[Vp-integration-subgroup] [Vp-reproduce-subgroup] White paper revision
Jacob Barhak
jacob.barhak at gmail.com
Wed Sep 29 00:30:16 PDT 2021
Hi Marcella,
Do you have an update on the status of the manuscript?
I loom forward to learn of the progress made.
Jacob
On Thu, Aug 19, 2021, 08:50 Torres, Marcella <mtorres at richmond.edu> wrote:
> At this point, I have submitted only the *title* of the proposed
> manuscript (that can be legally submitted) - that is all that is required -
> and am waiting to hear back about next steps. I will keep the group
> updated.
>
> Marcella
>
> Marcella Torres, Ph.D.
> Director of Mathematical Studies
> University of Richmond
> Jepson Hall Room 212
> 221 Richmond Way
> Richmond, VA 23173
> (804) 289-8081
> Pronouns: she/her
>
> ------------------------------
> *From:* Vp-reproduce-subgroup <
> vp-reproduce-subgroup-bounces at lists.simtk.org> on behalf of Jacob Barhak <
> jacob.barhak at gmail.com>
> *Sent:* Tuesday, August 17, 2021 8:13 AM
> *To:* James Osborne <jmosborne at unimelb.edu.au>
> *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>; 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.
>
> Well James,
>
> Its a bit more complicated that what you describe its not just editing
> work.
>
> Any version we submit must be approved for submission by all those listed.
>
> We have not reached this point for any other version other than the one we
> submitted before. So there is much more work than just references and
> polishing.
>
> The only version we can legally submit is this one:
>
> https://docs.google.com/document/d/1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM/edit?usp=sharing
>
>
> We actually have 5 other versions and may eventually get more versions
> after review and we can mention this. Yet to move the process forward we
> need to get feedback from the publishing venue.
>
> Marcella pointed out a new venue and so far there was only support, so I
> hope she can continue the process and ask for feedback on the version we
> agreed upon to submit before.
>
> The sooner the better.
>
>
> Jacob
>
>
>
> On Tue, Aug 17, 2021, 02:22 James Osborne <jmosborne at unimelb.edu.au>
> wrote:
>
> Just to clarify the versions were talking about...
>
> Here is the original submitted version that was rejected by the editor
> without review.
>
> https://docs.google.com/document/d/1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM/edit
>
> Here's the version we've been working on
>
> https://docs.google.com/document/d/1VvyP3YZQdQYjj8DFKOpQ4pn_0pdDGgiT/edit?amp%3Bpli=1
>
> Even in this state, I think it stands a better chance than the previously
> submitted one as if you remove all the comments and highlighting it's a
> cleaner story. This was a big issue with the original version and I don't
> think it's appropriate to resubmit anywhere without looking at this.
> The issue is that it will take a concerted effort to polish this updated
> version. Even sorting the references is non trivial.
> I think the only way of this happening is for a "First Author" to step
> forward and take the lead. They push work on the changes and chase people
> as needed but in return they get first/senior/corresponding authorship as
> appropriate.
>
> James
>
>
>
>
> On Tue, Aug 17, 2021 at 2:33 PM Jacob Barhak <jacob.barhak at gmail.com>
> wrote:
>
> 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 forh
>
>
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