[Vp-reproduce-subgroup] [Vp-integration-subgroup] White paper revision
James A Glazier
jaglazier at gmail.com
Mon Aug 16 09:04:00 PDT 2021
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://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
>> m: 402-547-8904 <callto:402-547-8904>| o: 402-472-3530
>> <callto:402-472-3530>
>> www.helikarlab.org
>> <http://helikarlab.org/>|www.thecellcollective.org
>> <https://cellcollective.org/>
>> twitter: @helikarlab
>> <http://twitter.com/helikarlab>, at biocollective
>> <http://twitter.com/biocollective>
>> ***The University of Nebraska E-Mail Confidentiality
>> Disclaimer***
>> The information in this e-mail may be privileged and
>> confidential, intended only for the use of the
>> addressee(s) above.
>> Any unauthorized use or disclosure of this information is
>> prohibited. If you have received this email by mistake,
>> please delete and immediately contact the 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 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
>>>> https://eric-forgoston.github.io/
>>>> <https://urldefense.com/v3/__https:/eric-forgoston.github.io/__;!!K6Z8K8YTIA!VdlFMCuGyTWxTFwAHTufvXzSxbtUQ9ckyDlofvqR1sm1Q-6-HD2vdZtc_2WF1l-OpF0$>
>>>>
>>>>
>>>>
>>>> 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$>
>>>>
>>>>
>>>>
>>>> On
>>>> Mon,
>>>> May
>>>> 24,
>>>> 2021
>>>> at
>>>> 6:55
>>>> AM
>>>> William
>>>> Waites
>>>> <wwaites at ieee.org
>>>> <mailto:wwaites at ieee.org>>
>>>> wrote:
>>>>
>>>> > Otherwise, all I saw was …
>>>>
>>>> There
>>>> was
>>>> editing
>>>> of
>>>> the
>>>> section
>>>> on
>>>> stochasticity
>>>> by
>>>> Eric
>>>> with
>>>> some
>>>> input
>>>> from
>>>> myself.
>>>>
>>>> _______________________________________________
>>>> Vp-reproduce-subgroup
>>>> mailing
>>>> list
>>>> Vp-reproduce-subgroup at lists.simtk.org
>>>> <mailto:Vp-reproduce-subgroup at lists.simtk.org>
>>>> https://lists.simtk.org/mailman/listinfo/vp-reproduce-subgroup
>>>> <https://urldefense.com/v3/__https:/lists.simtk.org/mailman/listinfo/vp-reproduce-subgroup__;!!K6Z8K8YTIA!VdlFMCuGyTWxTFwAHTufvXzSxbtUQ9ckyDlofvqR1sm1Q-6-HD2vdZtc_2WFyiepMXg$>
>>>>
>>>> _______________________________________________
>>>> Vp-reproduce-subgroup
>>>> mailing
>>>> list
>>>> Vp-reproduce-subgroup at lists.simtk.org
>>>> <mailto:Vp-reproduce-subgroup at lists.simtk.org>
>>>> https://lists.simtk.org/mailman/listinfo/vp-reproduce-subgroup
>>>> <https://urldefense.com/v3/__https:/lists.simtk.org/mailman/listinfo/vp-reproduce-subgroup__;!!K6Z8K8YTIA!VdlFMCuGyTWxTFwAHTufvXzSxbtUQ9ckyDlofvqR1sm1Q-6-HD2vdZtc_2WFyiepMXg$>
>>>>
>>>>
>>>>
>>>> --
>>>>
>>>> Alexander
>>>> Kulesza
>>>>
>>>> Team leader
>>>>
>>>> Modeling
>>>> &
>>>> simulation /
>>>> Biomodeling
>>>>
>>>> alexander.kulesza at novadiscovery.com
>>>> <mailto:alexander.kulesza at novadiscovery.com>
>>>>
>>>> +33 7
>>>> 82 92 44 62
>>>>
>>>> *nova*
>>>>
>>>> DISCOVERY
>>>>
>>>> www.novadiscovery.com
>>>> <https://urldefense.com/v3/__http:/www.novadiscovery.com/__;!!K6Z8K8YTIA!VdlFMCuGyTWxTFwAHTufvXzSxbtUQ9ckyDlofvqR1sm1Q-6-HD2vdZtc_2WF5R8SDjQ$>
>>>>
>>>> 1 Place
>>>> Verrazzano,
>>>> 69009 Lyon
>>>> +33 9
>>>> 72 53 13 01
>>>>
>>>>
>>>> /This
>>>> message
>>>> is
>>>> intended
>>>> only
>>>> for the
>>>> personal
>>>> and
>>>> confidential
>>>> use of
>>>> the
>>>> designated
>>>> recipient(s)
>>>> named
>>>> above.
