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

Jacob Barhak jacob.barhak at gmail.com
Mon Aug 9 07:31:27 PDT 2021 

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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>
>
>
>
> --
>
> Alexander Kulesza
>
> Team leader
>
> Modeling & simulation / Biomodeling
>
> alexander.kulesza at novadiscovery.com
>
> +33 7 82 92 44 62
>
> *nova*
>
> DISCOVERY
>
> www.novadiscovery.com
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> *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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