[Vp-reproduce-subgroup] [Vp-integration-subgroup] White paper revision
Yaling Liu
yal310 at lehigh.edu
Tue Oct 12 06:07:15 PDT 2021
I can cover part of the publication cost too.
We should split rather than let Jacob cover the cost.
Thanks.
Yaling
On Tue, Oct 12, 2021 at 2:00 AM Alexander Kulesza <
alexander.kulesza at novadiscovery.com> wrote:
> Hello all.
> I might find funding for a part of the publication costs as well when
> splitted.
>
> Best
> Alex
>
> Jacob Barhak <jacob.barhak at gmail.com> schrieb am Di., 12. Okt. 2021,
> 06:54:
>
>> Thanks Marcella,
>>
>> Below you will find my business mail address. It recently changed. .
>>
>> I assume payment is due upon publication and not upon review. If the
>> paper gets published fast, I will be happy to pay the entire $1900 fee
>> myself to accelerate the process - or we can discuss splitting it within
>> the group upon acceptance - this can be discussed later especially if
>> someone has funds secured for such publications. For now list me as the
>> payer so we can proceed.
>>
>> To be fully transparent I am adding the rest of the group to this
>> correspondence since all contributors should be aware.
>>
>> I look forward to the continuation of the process.
>>
>> Jacob
>>
>> --
>> Jacob Barhak Ph.D.
>> Sole Proprietor, Software Developer, and Computational Disease Modeler
>>
>> Jacob Barhak Analytics
>> 701 Brazos St
>> Suite 548
>> Austin TX, 78701
>>
>> Email: jacob.barhak at gmail.com
>>
>> https://sites.google.com/view/jacob-barhak/home
>>
>>
>> On Mon, Oct 11, 2021 at 3:05 PM Torres, Marcella <mtorres at richmond.edu>
>> wrote:
>>
>>> Hi Jacob,
>>>
>>> I appreciate the offer - currently I can't see an easy way to transition
>>> submissions, but I have listed you as corresponding author.
>>>
>>> The only thing that remains is that I need your full address to select
>>> you as payee, in the event the article is accepted. Once I complete that
>>> step, the paper will be submitted.
>>>
>>> Marcella
>>>
>>> Marcella Torres, Ph.D.
>>> Director of Mathematical Studies
>>> University of Richmond
>>> Jepson Hall Room 212
>>> 221 Richmond Way
>>> Richmond, VA 23173
>>> (804) 289-8081
>>> Pronouns: she/her
>>>
>>> ------------------------------
>>> *From:* Jacob Barhak <jacob.barhak at gmail.com>
>>> *Sent:* Monday, October 11, 2021 12:40 AM
>>> *To:* Torres, Marcella <mtorres at richmond.edu>
>>> *Cc:* James Osborne <jmosborne at unimelb.edu.au>;
>>> vp-reproduce-subgroup at lists.simtk.org <
>>> vp-reproduce-subgroup at lists.simtk.org>;
>>> vp-integration-subgroup at lists.simtk.org <
>>> vp-integration-subgroup at lists.simtk.org>; Jonathan Karr <
>>> jonrkarr at gmail.com>; John Gennari <gennari at uw.edu>; Winston Garira <
>>> Winston.Garira at univen.ac.za>; John Rice <john.rice at noboxes.org>
>>> *Subject:* Re: [Vp-reproduce-subgroup] [Vp-integration-subgroup] White
>>> paper revision
>>>
>>> *External Email:* Use caution in opening links, attachments, and buying
>>> gift cards.
>>>
>>> Hi Marcella,
>>>
>>> Your response is helpful.
>>>
>>> I can handle fees and paperwork if this accelerates the process.
>>>
>>>
>>> You can certainly list me as corresponding author, or if you prefer,
>>> you can delegate the submission task to me if you think it is better.
>>>
>>>
>>> If you prefer to continue submission, and need information for authors
>>> without process affiliation:
>>>
>>> For me, you can write write, independent, Austin, TX
>>> For John Rice you can write independent, Virginia Beach, VA.
>>>
>>> If you want me to act, just let me know your preference quickly so the
>>> paper gets submitted quickly.
