[Vp-integration-subgroup] [Vp-reproduce-subgroup] White paper revision
John Gennari
gennari at uw.edu
Mon Aug 9 08:06:01 PDT 2021
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
> <mailto: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
> <mailto: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
> <mailto:vp-reproduce-subgroup-bounces at lists.simtk.org>> on
> behalf of John Rice <john.rice at noboxes.org
> <mailto:john.rice at noboxes.org>>
> *Date: *Sunday, August 8, 2021 at 7:23 PM
> *To: *Yaling Liu <yal310 at lehigh.edu <mailto:yal310 at lehigh.edu>>
> *Cc: *vp-reproduce-subgroup at lists.simtk.org
> <mailto:vp-reproduce-subgroup at lists.simtk.org>
> <vp-reproduce-subgroup at lists.simtk.org
> <mailto:vp-reproduce-subgroup at lists.simtk.org>>,
> vp-integration-subgroup at lists.simtk.org
> <mailto:vp-integration-subgroup at lists.simtk.org>
> <vp-integration-subgroup at lists.simtk.org
> <mailto:vp-integration-subgroup at lists.simtk.org>>, Jonathan
> Karr <jonrkarr at gmail.com <mailto:jonrkarr at gmail.com>>, John
> Gennari <gennari at uw.edu <mailto:gennari at uw.edu>>, Faeder,
> James R <faeder at pitt.edu <mailto:faeder at pitt.edu>>, Winston
> Garira <Winston.Garira at univen.ac.za
> <mailto: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
> <mailto: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 <mailto: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 <mailto: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 <mailto:h.dobrovolny at tcu.edu>
> *******************************************************
>
> ------------------------------------------------------------------------
>
> *From:*Vp-reproduce-subgroup
> <vp-reproduce-subgroup-bounces at lists.simtk.org
> <mailto:vp-reproduce-subgroup-bounces at lists.simtk.org>>
> on behalf of Jacob Barhak <jacob.barhak at gmail.com
> <mailto:jacob.barhak at gmail.com>>
> *Sent:* August 7, 2021 11:18 AM
> *To:* Torres, Marcella
> *Cc:* vp-reproduce-subgroup at lists.simtk.org
> <mailto:vp-reproduce-subgroup at lists.simtk.org>;
> vp-integration-subgroup at lists.simtk.org
> <mailto: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
> <mailto: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
> <mailto: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
> <mailto:vp-reproduce-subgroup-bounces at lists.simtk.org>>
> on behalf of Jacob Barhak
> <jacob.barhak at gmail.com
> <mailto:jacob.barhak at gmail.com>>
> *Date: *Monday, August 2, 2021 at 11:45 AM
> *To: *Alexander Kulesza
> <alexander.kulesza at novadiscovery.com
> <mailto:alexander.kulesza at novadiscovery.com>>
> *Cc: *vp-reproduce-subgroup at lists.simtk.org
> <mailto:vp-reproduce-subgroup at lists.simtk.org><vp-reproduce-subgroup at lists.simtk.org
> <mailto:vp-reproduce-subgroup at lists.simtk.org>>,
> vp-integration-subgroup at lists.simtk.org
> <mailto:vp-integration-subgroup at lists.simtk.org><vp-integration-subgroup at lists.simtk.org
> <mailto:vp-integration-subgroup at lists.simtk.org>>,
> Jonathan Karr <jonrkarr at gmail.com
> <mailto:jonrkarr at gmail.com>>, John Gennari
> <gennari at uw.edu <mailto:gennari at uw.edu>>,
> Faeder, James R <faeder at pitt.edu
> <mailto:faeder at pitt.edu>>, Winston Garira
> <Winston.Garira at univen.ac.za
> <mailto: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
> <mailto: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
> <mailto: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
> <mailto: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
> <mailto: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
> <mailto: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
> <mailto: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
> <mailto: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
> <mailto: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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> <mailto:alexander.kulesza at novadiscovery.com>
>
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>
> --
>
> Alexander Kulesza
>
> Team leader
>
> Modeling & simulation / Biomodeling
>
> alexander.kulesza at novadiscovery.com
> <mailto:alexander.kulesza at novadiscovery.com>
>
> +33 7 82 92 44 62
>
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> --
>
> -- ------------------
>
> Yaling Liu, Professor
>
> Department of Mechanical Engineering and Mechanics
>
> Department of Bioengineering
>
> Lehigh University
>
> www.lehigh.edu/~yal310 <http://www.lehigh.edu/~yal310>
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