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<p>Dear Jacob:</p>
<p>I approve. Please go ahead and submit. There is a huge amount of
effort represented in the manuscript. I expect that referees may
ask for some reworking and cleanup to improve coherence, but I am
happy with you to submit it. Veronika and I did a short review on
the role of modeling in viral therapies: Zarnitsyna, Veronika I.,
Juliano Ferrari Gianlupi, Amit Hagar, T. J. Sego, and James A.
Glazier. "Advancing therapies for viral infections using
mechanistic computational models of the dynamic interplay between
the virus and host immune response." Current Opinion in Virology
50 (2021): 103-109. which you might add on revision.</p>
<p>Thank you for your heroic efforts.</p>
<p>JAG<br>
</p>
<p><br>
</p>
<div class="moz-cite-prefix">On 11/7/2021 3:12 PM, Yaling Liu wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CAJsuQ_hynE90npWTaBZ+8iyiqVz6kGnCa9M1XLqY=QpcObXVuQ@mail.gmail.com">
<meta http-equiv="content-type" content="text/html; charset=UTF-8">
<div dir="ltr">
<div
style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">Dear
Jacob,</div>
<div
style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)"><br>
</div>
<div
style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">I
approve the paper for submission.</div>
<div
style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)"><br>
</div>
<div
style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">Thanks.</div>
<div
style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)"><br>
</div>
<div
style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">Yaling</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Sun, Nov 7, 2021 at 9:59 AM
Winston Garira <<a
href="mailto:Winston.Garira@univen.ac.za"
moz-do-not-send="true" class="moz-txt-link-freetext">Winston.Garira@univen.ac.za</a>>
wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px
0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div dir="ltr">
<div
style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">Dear
Jacob,</div>
<div
style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)"><br>
</div>
<div
style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">I
approve the paper for submission.</div>
<div
style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)"><br>
</div>
<div
style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">Winston<br>
</div>
<hr style="display:inline-block;width:98%">
<div id="gmail-m_-5943549780352006519divRplyFwdMsg"
dir="ltr"><font style="font-size:11pt" face="Calibri,
sans-serif" color="#000000"><b>From:</b> William Waites
<<a href="mailto:wwaites@ieee.org" target="_blank"
moz-do-not-send="true" class="moz-txt-link-freetext">wwaites@ieee.org</a>><br>
<b>Sent:</b> Sunday, 07 November 2021 12:34<br>
<b>To:</b> Jacob Barhak <<a
href="mailto:jacob.barhak@gmail.com" target="_blank"
moz-do-not-send="true" class="moz-txt-link-freetext">jacob.barhak@gmail.com</a>><br>
<b>Cc:</b> James Osborne <<a
href="mailto:jmosborne@unimelb.edu.au" target="_blank"
moz-do-not-send="true" class="moz-txt-link-freetext">jmosborne@unimelb.edu.au</a>>;
<a href="mailto:vp-reproduce-subgroup@lists.simtk.org"
target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">vp-reproduce-subgroup@lists.simtk.org</a>
<<a
href="mailto:vp-reproduce-subgroup@lists.simtk.org"
target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">vp-reproduce-subgroup@lists.simtk.org</a>>;
James A Glazier <<a href="mailto:jaglazier@gmail.com"
target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">jaglazier@gmail.com</a>>;
<a href="mailto:vp-integration-subgroup@lists.simtk.org"
target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">vp-integration-subgroup@lists.simtk.org</a>
<<a
href="mailto:vp-integration-subgroup@lists.simtk.org"
target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">vp-integration-subgroup@lists.simtk.org</a>>;
Jonathan Karr <<a href="mailto:jonrkarr@gmail.com"
target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">jonrkarr@gmail.com</a>>;
John Gennari <<a href="mailto:gennari@uw.edu"
target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">gennari@uw.edu</a>>;
Faeder, James R <<a href="mailto:faeder@pitt.edu"
target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">faeder@pitt.edu</a>>;
Winston Garira <<a
href="mailto:Winston.Garira@univen.ac.za"
target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">Winston.Garira@univen.ac.za</a>><br>
<b>Subject:</b> Re: [Vp-integration-subgroup]
[Vp-reproduce-subgroup] Shayn Peirce-Cottler via
Frontiers: Manuscript</font>
<div> </div>
</div>
<div><font size="2"><span style="font-size:11pt">
<div>Dear Jacob,<br>
<br>
I approve. This version is much better than the
earlier one, though it’s a little long. I still
prefer the tighter structure of the one that John
started.<br>
<br>
Another example of a model that combines within-host
immune dynamics and between-host transmission we’ve
just put out (this is together with Ruchira Datta
and Veronika Zarnitsyna among others so comes partly
out of the MSM innate and adaptive immune response
subgroup) is here: <a
href="https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Farxiv.org%2Fabs%2F2111.02510&data=04%7C01%7CWinston.Garira%40univen.ac.za%7C4afdd5cc058a498bc11008d9a1da2418%7Cf38ba9d8554c48a2ae4213b1e7f3c797%7C0%7C0%7C637718780727672293%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=iRm%2FUvVD%2Fv%2F4ZwpUVFUltZxa6rkbq4uVWOzNdBqdXDk%3D&reserved=0"
target="_blank" moz-do-not-send="true">
