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

Sat Aug 7 21:46:14 PDT 2021

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
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________________________________
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

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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
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
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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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