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

Wed Jul 14 14:46:59 PDT 2021

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.
>>>>>
>>>>> _______________________________________________
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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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