https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Farxiv.org%2Fabs%2F2111.02510&data=04%7C01%7CWinston.Garira%40univen.ac.za%7C4afdd5cc058a498bc11008d9a1da2418%7Cf38ba9d8554c48a2ae4213b1e7f3c797%7C0%7C0%7C637718780727672293%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=iRm%2FUvVD%2Fv%2F4ZwpUVFUltZxa6rkbq4uVWOzNdBqdXDk%3D&reserved=0</a>
It gets some interesting results where phenomena
that are emergent at the population level arise from
simple dynamics at the individual level. Feel free
to ignore this though because (a) it’s just a
pre-print and (b) this is now fairly late in the
game.<br>
<br>
Could you add a second affiliation for me? School of
Informatics, University of Edinburgh<br>
<br>
Thank you everyone for pulling this together.<br>
<br>
Cheers,<br>
-w<br>
<br>
<br>
> On 6 Nov 2021, at 22:59, Jacob Barhak <<a
href="mailto:jacob.barhak@gmail.com"
target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">jacob.barhak@gmail.com</a>>
wrote:<br>
> <br>
> Greetings paper contributors,<br>
> <br>
> It is time for final approval of our
manuscript. Here is the manuscript I ask you to
approve towards submission to Frontiers in Systems
Biology:<br>
> <a
href="https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.google.com%2Fdocument%2Fd%2F1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM%2Fedit%3Fusp%3Dsharing&data=04%7C01%7CWinston.Garira%40univen.ac.za%7C4afdd5cc058a498bc11008d9a1da2418%7Cf38ba9d8554c48a2ae4213b1e7f3c797%7C0%7C0%7C637718780727672293%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=n56Rv%2BYvUgM6I7vvVXKyRUWqf74k6FPR9plverQXDU0%3D&reserved=0"
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> <br>
> I disabled all edits to it at this point so it
will not change unless I reopen it.
<br>
> <br>
> This is the list of contributors in no
particular order <br>
> • Jonathan Karr, Icahn Institute for
Data Science and Genomic Technology and Department
of Genetics and Genomic Sciences, Icahn School of
Medicine at Mount Sinai, New York, NY, USA<br>
> • Rahuman Sheriff, The European
Bioinformatics Institute (EMBL-EBI), London, UK<br>
> • James Osborne, School of Mathematics
and Statistics, University of Melbourne, Parkville,
Australia<br>
> • Gilberto Gonzalez Parra, Mathematics
Department, New Mexico Tech, Socorro, USA<br>
> • Eric Forgoston, Department of Applied
Mathematics and Statistics, Montclair State
University, Montclair, NJ, USA<br>
> • Ruth Bowness, Department of
Mathematical Sciences, University of Bath, Bath, UK<br>
> • Yaling Liu, Department of Mechanical
Engineering and Mechanics , Department of
Bioengineering, Lehigh University, Bethlehem, PA,
USA<br>
> • Robin Thompson, Mathematics Institute
& The Zeeman Institute for Systems Biology and
Infectious Disease Epidemiology Research, University
of Warwick, Coventry , UK<br>
> • Winston Garira - Department Of
Mathematics And Applied Mathematics , Modelling
Health and Environmental Linkages Research Group.
University of Venda, Limpopo, South Africa<br>
> • Jacob Barhak* - Jacob Barhak
Analytics, Austin, TX, USA<br>
> • John Rice - Independent Retired
Working Group Volunteer, Virginia Beach, VA, USA<br>
> • Marcella Torres*, School of Arts and
Sciences, University of Richmond, Richmond, USA<br>
> • Hana M. Dobrovolny , Department of
Physics & Astronomy, Texas Christian University,
Fort Worth, USA<br>
> • Tingting Tang, Department of
Mathematics and Statistics in San Diego State
University (SDSU) and SDSU Imperial Valley,
Calexico, CA, USA<br>
> • William Waites, Centre for
Mathematical Modelling of Infectious Diseases,
London School of Hygiene and Tropical Medicine,
London, UK<br>
> • James Glazier, Biocomplexity
Institute, Indiana University, Bloomington, USA<br>
> • James R. Faeder, Department of
Computational and Systems Biology, University of
Pittsburgh, Pittsburgh, USA<br>
> • Alexander Kulesza, Novadiscovery SA,
Lyon, France<br>
> <br>
> IF YOU ARE ON THIS LIST - YOU HAVE 3 TASKS DO
TO:<br>
> <br>
> TASK 1: <br>
> Please go over the paper and the Journal rules
here: <br>
> <a
href="https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.frontiersin.org%2Fabout%2Fpolicies-and-publication-ethics&data=04%7C01%7CWinston.Garira%40univen.ac.za%7C4afdd5cc058a498bc11008d9a1da2418%7Cf38ba9d8554c48a2ae4213b1e7f3c797%7C0%7C0%7C637718780727672293%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=xDeVGPtW3JEBn%2FKKU5GPMpxsI6vEo7HOuteuRiQHxEw%3D&reserved=0"
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<br>
> <br>
> Note that the guidelines allow to establish
authors levels of contribution according to
<a
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section 1.9 - however order is not dictated - I
suggest to keep this order which is more or less
random - I really do not want to discuss order or
authors - this is not the purpose of this paper.<br>
> Also to simplify the process, I detached the
manuscript from the working group - we can add it
back according to section 1.10 of the guidelines.
For simplicity I suggest we just submit the paper as
a group of authors - unless someone volunteers their
time to do more paperwork. The working group is
mentioned in the paper as well as correspondences.<br>
> <br>
> TASK 2: <br>
> Please check again your name and affiliation is
correct. this can be fixed in submission - and
apologies in advance for any mistakes. In cases of
dual affiliation, I listed only one, so please look
at the submission guidelines and give me the correct
information according to the guidelines - I will
have to enter it manually in the system upon
submission.