>>>> If you
>>>> are not
>>>> the
>>>> intended
>>>> recipient
>>>> of this
>>>> message
>>>> you are
>>>> hereby
>>>> notified
>>>> that
>>>> any
>>>> review,
>>>> dissemination,
>>>> distribution
>>>> or
>>>> copying
>>>> of this
>>>> message
>>>> is
>>>> strictly
>>>> prohibited.
>>>> Email
>>>> transmission
>>>> cannot
>>>> be
>>>> guaranteed
>>>> to be
>>>> secure
>>>> or
>>>> error-free.
>>>> Therefore,
>>>> we do
>>>> not
>>>> represent
>>>> that
>>>> this
>>>> information
>>>> is
>>>> complete
>>>> or
>>>> accurate
>>>> and it
>>>> should
>>>> not be
>>>> relied
>>>> upon as
>>>> such.
>>>> All
>>>> information
>>>> is
>>>> subject
>>>> to
>>>> change
>>>> without
>>>> notice./
>>>>
>>>> _______________________________________________
>>>> Vp-integration-subgroup
>>>> mailing list
>>>> Vp-integration-subgroup at lists.simtk.org
>>>> <mailto:Vp-integration-subgroup at lists.simtk.org>
>>>> https://lists.simtk.org/mailman/listinfo/vp-integration-subgroup
>>>> <https://urldefense.com/v3/__https:/lists.simtk.org/mailman/listinfo/vp-integration-subgroup__;!!K6Z8K8YTIA!VdlFMCuGyTWxTFwAHTufvXzSxbtUQ9ckyDlofvqR1sm1Q-6-HD2vdZtc_2WFn4YtY2g$>
>>>>
>>>> _______________________________________________
>>>> Vp-reproduce-subgroup
>>>> mailing list
>>>> Vp-reproduce-subgroup at lists.simtk.org
>>>> <mailto:Vp-reproduce-subgroup at lists.simtk.org>
>>>> https://lists.simtk.org/mailman/listinfo/vp-reproduce-subgroup
>>>> <https://urldefense.com/v3/__https:/lists.simtk.org/mailman/listinfo/vp-reproduce-subgroup__;!!K6Z8K8YTIA!VdlFMCuGyTWxTFwAHTufvXzSxbtUQ9ckyDlofvqR1sm1Q-6-HD2vdZtc_2WFyiepMXg$>
>>>>
>>>> _______________________________________________
>>>> Vp-integration-subgroup
>>>> mailing list
>>>> Vp-integration-subgroup at lists.simtk.org
>>>> <mailto:Vp-integration-subgroup at lists.simtk.org>
>>>> https://lists.simtk.org/mailman/listinfo/vp-integration-subgroup
>>>> <https://urldefense.com/v3/__https:/lists.simtk.org/mailman/listinfo/vp-integration-subgroup__;!!K6Z8K8YTIA!VdlFMCuGyTWxTFwAHTufvXzSxbtUQ9ckyDlofvqR1sm1Q-6-HD2vdZtc_2WFn4YtY2g$>
>>>>
>>>>
>>>>
>>>> --
>>>>
>>>> Alexander Kulesza
>>>>
>>>> Team leader
>>>>
>>>> Modeling & simulation /
>>>> Biomodeling
>>>>
>>>> alexander.kulesza at novadiscovery.com
>>>> <mailto:alexander.kulesza at novadiscovery.com>
>>>>
>>>> +33 7 82 92 44 62
>>>>
>>>> *nova*
>>>>
>>>> DISCOVERY
>>>>
>>>> www.novadiscovery.com
>>>> <https://urldefense.com/v3/__http:/www.novadiscovery.com/__;!!K6Z8K8YTIA!VdlFMCuGyTWxTFwAHTufvXzSxbtUQ9ckyDlofvqR1sm1Q-6-HD2vdZtc_2WF5R8SDjQ$>
>>>>
>>>> 1 Place Verrazzano, 69009 Lyon
>>>> +33 9 72 53 13 01
>>>>
>>>>
>>>> /This message is intended
>>>> only for the personal and
>>>> confidential use of the
>>>> designated recipient(s)
>>>> named above. If you are not
>>>> the intended recipient of
>>>> this message you are hereby
>>>> notified that any review,
>>>> dissemination, distribution
>>>> or copying of this message
>>>> is strictly prohibited.
