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

Sun Aug 8 16:08:47 PDT 2021

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$>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> On Mon, May 24, 2021 at 6:55 AM William Waites <wwaites at ieee.org>
>>>> wrote:
>>>>
>>>> > Otherwise, all I saw was …
>>>>
>>>> There was editing of the section on stochasticity by Eric with some
>>>> input from myself.
>>>>
>>>> _______________________________________________
>>>> Vp-reproduce-subgroup mailing list
>>>> Vp-reproduce-subgroup at lists.simtk.org
>>>> https://lists.simtk.org/mailman/listinfo/vp-reproduce-subgroup
>>>> <https://urldefense.com/v3/__https://lists.simtk.org/mailman/listinfo/vp-reproduce-subgroup__;!!K6Z8K8YTIA!VdlFMCuGyTWxTFwAHTufvXzSxbtUQ9ckyDlofvqR1sm1Q-6-HD2vdZtc_2WFyiepMXg$>
>>>>
>>>> _______________________________________________
>>>> Vp-reproduce-subgroup mailing list
>>>> Vp-reproduce-subgroup at lists.simtk.org
>>>> https://lists.simtk.org/mailman/listinfo/vp-reproduce-subgroup
>>>> <https://urldefense.com/v3/__https://lists.simtk.org/mailman/listinfo/vp-reproduce-subgroup__;!!K6Z8K8YTIA!VdlFMCuGyTWxTFwAHTufvXzSxbtUQ9ckyDlofvqR1sm1Q-6-HD2vdZtc_2WFyiepMXg$>
>>>>
>>>>
>>>>
>>>>
>>>> --
>>>>
>>>> Alexander Kulesza
>>>>
>>>> Team leader
>>>>
>>>> Modeling & simulation / Biomodeling
>>>>
>>>> alexander.kulesza at novadiscovery.com
>>>>
>>>> +33 7 82 92 44 62
>>>>
>>>> *nova*
>>>>
>>>> DISCOVERY
>>>>
>>>> www.novadiscovery.com
>>>> <https://urldefense.com/v3/__http://www.novadiscovery.com/__;!!K6Z8K8YTIA!VdlFMCuGyTWxTFwAHTufvXzSxbtUQ9ckyDlofvqR1sm1Q-6-HD2vdZtc_2WF5R8SDjQ$>
>>>>
>>>> 1 Place Verrazzano, 69009 Lyon
>>>> +33 9 72 53 13 01
>>>>
>>>>
>>>> *This message is intended only for the personal and confidential use of
>>>> the designated recipient(s) named above. If you are not the intended
>>>> recipient of this message you are hereby notified that any review,
>>>> dissemination, distribution or copying of this message is strictly
>>>> prohibited. Email transmission cannot be guaranteed to be secure or
>>>> error-free. Therefore, we do not represent that this information is
>>>> complete or accurate and it should not be relied upon as such. All
>>>> 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
>>>> <https://urldefense.com/v3/__https://lists.simtk.org/mailman/listinfo/vp-integration-subgroup__;!!K6Z8K8YTIA!VdlFMCuGyTWxTFwAHTufvXzSxbtUQ9ckyDlofvqR1sm1Q-6-HD2vdZtc_2WFn4YtY2g$>
>>>>
>>>> _______________________________________________
>>>> Vp-reproduce-subgroup mailing list
>>>> Vp-reproduce-subgroup at lists.simtk.org
>>>> https://lists.simtk.org/mailman/listinfo/vp-reproduce-subgroup
>>>> <https://urldefense.com/v3/__https://lists.simtk.org/mailman/listinfo/vp-reproduce-subgroup__;!!K6Z8K8YTIA!VdlFMCuGyTWxTFwAHTufvXzSxbtUQ9ckyDlofvqR1sm1Q-6-HD2vdZtc_2WFyiepMXg$>
>>>>
>>>> _______________________________________________
>>>> Vp-integration-subgroup mailing list
>>>> Vp-integration-subgroup at lists.simtk.org
>>>> https://lists.simtk.org/mailman/listinfo/vp-integration-subgroup
>>>> <https://urldefense.com/v3/__https://lists.simtk.org/mailman/listinfo/vp-integration-subgroup__;!!K6Z8K8YTIA!VdlFMCuGyTWxTFwAHTufvXzSxbtUQ9ckyDlofvqR1sm1Q-6-HD2vdZtc_2WFn4YtY2g$>
>>>>
>>>>
>>>>
>>>>
>>>> --
>>>>
>>>> Alexander Kulesza
>>>>
>>>> Team leader
>>>>
>>>> Modeling & simulation / Biomodeling
>>>>
>>>> alexander.kulesza at novadiscovery.com
>>>>
>>>> +33 7 82 92 44 62
>>>>
>>>> *nova*
>>>>
>>>> DISCOVERY
>>>>
>>>> www.novadiscovery.com
>>>> <https://urldefense.com/v3/__http://www.novadiscovery.com/__;!!K6Z8K8YTIA!VdlFMCuGyTWxTFwAHTufvXzSxbtUQ9ckyDlofvqR1sm1Q-6-HD2vdZtc_2WF5R8SDjQ$>
>>>>
>>>> 1 Place Verrazzano, 69009 Lyon
>>>> +33 9 72 53 13 01
>>>>
>>>>
>>>> *This message is intended only for the personal and confidential use of
>>>> the designated recipient(s) named above. If you are not the intended
>>>> recipient of this message you are hereby notified that any review,
>>>> dissemination, distribution or copying of this message is strictly
>>>> prohibited. Email transmission cannot be guaranteed to be secure or
>>>> error-free. Therefore, we do not represent that this information is
>>>> complete or accurate and it should not be relied upon as such. All
>>>> 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
>

-- 
-- ------------------
Yaling Liu, Professor
Department of Mechanical Engineering and Mechanics
Department of Bioengineering
Lehigh University
www.lehigh.edu/~yal310
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.simtk.org/pipermail/vp-integration-subgroup/attachments/20210808/e594f4bb/attachment-0001.html>