[Vp-integration-subgroup] [Vp-reproduce-subgroup] White paper revision
Jacob Barhak
jacob.barhak at gmail.com
Mon Aug 16 21:33:16 PDT 2021
Thanks James,
This will for sure not be the final version of the paper. We will have
revisions and already had discussions.
The attempt here is to get the ball rolling and to we need to start
somewhere, so the proper entry point is the last agreement.
If the editor will be positive, I believe we can reach a nice revised
version that everyone will be gappy with with augmented list of authors.
For now I just wanted to verify that Marcella is willing to do the initial
communications with the editor.
Hopefully its ok with her.
Jacob
On Mon, Aug 16, 2021, 11:04 James A Glazier <jaglazier at gmail.com> wrote:
> Dear Jacob:
>
> I see a lot of progress but the text is still fragmentary. I think you
> will have a hard time having it reviewed before you clean it up some more.
>
> Frontiers is a reasonable place for it, and it does give you the
> opportunity to do multiple rounds of review.
>
> JAG
> On 8/16/2021 11:59 AM, Jacob Barhak wrote:
>
> Hi Marcella,
>
> So far there were no objections and support in your suggested venue was
> provided by 9 out of the 17 original authors + support by many that joined
> later.
>
> I have seen no objection to the venue by anyone. - meaning that we can
> probably move on to the new venue and start the process.
>
> I suggest you move on and contact the editor and follow the proper process
> for the venue and ask for feedback.
>
> Please indicate that we are seeking review to guide further revisions that
> we have already begun, yet not completed, so there may be changes in title,
> authors, and text, yet the core paper has been approved by 17 authors and
> major arguments will most probably stay.
>
> The version we can currently legally submit is this one that we approved:
>
> https://docs.google.com/document/d/1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM/edit?usp=sharing
>
> I locked that version for changes until the review process is complete.
>
> For the many who wanted revisions - we will have them still - yet since we
> have not reached agreement on a revised version, it will have to wait until
> after review. is provided and we can incorporate reviewers comments in the
> revisions.
>
> Marcella, please let us know if you will handle submission and
> communications with the publication venue. - Frontiers in Systems Biology
>
> Regarding submission, I suggest starting with doing things that do not
> take effort - like communicating with the editor about this paper and
> declaring intention to see the response we get.
>
> While we wait for responses, we can continue discussion and give a last
> chance for objections to Frontiers in Systems Biology to arrive from the
> original 17 contributors. If any objection to the venue appears before we
> get a response, we will have to stop the process.
>
> Hopefully the large support in the new venue will persist.
>
> I suggest we start a new email thread regarding submission and that we all
> get updated on the process to keep things transparent.
>
> Jacob
>
>
>
>
>
>
>
> On Wed, Aug 11, 2021 at 1:08 AM Gilberto Gonzalez-Parra <
> gilberto.gonzalezparra at nmt.edu> wrote:
>
>> Hi all,
>>
>> I think the new version is better, even though it is not ready. The main
>> points are there, which include the importance of reproducibility and
>> integration in modeling biology systems.
>>
>> Probably, one or two co-authors need to take the lead to polish the
>> article and references. I suggest that these authors take some of the
>> top positions in the list of authors (in some places author position is
>> taken into account).
>>
>> Venue seems fine.
>>
>>
>> ***************************************************************************
>> Gilberto C. Gonzalez-Parra, Ph.D in Applied Mathematics.
>> Faculty of the Mathematics Department
>> New Mexico Tech, NM, USA.
>>
>> ****************************************************************************
>>
>>
>> On Tue, Aug 10, 2021 at 1:24 PM Rahuman Sheriff <sheriff at ebi.ac.uk>
>> wrote:
>>
>>> I also agree with the venue and the suggestion to tidy up the manuscript
>>> with a strict deadline.
>>> Sheriff
>>>
>>>
>>> On 10 Aug 2021, at 10:43, James Osborne <jmosborne at unimelb.edu.au>
>>> wrote:
>>>
>>> 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>
>>>> ***The University of Nebraska E-Mail Confidentiality Disclaimer***
>>>> The information in this e-mail may be privileged and confidential,
>>>> intended only for the use of the addressee(s) above.
>>>> Any unauthorized use or disclosure of this information is prohibited.
>>>> If you have received this email by mistake,
>>>> please delete and immediately contact the sender.
>>>> 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
>>>>>>
>>>>>>
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