[Vp-integration-subgroup] [Vp-reproduce-subgroup] White paper revision
Tomas Helikar
thelikar2 at unl.edu
Tue Aug 10 00:10:06 PDT 2021
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
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<callto:402-472-3530>
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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
>> <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$>
>>
>> On Mon, May
>> 24, 2021 at
>> 6:55 AM
>> William
>> Waites
>> <wwaites at ieee.org
>> <mailto:wwaites at ieee.org>>
>> wrote:
>>
>> > Otherwise, all I saw was …
>>
>> There was
>> editing
>> of the
>> section
>> on
>> stochasticity
>> by Eric
>> with some
>> input
>> from myself.
>>
>> _______________________________________________
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>>
>>
>> --
>>
>> Alexander Kulesza
>>
>> Team leader
>>
>> Modeling &
>> simulation / Biomodeling
>>
>> alexander.kulesza at novadiscovery.com
>> <mailto:alexander.kulesza at novadiscovery.com>
>>
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>>
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>> --
>>
>> Alexander Kulesza
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>> Team leader
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>> --
>>
>> -- ------------------
>>
>> Yaling Liu, Professor
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>> Department of Mechanical Engineering and Mechanics
>>
>> Department of Bioengineering
>>
>> Lehigh University
>>
>> www.lehigh.edu/~yal310
>> <https://urldefense.com/v3/__http://www.lehigh.edu/*yal310__;fg!!PvXuogZ4sRB2p-tU!RpcLpR1RAgDlcdjrW-GQkhhfcfr8Fu1ojChx271t6XEjc3XFfFqLOojpDQcZr6uP$>
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