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

Thu Jul 29 07:54:15 PDT 2021

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
>
> 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/
>>>
>>>
>>> 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/
>>>>>
>>>>>
>>>>> 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
>>>>>>
>>>>> _______________________________________________
>>>>> Vp-reproduce-subgroup mailing list
>>>>> Vp-reproduce-subgroup at lists.simtk.org
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>>>>>
>>>>
>>>>
>>>> --
>>>> Alexander Kulesza
>>>> Team leader
>>>> Modeling & simulation / Biomodeling
>>>> alexander.kulesza at novadiscovery.com
>>>> +33 7 82 92 44 62
>>>> nova
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>>>> www.novadiscovery.com
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>>>> +33 9 72 53 13 01
>>>>
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