[Vp-reproduce-subgroup] [Vp-integration-subgroup] White paper revision
Torres, Marcella
mtorres at richmond.edu
Sun Oct 10 08:31:54 PDT 2021
Hi Jacob and group members,
Sorry for the delay. I was waiting for a response from Frontiers, but it turns out that once I log into my account, I can continue the submission process.
I am assuming you, Jacob, are willing to be a corresponding author? I can list myself as well, but I'm expecting to give birth sometime in the next 2-3 weeks so may be unavailable for a short period.
As I'm filling out the author information, I will need title, city, and state information for those without an institutional affiliation: I think this includes Jacob and John Rice.
There is also the matter of fees; I think this was discussed, but I don't remember who had funding:
[cid:4cf62db0-0275-4ab9-a45b-d67c8028d24f]
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: Jacob Barhak <jacob.barhak at gmail.com>
Sent: Wednesday, September 29, 2021 3:30 AM
To: Torres, Marcella <mtorres at richmond.edu>
Cc: James Osborne <jmosborne at unimelb.edu.au>; 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
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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<mailto: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<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: Tuesday, August 17, 2021 8:13 AM
To: James Osborne <jmosborne at unimelb.edu.au<mailto:jmosborne at unimelb.edu.au>>
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>>; 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
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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<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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
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On 8/9/21 5:06 PM, John Gennari wrote:
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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
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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>
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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
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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
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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 forh
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