
>>
>> As you can see, there was no response to your email - in fact the paper
>> writing stopped - I waited sufficient time to make sure this is the case to
>> prove a point. If there is no one to tend to the editing, then there will
>> not be any progress and the paper will lose focus -
>> partially because people will pull it in many directions and resolution
>> will take time no one is willing to provide to move it forward. And this is
>> what happened here.
>>
>>
>>
>> I remind you that I wrote what needs to be done to make progress. See the
>> 4 points in this archived email:
>>
>>
>> https://lists.simtk.org/pipermail/vp-reproduce-subgroup/2021-May/000098.html
>> <https://urldefense.com/v3/__https:/lists.simtk.org/pipermail/vp-reproduce-subgroup/2021-May/000098.html__;!!K6Z8K8YTIA!VdlFMCuGyTWxTFwAHTufvXzSxbtUQ9ckyDlofvqR1sm1Q-6-HD2vdZtc_2WFEHRSJVg$>
>>
>>
>>
>> By now it's fairly safe to declare that the group failed to fulfil those
>> points in reasonable time, and the revised version is in a worse condition
>> towards publication than the version we all agreed to submit before.
>>
>>
>>
>> This situation raises the question.
>>
>>
>>
>> Is there more benefit from submitting the findings we had before as they
>> were to a 3rd party for publication than waiting for revisions to end?
>>
>>
>>
>> I personally doubt that any further revisions will allow publication in
>> reasonable time - which as I mentioned before delays science rather than
>> advancing it.
>>
>>
>>
>> I assume that this email will start a debate with different opinions,
>> that may take a long time and this is not my intention. My purpose is
>> practical -  I am trying to salvage the paper so it gets published quickly.
>> It is better than waiting forever...
>>
>>
>>
>> I believe that what we accumulated and summarized in a table is worth
>> publication as we agreed before. We did reach a consensus and I hope
>> individuals will realize this is the most practical course of action.
>>
>>
>>
>> Revisions can continue and information added for future versions, yet I
>> do ask that this paper be submitted quickly to a venue that will accept it
>> in the form we agreed upon.
>>
>>
>>
>> If we do not do this, we will be guilty of delaying science.
>>
>>
>>
>> Hopefully contributors will realize this and we can proceed to fix the
>> situation quickly.
>>
>>
>>
>>            Jacob
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> On Mon, Jun 21, 2021 at 1:06 PM Gilberto Gonzalez-Parra <
>> gilberto.gonzalezparra at nmt.edu> wrote:
>>
>> Dear all,
>>
>>
>>
>> I like Eric's idea  i.e.  "section heads can look at the technical
>> aspects of their respective sections this week."
>>
>>
>>
>> There are many suggestions and I think the section heads can focus in one
>> section to make the work more manageable. Then we can read the whole
>> manuscript to check the consistency of the manuscript. Overall, I think we
>> can focus on two main ideas. One to point out the challenges of Biosimulation
>> Model Reproducibility and Model Integration, and some initial basic ideas
>> to tackle these issues. That might be the main message of the article (??)
>>
>>
>>
>> Best,
>>
>>
>>
>>
>>
>> ***************************************************************************
>>
>> Gilberto C. Gonzalez-Parra, Ph.D in Applied Mathematics.
>>
>> Faculty of the Mathematics Department
>>
>> New Mexico Tech, NM, USA.
>>
>>
>> ****************************************************************************
>>
>>
>>
>>
>>
>> On Mon, Jun 21, 2021 at 8:16 AM Eric Forgoston <
>> eric.forgoston at montclair.edu> wrote:
>>
>> Dear all,
>>
>>
>>
>> It seems that progress has mostly stalled - there are numerous
>> comments/edits that have been suggested and are waiting to be acted upon by
>> the section heads.
>>
>>
>>
>> I suggest a renewed effort over the next week or so: perhaps section
>> heads can look at the technical aspects of their respective sections this
>> week. Then, if interested, I can set up a poll for a discussion next week
>> that will serve to resolve and finalise any remaining issues.
>>
>>
>>
>> Thoughts?
>>
>>
>>
>> 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/
>> <https://urldefense.com/v3/__https:/eric-forgoston.github.io/__;!!K6Z8K8YTIA!VdlFMCuGyTWxTFwAHTufvXzSxbtUQ9ckyDlofvqR1sm1Q-6-HD2vdZtc_2WF1l-OpF0$>
>>
>>
>>
>>
>>
>> On Mon, Jun 21, 2021 at 5:54 AM Alexander Kulesza <
>> alexander.kulesza at novadiscovery.com> wrote:
>>
>> Hello all,
>>
>>
>>
>> regarding the manuscript, what is the deadline for contributions? I try
>> to find another slot for a  working session this and next week. Please let
>> me know where help is needed in terms of editing.
>>
>>
>>
>> ALexander
>>
>>
>>
>> On Mon, 24 May 2021 at 18:00, John Gennari <gennari at uw.edu> wrote:
>>
>>
>>
>> Eric:
>>
>> Yes, I do see your changes. Thanks!
>>
>> -John G.
>>
>> On 5/24/2021 4:47 AM, Eric Forgoston wrote:
>>
>> Hi Jacob and all,
>>
>> I did rewrite the stochastic section adding in material from me and
>> comments from William and James G. The only material I removed had been
>> written by myself originally.
>>
>> Additional comments are welcome.
>>
>>
>>
>> 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/
>> <https://urldefense.com/v3/__https:/eric-forgoston.github.io/__;!!K6Z8K8YTIA!VdlFMCuGyTWxTFwAHTufvXzSxbtUQ9ckyDlofvqR1sm1Q-6-HD2vdZtc_2WF1l-OpF0$>
>>
>>
>>
>>
>>
>> On Mon, May 24, 2021 at 6:55 AM William Waites <wwaites at ieee.org> wrote:
>>
>> > Otherwise, all I saw was …
>>
>> There was editing of the section on stochasticity by Eric with some input
>> from myself.
>>
>> _______________________________________________
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>>
>>
>>
>>
>> --
>>
>> Alexander Kulesza
>>
>> Team leader
>>
>> Modeling & simulation / Biomodeling
>>
>> alexander.kulesza at novadiscovery.com
>>
>> +33 7 82 92 44 62
>>
>> *nova*
>>
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>>
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>>
>>
>>
>> --
>>
>> Alexander Kulesza
>>
>> Team leader
>>
>> Modeling & simulation / Biomodeling
>>
>> alexander.kulesza at novadiscovery.com
>>
>> +33 7 82 92 44 62
>>
>> *nova*
>>
>> DISCOVERY
>>
>> www.novadiscovery.com
>> <https://urldefense.com/v3/__http:/www.novadiscovery.com/__;!!K6Z8K8YTIA!VdlFMCuGyTWxTFwAHTufvXzSxbtUQ9ckyDlofvqR1sm1Q-6-HD2vdZtc_2WF5R8SDjQ$>
>>
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>> +33 9 72 53 13 01
>>
>>
>> *This message is intended only for the personal and confidential use of
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>>
>>
>> --
>>
>> -- ------------------
>>
>> Yaling Liu, Professor
>>
>> Department of Mechanical Engineering and Mechanics
>>
>> Department of Bioengineering
>>
>> Lehigh University
>>
>> www.lehigh.edu/~yal310
>>
>> _______________________________________________
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