<br>
> <br>
> TASK 3: <br>
> REPLY TO ALL TO THIS MESSAGE and note one of
the following options:<br>
> <br>
> 1. APPROVE: this means you agree that the
manuscript represents your views correctly You also
approve the corresponding author to act on your
behalf for the rest of the publication process -
currently I am the corresponding author and will add
Marcella if possible yet if anyone else wants to
volunteer - please do.<br>
> <br>
> 2. DISAPPROVE: This means you cannot have your
name signed on this manuscript and the group should
discuss some matters in further details before
submission to properly represent you - this means
you are still interested in being an author, yet
need your views represented properly - this will
delay us all, so if you choose this option, this
means you will have to spend time on discussions and
explain why you have not acted by now and you are
asking to delay now. This option will take a lot of
time from you and others, yet you certainly have the
right to choose this option. <br>
> <br>
> 3. ABSTAIN: This means you are ok with removing
your name from the author list and allowing the rest
of us to submit the manuscript with your
contribution without taking responsibility - your
name will be added to acknowledgements instead. In
legal terms it means you waive copyright on the text
you added so we can legally send this text to the
Journal despite your name not listed in the author
list.
<br>
> <br>
> I also ask John Gennari for the last time to
rejoin the group and approve the manuscript as an
author sinceI believe he had major contributions -
hopefully he will reconsider and accept this
responsibility and privilege. Otherwise he makes our
lives harder to protect that paper, especially with
elements lik SemGen and Annotaions where he is an
expert.
<br>
> <br>
> I will need a public response from all of you -
if you send me a private email I will forward it to
the list to become public record - please avoid
doing so since you are making me work twice- so
PLEASE PRESS REPLY ALL.<br>
> <br>
> Hopefully we can get this approval round done
quickly and move forward and submit.
<br>
> <br>
> Jacob<br>
> <br>
> <br>
> <br>
> <br>
> On Thu, Nov 4, 2021 at 12:30 AM Jacob Barhak
<<a href="mailto:jacob.barhak@gmail.com"
target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">jacob.barhak@gmail.com</a>>
wrote:<br>
> Thanks James, And Greetings to all
contributors, <br>
> <br>
> James, your suggestions are almost all accepted
- yes we needed American English and modelling is
not the American form - thanks for noticing. The
reference will stay as is or corrected during proofs
I see no better way to reference it other than the
automatically generated text. <br>
> <br>
> At this point 3 people went over the manuscript
and it seems ready to go.<br>
> <br>
> However, to avoid any misunderstandings I would
like formal public approval from all Authors to make
sure we are all on the same page. There were several
discussions and different voices and I want to make
sure this version is something all authors agree on.
Here is the manuscript:<br>
> <a
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> <br>
> If you want to see the comment history, please
send me a request so I can add you as an editor.<br>
> <br>
> Before you rush approving, I would ask you to
take a minute and read section 1.3. Authorship and
Author Responsibilities in
<br>
> <a
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> <br>
> If you approve this manuscript, this means you
are comfortable with releasing this for publication
using the CC-BY, version 4.0 license with the terms
above.
<br>
> <br>
> Please double check your name and affiliation -
I will have to copy it - if there is a mistake, let
me know.
<br>
> <br>
> If after checking all these you are ok, please:<br>
> REPLY TO ALL TO THIS MESSAGE WITH THE TEXT "I
APPROVE THE MANUSCRIPT"<br>
> <br>
> I ask that you do not send any approve message
before Saturday - 6 - Nov - I want to give a last
chance for edits or discussions before everyone
approves. WE had plenty of time, yet I want to make
sure there is no late arrival that is very important
so I am giving this two more days. <br>
> <br>
> On Oct 6th I will lock the manuscript and
remove all comments and mark them as resolved.
<br>
> <br>
> I hope you all find it in good shape.<br>
> <br>
> Jacob<br>
> <br>
> <br>
> <br>
> <br>
> On Wed, Nov 3, 2021 at 5:15 AM James Osborne
<<a href="mailto:jmosborne@unimelb.edu.au"
target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">jmosborne@unimelb.edu.au</a>>
wrote:<br>
> Jacob <br>
> <br>
> I did another readability pass and fixed a few
grammatical errors and fixed some British English vs
American English inconsistencies (went on the
American side). Everything as suggestions so you can
leave if you choose.<br>
> <br>
> For what it's worth thank you for your efforts
knocking this into shape.<br>
> <br>
> James <br>
> <br>
> On Wed, Nov 3, 2021 at 4:42 PM Jacob Barhak
<<a href="mailto:jacob.barhak@gmail.com"
target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">jacob.barhak@gmail.com</a>>
wrote:<br>
> Hi James,<br>
> <br>
> Eric Forgoston was kind enough to gp through
the paper and made edits - I resolved most issues
and only a few comments are left for experts on
annotation and to resolve some differences between
John Rice and Alex.
<br>
> <br>
> I ask that we avoid endless edits and start the
approval process for submission. We should not drag
editing anymore - Eric's last edits were at the
level of punctuation and proofs so we should be
good. And this is after many edits and checks I made
myself and I know Hana and Alex also made edits. <br>
> <br>
> Unless someone shouts, I will start the
approval process tomorrow - so I ask contributors to
give the papr a last peek before you are asked to
say Yes/NO towards submission with your name on it.