>>>> Email transmission cannot
>>>> be guaranteed to be secure
>>>> or error-free. Therefore,
>>>> we do not represent that
>>>> this information is
>>>> complete or accurate and it
>>>> should not be relied upon
>>>> as such. All information is
>>>> subject to change without
>>>> notice./
>>>>
>>>> _______________________________________________
>>>> Vp-integration-subgroup mailing list
>>>> Vp-integration-subgroup at lists.simtk.org
>>>> <mailto:Vp-integration-subgroup at lists.simtk.org>
>>>> https://lists.simtk.org/mailman/listinfo/vp-integration-subgroup
>>>> <https://urldefense.com/v3/__https://lists.simtk.org/mailman/listinfo/vp-integration-subgroup__;!!PvXuogZ4sRB2p-tU!RpcLpR1RAgDlcdjrW-GQkhhfcfr8Fu1ojChx271t6XEjc3XFfFqLOojpDX4XS_Qo$>
>>>>
>>>>
>>>>
>>>> --
>>>>
>>>> -- ------------------
>>>>
>>>> Yaling Liu, Professor
>>>>
>>>> Department of Mechanical Engineering and Mechanics
>>>>
>>>> Department of Bioengineering
>>>>
>>>> Lehigh University
>>>>
>>>> www.lehigh.edu/~yal310
>>>> <https://urldefense.com/v3/__http://www.lehigh.edu/*yal310__;fg!!PvXuogZ4sRB2p-tU!RpcLpR1RAgDlcdjrW-GQkhhfcfr8Fu1ojChx271t6XEjc3XFfFqLOojpDQcZr6uP$>
>>>>
>>>> _______________________________________________
>>>> Vp-reproduce-subgroup mailing list
>>>> Vp-reproduce-subgroup at lists.simtk.org
>>>> <mailto:Vp-reproduce-subgroup at lists.simtk.org>
>>>> https://lists.simtk.org/mailman/listinfo/vp-reproduce-subgroup
>>>> <https://urldefense.com/v3/__https://lists.simtk.org/mailman/listinfo/vp-reproduce-subgroup__;!!PvXuogZ4sRB2p-tU!RpcLpR1RAgDlcdjrW-GQkhhfcfr8Fu1ojChx271t6XEjc3XFfFqLOojpDdCf8WCB$>
>>>>
>>>> _______________________________________________
>>>> Vp-reproduce-subgroup mailing list
>>>> Vp-reproduce-subgroup at lists.simtk.org
>>>> <mailto:Vp-reproduce-subgroup at lists.simtk.org>
>>>> https://lists.simtk.org/mailman/listinfo/vp-reproduce-subgroup
>>>> <https://urldefense.com/v3/__https://lists.simtk.org/mailman/listinfo/vp-reproduce-subgroup__;!!PvXuogZ4sRB2p-tU!RpcLpR1RAgDlcdjrW-GQkhhfcfr8Fu1ojChx271t6XEjc3XFfFqLOojpDdCf8WCB$>
>>>>
>>>
>>> _______________________________________________
>>> Vp-integration-subgroup mailing list
>>> Vp-integration-subgroup at lists.simtk.org <mailto:Vp-integration-subgroup at lists.simtk.org>
>>> https://urldefense.com/v3/__https://lists.simtk.org/mailman/listinfo/vp-integration-subgroup__;!!PvXuogZ4sRB2p-tU!RpcLpR1RAgDlcdjrW-GQkhhfcfr8Fu1ojChx271t6XEjc3XFfFqLOojpDX4XS_Qo$ <https://urldefense.com/v3/__https://lists.simtk.org/mailman/listinfo/vp-integration-subgroup__;!!PvXuogZ4sRB2p-tU!RpcLpR1RAgDlcdjrW-GQkhhfcfr8Fu1ojChx271t6XEjc3XFfFqLOojpDX4XS_Qo$>
>>
>> _______________________________________________
>> Vp-integration-subgroup mailing list
>> Vp-integration-subgroup at lists.simtk.org
>> <mailto:Vp-integration-subgroup at lists.simtk.org>
>> https://lists.simtk.org/mailman/listinfo/vp-integration-subgroup
>> <https://lists.simtk.org/mailman/listinfo/vp-integration-subgroup>
>
> _______________________________________________
> Vp-integration-subgroup mailing list
> Vp-integration-subgroup at lists.simtk.org
> <mailto:Vp-integration-subgroup at lists.simtk.org>
> https://lists.simtk.org/mailman/listinfo/vp-integration-subgroup
> <https://lists.simtk.org/mailman/listinfo/vp-integration-subgroup>
>
> _______________________________________________
> Vp-integration-subgroup mailing list
> Vp-integration-subgroup at lists.simtk.org
> <mailto:Vp-integration-subgroup at lists.simtk.org>
> https://lists.simtk.org/mailman/listinfo/vp-integration-subgroup
> <https://lists.simtk.org/mailman/listinfo/vp-integration-subgroup>
>
>
> _______________________________________________
> Vp-reproduce-subgroup mailing list
> Vp-reproduce-subgroup at lists.simtk.org
> https://lists.simtk.org/mailman/listinfo/vp-reproduce-subgroup
--
James A. Glazier, PhD
Professor of Intelligent Systems Engineering, Adjunct Professor of Physics
Director, Biocomplexity Institute
Indiana University, Bloomington
(812) 391-2159 (cell)
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.simtk.org/pipermail/vp-reproduce-subgroup/attachments/20210816/44dd18d5/attachment-0001.html>
More information about the Vp-reproduce-subgroup
mailing list