>>>
>>> Jacob
>>>
>>>
>>>
>>>
>>> On Sun, Oct 10, 2021, 10:31 Torres, Marcella <mtorres at richmond.edu>
>>> wrote:
>>>
>>> Hi Jacob and group members,
>>>
>>> Sorry for the delay. I was waiting for a response from Frontiers, but it
>>> turns out that once I log into my account, I can continue the submission
>>> process.
>>> I am assuming you, Jacob, are willing to be a corresponding author? I
>>> can list myself as well, but I'm expecting to give birth sometime in the
>>> next 2-3 weeks so may be unavailable for a short period.
>>>
>>> As I'm filling out the author information, I will need title, city, and
>>> state information for those without an institutional affiliation: I think
>>> this includes Jacob and John Rice.
>>>
>>> There is also the matter of fees; I think this was discussed, but I
>>> don't remember who had funding:
>>>
>>>
>>>
>>>
>>> Marcella Torres, Ph.D.
>>> Director of Mathematical Studies
>>> University of Richmond
>>> Jepson Hall Room 212
>>> 221 Richmond Way
>>> Richmond, VA 23173
>>> (804) 289-8081
>>> Pronouns: she/her
>>>
>>> ------------------------------
>>> *From:* Jacob Barhak <jacob.barhak at gmail.com>
>>> *Sent:* Wednesday, September 29, 2021 3:30 AM
>>> *To:* Torres, Marcella <mtorres at richmond.edu>
>>> *Cc:* James Osborne <jmosborne at unimelb.edu.au>;
>>> vp-reproduce-subgroup at lists.simtk.org <
>>> vp-reproduce-subgroup at lists.simtk.org>;
>>> vp-integration-subgroup at lists.simtk.org <
>>> vp-integration-subgroup at lists.simtk.org>; Jonathan Karr <
>>> jonrkarr at gmail.com>; John Gennari <gennari at uw.edu>; Winston Garira <
>>> 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 Marcella,
>>>
>>> Do you have an update on the status of the manuscript?
>>>
>>> I loom forward to learn of the progress made.
>>>
>>> Jacob
>>>
>>> On Thu, Aug 19, 2021, 08:50 Torres, Marcella <mtorres at richmond.edu>
>>> wrote:
>>>
>>> At this point, I have submitted only the *title* of the proposed
>>> manuscript (that can be legally submitted) - that is all that is required -
>>> and am waiting to hear back about next steps. I will keep the group
>>> updated.
>>>
>>> Marcella
>>>
>>> Marcella Torres, Ph.D.
>>> Director of Mathematical Studies
>>> University of Richmond
>>> Jepson Hall Room 212
>>> 221 Richmond Way
>>> Richmond, VA 23173
>>> (804) 289-8081
>>> Pronouns: she/her
>>>
>>> ------------------------------
>>> *From:* Vp-reproduce-subgroup <
>>> vp-reproduce-subgroup-bounces at lists.simtk.org> on behalf of Jacob
>>> Barhak <jacob.barhak at gmail.com>
>>> *Sent:* Tuesday, August 17, 2021 8:13 AM
>>> *To:* James Osborne <jmosborne at unimelb.edu.au>
>>> *Cc:* vp-reproduce-subgroup at lists.simtk.org <
>>> vp-reproduce-subgroup at lists.simtk.org>;
>>> vp-integration-subgroup at lists.simtk.org <
>>> vp-integration-subgroup at lists.simtk.org>; Jonathan Karr <
>>> jonrkarr at gmail.com>; John Gennari <gennari at uw.edu>; Winston Garira <
>>> 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.