<br>
> <br>
> Hopefully this last warning is sufficient and
you will all find the paper in good shape.
<br>
> <br>
> Jacob<br>
> <br>
> On Thu, Oct 28, 2021 at 9:26 PM Jacob Barhak
<<a href="mailto:jacob.barhak@gmail.com"
target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">jacob.barhak@gmail.com</a>>
wrote:<br>
> Hi James,<br>
> <br>
> Apologies - I must have missed your email
request. If anyone else wants access and did not get
it, please let me know - I will do my best to give
you access within a day.
<br>
> <br>
> For those who have access. Please no more
additions - from now on just corrections of typos,
grammer, and grave errors. Anything else, please
leave a comment and we can discuss it.<br>
> <br>
> I really want the paper out quickly - hopefully
we can finish this and submit quickly.<br>
> <br>
> Jacob<br>
> <br>
> On Thu, Oct 28, 2021 at 3:17 PM James A Glazier
<<a href="mailto:jaglazier@gmail.com"
target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">jaglazier@gmail.com</a>>
wrote:<br>
> Dear Jacob:<br>
> <br>
> I would like to review the document. I had
asked for access a few weeks ago. Happy to look in
the next few days.<br>
> <br>
> JAG<br>
> <br>
> On 10/24/2021 4:40 AM, Jacob Barhak wrote:<br>
>> Hi Eric, <br>
>> <br>
>> You are the last one I remember who wanted
to edit. Please check the manuscript<br>
>> <a
href="https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.google.com%2Fdocument%2Fd%2F1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM%2Fedit%3Fusp%3Dsharing&data=04%7C01%7CWinston.Garira%40univen.ac.za%7C4afdd5cc058a498bc11008d9a1da2418%7Cf38ba9d8554c48a2ae4213b1e7f3c797%7C0%7C0%7C637718780727672293%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=n56Rv%2BYvUgM6I7vvVXKyRUWqf74k6FPR9plverQXDU0%3D&reserved=0"
target="_blank" moz-do-not-send="true">
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>> <br>
>> I finished editing the references and am
almost ready for transformation to match the
guidelines. I finished addressing the editor
requesting for removal of bullet points everywhere
but the stochastic section .
<br>
>> <br>
>> I ask that you do not add any more
references and focus only on text in the stochastic
section. Handling the references took about 4 hours
alone and still needs inspection.
<br>
>> <br>
>> However, I will appreciate help with minor
proofs - I made significant changes so there is a
chance for typos still. Some of the changes have
been made after more than 12 hours of consecutive
work. So polish will help - yet no more major
changes.
<br>
>> <br>
>> The tasks left to do are:<br>
>> - Ask John Gennari to inspect the paper
again - it has major contributions from his version
and he should join the authors list - I must be ask
again
<br>
>> - Finish the edits to the stochastic
section - Eric - you asked for this<br>
>> - Finish formatting to fit the Journal
guidelines <br>
>> - Add a cover letter and split the paper
into sections to be uploaded to the journal web site<br>
>> - Approve the version with all authors - we
must do this again and get full approval - this may
take a while<br>
>> - Determine who else wants to be listed as
corresponding author - currently I marked Marcell
and myself, yet others may want to correspond.
<br>
>> - Upload the paper to the journal
submission system<br>
>> <br>
>> I hope for no obstacles and full
cooperation to make the process smooth.<br>
>> <br>
>> Jacob<br>
>> <br>
>> <br>
>> <br>
>> On Sat, Oct 23, 2021 at 9:08 PM Jacob
Barhak <<a href="mailto:jacob.barhak@gmail.com"
target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">jacob.barhak@gmail.com</a>>
wrote:<br>
>> So Gilberto,<br>
>> <br>
>> The last approved version is the only one
we can continue from - this is unfortunate that
there is a need to back port some modifications -
hence the conversation with Eric and Hana - yet to
maintain traceability and honor all contributors -
this is necessary.<br>
>> <br>
>> And yes, there will be some differences -
it's unavoidable. Yet I pretty much merged the other
traceable versions by now. If I missed anything - I
apologize - there is a limit to human capabilities.
<br>
>> <br>
>> We discussed this multiple times on this
list, if this is a stopper for you, let me know
immediately so I will stop work to resolve this
issue.<br>
>> <br>
>> Otherwise, I will continue - I think I
resolved most points except from references and
removal of bullets - still working on that and I
will have to deal with modifying conclusions at the
end.
<br>
>> <br>
>> And Gilberto, if you want to contribute
time towards changing order of sections and handle
references to comply with the target journal
guidelines, please go online on the Jitsi
channel.and I will show you the extent of work
needed. I will be here for at least 3 more hours -
until midnight - yet to be efficient, please join on
jitsi if you want to talk while I continue
modifications.
<br>
>> <br>
>> I hope I can finish most of the work except
references perhaps by midnight. <br>
>> <br>
>> Jacob<br>
>> <br>
>> <br>
>> <br>
>> On Sat, Oct 23, 2021 at 8:32 PM Gilberto
Gonzalez-Parra <<a
href="mailto:gilberto.gonzalezparra@nmt.edu"
target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">gilberto.gonzalezparra@nmt.edu</a>>
wrote:<br>
>> Hi Jacob,<br>
>> <br>
>> I noticed that we are not using the last
version that has many modifications. Are you using
the previous version that was originally submitted
to cureus ? and trying to incorporate the changes of
the last version ?<br>
>> <br>
>> I noticed that the section/challenge
Barriers to model implementation and real-world use
was removed. I think in one of the emails it says
that there is no solution proposed for this. I can
write some general ideas for this.
