[Vp-integration-subgroup] [Vp-reproduce-subgroup] White paper revision
Tomas Helikar
thelikar2 at unl.edu
Tue Aug 17 05:20:08 PDT 2021
Hi Jacob,
I think the point the group is making is that there was feedback on the
manuscript from the previous journal, which required substantially
revising the manuscript; that's what the group has been trying to do
(though the effort has slowed down a bit).
The previous journal editor raised some valid concerns about the
manuscript state, and many members of the group agreed that a revision
is indeed needed before moving to the next venue. Submitting the same
version of the manuscript to another journal will, I'm afraid, result in
the same outcome of rejection. If the rejection in the suggested journal
is hard (i.e., no invitation to resubmit a revised version), then we
lose a venue for possible publication of the manuscript.
Best,
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>
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On 8/17/21 2:13 PM, Jacob Barhak wrote:
> Non-NU Email
> ------------------------------------------------------------------------
> 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
> <https://urldefense.com/v3/__https://docs.google.com/document/d/1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM/edit?usp=sharing__;!!PvXuogZ4sRB2p-tU!XQgHtF8amUyDkO2BuwhFFjU3o8r5NAnbMvGk-yuQH46H9g16qJU5-M0UBMdg_AMv$>
>
>
> We actually have 5 other versions and may eventually get more versions
> after review and we can mention this. Yet to move the process forward
> we need to get feedback from the publishing venue.
>
> Marcella pointed out a new venue and so far there was only support,
> so I hope she can continue the process and ask for feedback on the
> version we agreed upon to submit before.
>
> The sooner the better.
>
>
> Jacob
>
>
>
> On Tue, Aug 17, 2021, 02:22 James Osborne <jmosborne at unimelb.edu.au
> <mailto:jmosborne at unimelb.edu.au>> wrote:
>
> Just to clarify the versions were talking about...
>
> Here is the original submitted version that was rejected by the
> editor without review.
> https://docs.google.com/document/d/1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM/edit
> <https://urldefense.com/v3/__https://docs.google.com/document/d/1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM/edit__;!!PvXuogZ4sRB2p-tU!XQgHtF8amUyDkO2BuwhFFjU3o8r5NAnbMvGk-yuQH46H9g16qJU5-M0UBPvBUk-K$>
>
> Here's the version we've been working on
> https://docs.google.com/document/d/1VvyP3YZQdQYjj8DFKOpQ4pn_0pdDGgiT/edit?amp%3Bpli=1
> <https://urldefense.com/v3/__https://docs.google.com/document/d/1VvyP3YZQdQYjj8DFKOpQ4pn_0pdDGgiT/edit?amp*3Bpli=1__;JQ!!PvXuogZ4sRB2p-tU!XQgHtF8amUyDkO2BuwhFFjU3o8r5NAnbMvGk-yuQH46H9g16qJU5-M0UBMkV18u-$>
>
> 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
>> <https://urldefense.com/v3/__https://docs.google.com/document/d/1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM/edit?usp=sharing__;!!PvXuogZ4sRB2p-tU!XQgHtF8amUyDkO2BuwhFFjU3o8r5NAnbMvGk-yuQH46H9g16qJU5-M0UBMdg_AMv$>
>>
>> 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
>>> m: 402-547-8904 <callto:402-547-8904>| o:
>>> 402-472-3530 <callto:402-472-3530>
>>> www.helikarlab.org
>>> <https://urldefense.com/v3/__http://helikarlab.org/__;!!PvXuogZ4sRB2p-tU!XQgHtF8amUyDkO2BuwhFFjU3o8r5NAnbMvGk-yuQH46H9g16qJU5-M0UBNn_4S2A$>|www.thecellcollective.org
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>>> ***The University of Nebraska E-Mail
>>> Confidentiality Disclaimer***
>>> The information in this e-mail may be
>>> privileged and confidential, intended only
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>>> 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
>>>>> <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
>>>>>
>>>>> *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
>>>>> <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>
>>>>> *******************************************************
>>>>>
>>>>>
>>>>> ------------------------------------------------------------------------
>>>>>
>>>>> *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
>>>>>
>>>>>
>>>>> *[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
>>>>> <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 forh
>>>>>
>
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