>>>
>>> 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
>>>
>>>
>>> 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>
>>> 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
>>>
>>> Here's the version we've been working on
>>>
>>> https://docs.google.com/document/d/1VvyP3YZQdQYjj8DFKOpQ4pn_0pdDGgiT/edit?amp%3Bpli=1
>>>
>>> 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>
>>> 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> 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
>>>
>>> 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> 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>
>>> 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>
>>> 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> 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>, @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>
>>> 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>
>>> 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> on behalf of John Rice <
>>> john.rice at noboxes.org>
>>> *Date: *Sunday, August 8, 2021 at 7:23 PM
>>> *To: *Yaling Liu <yal310 at lehigh.edu>
>>> *Cc: *vp-reproduce-subgroup at lists.simtk.org <
>>> vp-reproduce-subgroup at lists.simtk.org>,
>>> vp-integration-subgroup at lists.simtk.org <
>>> vp-integration-subgroup at lists.simtk.org>, Jonathan Karr <
>>> jonrkarr at gmail.com>, John Gennari <gennari at uw.edu>, Faeder, James R <
>>> faeder at pitt.edu>, Winston Garira <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> 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>
>>> 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>
>>> 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
>>> *******************************************************
>>>
>>> ------------------------------
>>>
>>> *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
>>>
>>>
>>> *[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> 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>
>>> 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> on behalf of Jacob
>>> Barhak <jacob.barhak at gmail.com>
>>> *Date: *Monday, August 2, 2021 at 11:45 AM
>>> *To: *Alexander Kulesza <alexander.kulesza at novadiscovery.com>
>>> *Cc: *vp-reproduce-subgroup at lists.simtk.org <
>>> vp-reproduce-subgroup at lists.simtk.org>,
>>> vp-integration-subgroup at lists.simtk.org<
>>> vp-integration-subgroup at lists.simtk.org>, Jonathan Karr <
>>> jonrkarr at gmail.com>, John Gennari <gennari at uw.edu>, Faeder, James R <
>>> faeder at pitt.edu>, Winston Garira <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> 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$>
>>> which intends to get agreement or disgreement of the group for the
>>> different optuions that exist.
>>>
>>>
>>> Please let me know what you think.
>>>
>>> Alexander
>>>
>>>
>>>
>>>
>>> On Thu, 29 Jul 2021 at 16:54, Jacob Barhak <jacob.barhak at gmail.com>
>>> wrote:
>>>
>>> Greetings contributors,
>>>
>>>
>>> Two of the contributors approach me about this message privately.
>>> However, there were many more who participated and no one responded
>>> publicly in 2 weeks.
>>>
>>>
>>> Do you not want this paper be circulated?
>>>
>>>
>>> I am asking those questions publicly since this deserves a public
>>> discussion.
>>>
>>>
>>> Hopefully this reminder will stir up the group.
>>>
>>>
>>> Jacob
>>>
>>>
>>> On Wed, Jul 14, 2021 at 4:46 PM Jacob Barhak <jacob.barhak at gmail.com>
>>> wrote:
>>>
>>> Hi Gilberto,
>>>
>>>
>>> As you can see, there was no response to your email - in fact the paper
>>> writing stopped - I waited sufficient time to make sure this is the case to
>>> prove a point. If there is no one to tend to the editing, then there will
>>> not be any progress and the paper will lose focus -
>>> partially because people will pull it in many directions and resolution
>>> will take time no one is willing to provide to move it forward. And this is
>>> what happened here.
>>>
>>>
>>> I remind you that I wrote what needs to be done to make progress. See
>>> the 4 points in this archived email:
>>>
>>>
>>> https://lists.simtk.org/pipermail/vp-reproduce-subgroup/2021-May/000098.html
>>> <https://urldefense.com/v3/__https:/lists.simtk.org/pipermail/vp-reproduce-subgroup/2021-May/000098.html__;!!K6Z8K8YTIA!VdlFMCuGyTWxTFwAHTufvXzSxbtUQ9ckyDlofvqR1sm1Q-6-HD2vdZtc_2WFEHRSJVg$>
>>>
>>>
>>> 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
>>>
>>> _______________________________________________
>> Vp-integration-subgroup mailing list
>> Vp-integration-subgroup at lists.simtk.org
>> https://lists.simtk.org/mailman/listinfo/vp-integration-subgroup
>>
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--
-- ------------------
Yaling Liu, Professor
Department of Bioengineering, Director of Graduate Studies
Department of Mechanical Engineering and Mechanics
Lehigh University
www.lehigh.edu/~yal310
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