<br>
>> <br>
>> In the current version in the table it
appears "<br>
>> Model<br>
>> application and implementation barriers<br>
>> " just after "<br>
>> Missing Annotations in Models"<br>
>> <br>
>> but later in the document appears just
before stochastic modeling. I think we should keep
the same order that is in the table. The article<br>
>> would look better organized.<br>
>> <br>
>> Best,<br>
>> <br>
>>
***************************************************************************<br>
>> Gilberto C. Gonzalez-Parra, Ph.D in Applied
Mathematics.<br>
>> Faculty of the Mathematics Department<br>
>> New Mexico Tech, NM, USA.<br>
>>
****************************************************************************<br>
>> <br>
>> <br>
>> On Sat, Oct 23, 2021 at 5:38 PM Jacob
Barhak <<a href="mailto:jacob.barhak@gmail.com"
target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">jacob.barhak@gmail.com</a>>
wrote:<br>
>> Hi Eric, and also greeting for the other
paper contributors <br>
>> <br>
>> Here is a real time update just to give an
idea of current editing status.<br>
>> <br>
>> It took almost 6 hours to get the
manuscript to the point that contributions from
Sheriff, Alex, John Gennari, and Hana were
integrated. I assume Eric will add his edits later -
since those are in one section, it should not cause
any conflict. However, Eric, please be careful when
editing the stochastic section. Pease look at the
comments Hana and I exchanged. I am also adding the
chat between us so it will be easier on you:<br>
>> <br>
>> "<br>
>> Hi Hana<br>
>> Can you see the chat?<br>
>> I can. There's just a lot going on around
here right now, so I'm not fast with typing<br>
>> I put the references in the comments, can
you see them?<br>
>> Yes I See them - yet you will have to
ensure that this is your text - you see, you copied
text from a document where we do not have
contributor history - this was the main issue - so
you will have not to prove this was your text and
only your text - this is the problem I am faced
with - I have to establish tracability - in this
document I know you added the text - yet I cannot
verify that you did not include text from anonymous
since I already concluded you added text from Alex -
this is how I stumbled on this - I apologize yet I
really am serious about tracing back authorship..<br>
>> And thanks fro helping<br>
>> If you want, you can join jitsi: <a
href="https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmeet.jit.si%2FCollaborativePaperEditing&data=04%7C01%7CWinston.Garira%40univen.ac.za%7C4afdd5cc058a498bc11008d9a1da2418%7Cf38ba9d8554c48a2ae4213b1e7f3c797%7C0%7C0%7C637718780727672293%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=kxHZrZGrcqae4B9YRD1zyUSnZDw3oie7lAmHMAzQb7Q%3D&reserved=0"
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and we can chat using voice<br>
>> I just saw your comment - it is public
confirmation - this is good enough thank you
<br>
>> The first two paragraphs are from the
original paper. The third paragraph is from Alex.
The last two are mine. It looks like someone (other
than me) italicized the in vitro and in vivo and
changed the verb on the "Even data that are..." (I
had is), but everything else is mine.<br>
>> If you can modify things to the original
version you added - it will be better - if someone
manipulated the text I want to remove it - even if
it is small changes
<br>
>> I know you're trying to get things done
today, but I'll be out tonight, so if anything else
comes up, I probably won't get to it until the
morning.
<br>
>> Well, "are" is the correct verb there, so
that should probably stay. I can remove the
italicization.<br>
>> Do not worry - I am making good progress
and may not need help until I am done - I appreciate
the help and the fact you are working on it over the
weekend - I will later also make this chat public
for transparency. I do believe you have contributed
a lot to this paper - its not the first time you are
going over it - I can only thank you .
<br>
>> the are was my change today I believe so
its not a problem - yet google suggests is instead I
guess is and are both acceptable with data ....
nevermind that.<br>
>> "<br>
>> <br>
>> I did my best to keep all ideas and other
texts intact and there are many comments to mark
changes - the paper became longer, yet not too much
and I feel it is still reasonable .<br>
>> <br>
>> I am now moving to the next part of
complying with the requests of the editor:<br>
>> 1) Determine authorship<br>
>> 2) Converging format to journal guidelines
- this also means references<br>
>> 3) Detach from group - some elements
already marked<br>
>> 4) Revise bullet points into paragraphs<br>
>> <br>
>> I plan to continue editing until midnight
CST with a break for dinner - so if anyone has
comments - please feel free to join the open channel
that shows the editing and influence real-time.<br>
>> <br>
>> Hopefully you will find the merged version
in order. <br>
>> <br>
>> Jacob<br>
>> <br>
>> <br>
>> <br>
>> <br>
>> <br>
>> <br>
>> On Sat, Oct 23, 2021 at 2:50 PM Jacob
Barhak <<a href="mailto:jacob.barhak@gmail.com"
target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">jacob.barhak@gmail.com</a>>
wrote:<br>
>> Hi Eric,<br>
>> <br>
>> You wanted to edit the stochastic section -
you are welcome to do it. Yet I ask no more
references or deletions - I am overloaded already.
