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

[James Osborne]

I'm fine with Frontiers.

My 2 cents is that the revised version would be more likely to get
published. I think we should find time to tidy up what we need.

James

On Tue, Aug 10, 2021 at 5:11 PM Tomas Helikar <thelikar2 at unl.edu> wrote:

> Hi everyone,
>
> I'm also fine with this journal. But we need to finalize the revised
> version -- lots of work was done on it already.
>
> Perhaps we can recirculate the last version of the google doc version of
> it and set a deadline for finishing it? I don't believe it would take more
> than a couple of weeks to finalize.
>
> Best wishes,
>
> T.
> Tomas Helikar, Ph.D.
> Susan J Rosowski Associate Professor
> Department of Biochemistry | University of Nebraska-Lincoln
> m: 402-547-8904 <callto:402-547-8904> | o: 402-472-3530
> <callto:402-472-3530>
> www.helikarlab.org <http://helikarlab.org> | www.thecellcollective.org
> <https://cellcollective.org>
> twitter: @helikarlab <http://twitter.com/helikarlab>, @biocollective
> <http://twitter.com/biocollective>
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> On 8/9/21 5:06 PM, John Gennari wrote:
>
> Non-NU Email
> ------------------------------
>
> I agree with Jon Karr. The venue is fine, but we need at least a quick
> review for readability before submission.
>
> -John G.
> On 8/9/2021 7:49 AM, Jonathan Karr wrote:
>
> 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$>
>>>
>>>
>>>
>>>
>>>
>>> On Mon, May 24, 2021 at 6:55 AM William Waites <wwaites at ieee.org> wrote:
>>>
>>> > Otherwise, all I saw was …
>>>
>>> There was editing of the section on stochasticity by Eric with some
>>> input from myself.
>>>
>>> _______________________________________________
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>>>
>>>
>>>
>>>
>>> --
>>>
>>> Alexander Kulesza
>>>
>>> Team leader
>>>
>>> Modeling & simulation / Biomodeling
>>>
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>>>
>>> +33 7 82 92 44 62
>>>
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>>>
>>>
>>> --
>>>
>>> Alexander Kulesza
>>>
>>> Team leader
>>>
>>> Modeling & simulation / Biomodeling
>>>
>>> alexander.kulesza at novadiscovery.com
>>>
>>> +33 7 82 92 44 62
>>>
>>> *nova*
>>>
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>>> information is subject to change without notice.*
>>>
>>> _______________________________________________
>>> Vp-integration-subgroup mailing list
>>> Vp-integration-subgroup at lists.simtk.org
>>> https://lists.simtk.org/mailman/listinfo/vp-integration-subgroup
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>>>
>>>
>>>
>>>
>>> --
>>>
>>> -- ------------------
>>>
>>> Yaling Liu, Professor
>>>
>>> Department of Mechanical Engineering and Mechanics
>>>
>>> Department of Bioengineering
>>>
>>> Lehigh University
>>>
>>> www.lehigh.edu/~yal310
>>> <https://urldefense.com/v3/__http://www.lehigh.edu/*yal310__;fg!!PvXuogZ4sRB2p-tU!RpcLpR1RAgDlcdjrW-GQkhhfcfr8Fu1ojChx271t6XEjc3XFfFqLOojpDQcZr6uP$>
>>>
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>>>
>>
> _______________________________________________
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