<br>
>> <br>
>> The version benign edited is:<br>
>> <a
href="https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.google.com%2Fdocument%2Fd%2F1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM%2Fedit&data=04%7C01%7CWinston.Garira%40univen.ac.za%7C4afdd5cc058a498bc11008d9a1da2418%7Cf38ba9d8554c48a2ae4213b1e7f3c797%7C0%7C0%7C637718780727672293%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=jRu17cEBk1FL0FlwjwNuvx1b5GTWrgBkm0OVXBeVhWE%3D&reserved=0"
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>> <br>
>> You will need to login so that your edits
will be traceable.<br>
>> <br>
>> You can join me while editing in:<br>
>> <a
href="https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmeet.jit.si%2FCollaborativePaperEditing&data=04%7C01%7CWinston.Garira%40univen.ac.za%7C4afdd5cc058a498bc11008d9a1da2418%7Cf38ba9d8554c48a2ae4213b1e7f3c797%7C0%7C0%7C637718780727672293%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=kxHZrZGrcqae4B9YRD1zyUSnZDw3oie7lAmHMAzQb7Q%3D&reserved=0"
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>> <br>
>> I am sharing my screen there while editing.
<br>
>> <br>
>> You might be able to help me with other
sections as well.<br>
>> <br>
>> Jacob<br>
>> <br>
>> <br>
>> On Sat, Oct 23, 2021 at 2:44 PM Eric
Forgoston <<a
href="mailto:eric.forgoston@montclair.edu"
target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">eric.forgoston@montclair.edu</a>>
wrote:<br>
>> Hi Jacob,<br>
>> <br>
>> If you give me a link to the paper you are
editing and edit access to the paper I can update
the stochastic section.<br>
>> <br>
>> Cheers,<br>
>> <br>
>> Eric<br>
>> ---------------------<br>
>> Dr. Eric Forgoston<br>
>> Professor of Applied Mathematics<br>
>> Chair, Department of Applied Mathematics
and Statistics<br>
>> Montclair State University<br>
>> Montclair, NJ 07043 USA<br>
>> +1 973 655-7242 <br>
>> <a
href="https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Feric-forgoston.github.io%2F&data=04%7C01%7CWinston.Garira%40univen.ac.za%7C4afdd5cc058a498bc11008d9a1da2418%7Cf38ba9d8554c48a2ae4213b1e7f3c797%7C0%7C0%7C637718780727682287%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=KiG9WrIyZdyq8WdZIIzMD2GV86jcFjgPzhkKxwChSRM%3D&reserved=0"
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>> <br>
>> <br>
>> On Sat, Oct 23, 2021 at 1:39 PM Jacob
Barhak <<a href="mailto:jacob.barhak@gmail.com"
target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">jacob.barhak@gmail.com</a>>
wrote:<br>
>> Greetings Paper Contributors,<br>
>> <br>
>> The paper editing process started and you
can follow it live on:<br>
>> <a
href="https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmeet.jit.si%2FCollaborativePaperEditing&data=04%7C01%7CWinston.Garira%40univen.ac.za%7C4afdd5cc058a498bc11008d9a1da2418%7Cf38ba9d8554c48a2ae4213b1e7f3c797%7C0%7C0%7C637718780727682287%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=KHnJGERu2bWXaAIOyq8eOupzextaxY7R2rnFh6L9C4Y%3D&reserved=0"
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>> <br>
>> I will keep the channel open as long as I
am editing so that the process will be as
transparent as possible.
<br>
>> <br>
>> The first step would be to reconcile the
differences between those 4 versions traceable back
to authors:<br>
>> <a
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- the submitted version<br>
>> <a
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- first committed version<br>
>> <a
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- first committed version<br>
>> <a
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- its the first document posted<br>
>> <br>
>> After this step is done I will move towards
adhering to those instructions:<br>
>> <a
href="https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.frontiersin.org%2Fabout%2Fauthor-guidelines&data=04%7C01%7CWinston.Garira%40univen.ac.za%7C4afdd5cc058a498bc11008d9a1da2418%7Cf38ba9d8554c48a2ae4213b1e7f3c797%7C0%7C0%7C637718780727682287%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=qkqzufzA1m6zgRR9gppIq4%2B2LYYByiBhRQAamQntqTM%3D&reserved=0"
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>> <br>
>> I estimate I will be working till late
today with very few breaks and hopefully make
sufficient progress.<br>
>> <br>
>> Feel free to visit and perhaps even help.
If you do, please raise your voice so I can hear you
- I am sharing my screen and not seeing the video
when I edit - so you will have to let me know you
are in the room.
<br>
>> <br>
>> Hopefully some of you will visit.<br>
>> <br>
>> Jacob<br>
>> <br>
>> On Fri, Oct 22, 2021 at 2:52 PM Jacob
Barhak <<a href="mailto:jacob.barhak@gmail.com"
target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">jacob.barhak@gmail.com</a>>
wrote:<br>
>> Thanks Sheriff, <br>
>> <br>
>> With your green light I can start editing<br>
>> <br>
>> Eric, the base of John's version will be
merged to the best of my ability, yet unfortunately,
it has omissions and later version based on it are
not traceable back to contributors, so I can only
use some of the base.
<br>
>> <br>
>> If you want to repeat edits so those will
be traceable it is possible. Yet we cannot copy
verbatim without going to details.
<br>
>> <br>
>> To make things easier, I will open a
channel over the weekend during edits where anyone
can join and communicate while watching the edits
live.
<br>
>> <br>
>> Hopefully it will make things smoother. <br>
>> <br>
>> Jacob<br>
>> <br>
>> <br>
>> <br>
>> <br>
>> <br>
>> <br>
>> On Fri, Oct 22, 2021, 13:40 Eric Forgoston
<<a href="mailto:eric.forgoston@montclair.edu"
target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">eric.forgoston@montclair.edu</a>>
wrote:<br>
>> Dear Jacob and all,<br>
>> <br>
>> I suggest, as others have done, to use the
John G. version as structurally it has already
cleaned up most of the issues raised by the Editor,
and also has many revised and improved sections. In
particular, the stochastic section that I worked on
with others is far superior to the one in the paper
submitted to Frontiers.<br>
>> <br>
>> Best wishes,<br>
>> <br>
>> Eric<br>
>> ---------------------<br>
>> Dr. Eric Forgoston<br>
>> Professor of Applied Mathematics<br>
>> Chair, Department of Applied Mathematics
and Statistics<br>
>> Montclair State University<br>
>> Montclair, NJ 07043 USA<br>
>> +1 973 655-7242 <br>
>> <a
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>> <br>
>> <br>
>> On Fri, Oct 22, 2021 at 12:57 PM Rahuman
Sheriff <<a href="mailto:sheriff@ebi.ac.uk"
target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">sheriff@ebi.ac.uk</a>>
wrote:<br>
>> Congratulations Marcella,<br>
>> <br>
>> Hi Jacob and all,<br>
>> <br>
>> As Tomas mentioned, John G’s version is bit
more organised. <br>
>> Although it would be nice to take that one
forward, I also fine with you recovering your
version incorporating requested changes including
mine.
<br>
>> I would prefer this manuscript progresses
ahead, instead of another long discussion.
<br>
>> Green signal from my side.<br>
>> Best regards<br>
>> Sheriff<br>
>> <br>
>> <br>
>>> On 22 Oct 2021, at 01:49, Jacob Barhak
<<a href="mailto:jacob.barhak@gmail.com"
target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">jacob.barhak@gmail.com</a>>
wrote:<br>
>>> <br>
>>> Congratulations Marcella, <br>
>>> <br>
>>> Indeed you bring good news. <br>
>>> <br>
>>> You should not worry about the
manuscript. You have done plenty and we can handle
if from now on, you can focus on your family.
<br>
>>> <br>
>>> Jacob<br>
>>> <br>
>>> On Thu, Oct 21, 2021, 10:33 Torres,
Marcella <<a href="mailto:mtorres@richmond.edu"
target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">mtorres@richmond.edu</a>>
wrote:<br>
>>> This streamlined approach sounds good
to me; thanks Jacob for offering to coordinate
edits. I think the one month deadline is a good
maximum, since Frontiers favors quick turnaround.<br>
>>> <br>
>>> I don't insist on participating in the
revisions, but I am available to help with cleaning
up grammar, typos, and so on - I noticed quite a few
minor issues when reviewing the document for
submission. However, my son was born a few days ago
and I have limited time. <br>
>>> <br>
>>> Marcella<br>
>>> From: Jacob Barhak <<a
href="mailto:jacob.barhak@gmail.com"
target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">jacob.barhak@gmail.com</a>><br>
>>> Sent: Wednesday, October 20, 2021
11:53:58 PM<br>
>>> To: Alexander Kulesza <<a
href="mailto:alexander.kulesza@novadiscovery.com"
target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">alexander.kulesza@novadiscovery.com</a>><br>
>>> Cc: Hana <<a
href="mailto:h.dobrovolny@tcu.edu" target="_blank"
moz-do-not-send="true"
class="moz-txt-link-freetext">h.dobrovolny@tcu.edu</a>>;
James Osborne <<a
href="mailto:jmosborne@unimelb.edu.au"
target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">jmosborne@unimelb.edu.au</a>>;
John Rice <<a href="mailto:john.rice@noboxes.org"
target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">john.rice@noboxes.org</a>>;
Torres, Marcella <<a
href="mailto:mtorres@richmond.edu" target="_blank"
moz-do-not-send="true"
class="moz-txt-link-freetext">mtorres@richmond.edu</a>>;
<a
href="mailto:vp-reproduce-subgroup@lists.simtk.org"
target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">vp-reproduce-subgroup@lists.simtk.org</a>
<<a
href="mailto:vp-reproduce-subgroup@lists.simtk.org"
target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">vp-reproduce-subgroup@lists.simtk.org</a>>;
<a
href="mailto:vp-integration-subgroup@lists.simtk.org"
target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">vp-integration-subgroup@lists.simtk.org</a>
<<a
href="mailto:vp-integration-subgroup@lists.simtk.org"
target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">vp-integration-subgroup@lists.simtk.org</a>>;
Jonathan Karr <<a
href="mailto:jonrkarr@gmail.com" target="_blank"
moz-do-not-send="true"
class="moz-txt-link-freetext">jonrkarr@gmail.com</a>>;
John Gennari <<a href="mailto:gennari@uw.edu"
target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">gennari@uw.edu</a>>;
Winston Garira <<a
href="mailto:Winston.Garira@univen.ac.za"
target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">Winston.Garira@univen.ac.za</a>><br>
>>> Subject: Re: [Vp-integration-subgroup]
Fwd: Shayn Peirce-Cottler via Frontiers: Manuscript<br>
>>> <br>
>>> External Email: Use caution in opening
links, attachments, and buying gift cards.<br>
>>> <br>
>>> Thanks Alex, Thanks John,<br>
>>> <br>
>>> Your contribution is appreciated and
since John cleared us to move forward it simplifies
things. I hope he will change his mind about
authorship since he contributed a lot, yet I will
respect his wishes - perhaps after seeing the final
version he will change his mind. <br>
>>> <br>
>>> If Sheriff gives me a green light I can
incorporate his modifications as well. I do ask that
if any of the listed authors has any serious
concerns and plans to not approve a modified version
that addresses the editors requests alone alongside
those I mentioned above, to step up before the work
is done so we can resolve things before energy is
spent.
<br>
>>> <br>
>>> If there will be no blocks I plan to
start work over the weekend if I see no objections
by then.<br>
>>> <br>
>>> I appreciate the offer to help with
bibliography, from experience I know it is perhaps
the most time consuming. However, since we have many
links and specialized publications in our list - I
am not sure if any tool can make it easier - the
last time I had to do a lot of manual work to fit a
specific format and find all missing links and also
fix some errors - no tool would have helped me then.
This time I think it will be a bit easier. Yet I ask
for no more references to be added - I also want to
add more references, yet I am stopping myself. We
can always expand the work in another future version
if we have new findings.
<br>
>>> <br>
>>> Again note that I will only try to
address the requests of the editor at this point
without trying to perfect anything beyond what I
wrote above and I want to keep things as traceable
as possible. Once I am done,we will see if we can
approve this manuscript for publication.<br>
>>> <br>
>>> Unless any blockers appear, if anyone
wants to actively participate in the editing over
the weekend, please let me know so we can
communicate better.<br>
>>> <br>
>>> Jacob<br>
>>> <br>
>>> <br>
>>> <br>
>>> <br>
>>> <br>
>>> <br>
>>> <br>
>>> <br>
>>> <br>
>>> <br>
>>> On Tue, Oct 19, 2021 at 2:02 AM
Alexander Kulesza <<a
href="mailto:alexander.kulesza@novadiscovery.com"
target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">alexander.kulesza@novadiscovery.com</a>>
wrote:<br>
>>> Dear Jacob,<br>
>>> thanks for forwarding and you
suggestions, which seems more than reasonable. <br>
>>> <br>
>>> My contributions from May 19th, May31st
and June 2nd are in <a
href="https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.google.com%2Fdocument%2Fd%2F1VvyP3YZQdQYjj8DFKOpQ4pn_0pdDGgiT%2Fedit%3Fusp%3Dsharing%26ouid%3D113860487708206439519%26rtpof%3Dtrue%26sd%3Dtrue&data=04%7C01%7CWinston.Garira%40univen.ac.za%7C4afdd5cc058a498bc11008d9a1da2418%7Cf38ba9d8554c48a2ae4213b1e7f3c797%7C0%7C0%7C637718780727682287%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=5DkphKFgmXWvV4azKVy0EyqJwh3cnPbocnBSE%2BL8CZQ%3D&reserved=0"
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<br>
>>> <br>
>>> The other document <a
href="https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.google.com%2Fdocument%2Fd%2F1esZvWWVBvpwvuFUi3C3161lthZkEBFyMRrwwozitBi4%2Fedit%3Fusp%3Dsharing&data=04%7C01%7CWinston.Garira%40univen.ac.za%7C4afdd5cc058a498bc11008d9a1da2418%7Cf38ba9d8554c48a2ae4213b1e7f3c797%7C0%7C0%7C637718780727682287%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=i69lTB9BmMlCGAivRn4Z5ZXIayBAK9UYcKmumIsr6TY%3D&reserved=0"
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I created initially to suggest my edits without
editing the core version can be disregarded as I
have tranferred all of them into the main document,
cited above.
<br>
>>> <br>
>>> If we were on Latex, I could offer to
create the bibliography but unfortunately we lack a
bibliography manager integrated in Word/GDoc. If we
were to work with Mendeley and someone could create
a group for this paper that has a shared library I
could offer to transfer citations from the paper
into that database too. <br>
>>> <br>
>>> Please let me know.<br>
>>> A<br>
>>> <br>
>>> <br>
>>> <br>
>>> On Tue, 19 Oct 2021 at 05:51, Jacob
Barhak <<a href="mailto:jacob.barhak@gmail.com"
target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">jacob.barhak@gmail.com</a>>
wrote:<br>
>>> Greetings white paper contributors,<br>
>>> <br>
>>> Below is the response from the editor
to my request and my thank you.<br>
>>> <br>
>>> The editor grants us the extension by
rejecting the paper and allowing time to come up
with a better version. There is no time limit now,
yet I want to get her a revised version within a
month.
<br>
>>> <br>
>>> The requests are simple and easy to
satisfy - and I know there are many of you who want
more revisions, yet I suggest we reduce them to only
what is manageable and necessary. Otherwise we will
never get this paper published despite its
importance.
<br>
>>> <br>
>>> The most time consuming effort would be
adhering to the journal format as defined here:<br>
>>> <a
href="https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.frontiersin.org%2Fabout%2Fauthor-guidelines&data=04%7C01%7CWinston.Garira%40univen.ac.za%7C4afdd5cc058a498bc11008d9a1da2418%7Cf38ba9d8554c48a2ae4213b1e7f3c797%7C0%7C0%7C637718780727682287%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=qkqzufzA1m6zgRR9gppIq4%2B2LYYByiBhRQAamQntqTM%3D&reserved=0"
target="_blank" moz-do-not-send="true">
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>>> <br>
>>> I think the most time consuming task
would be dealing with the references - otherwise the
format guidelines seem reasonable.<br>
>>> <br>
>>> We can also add some revisions we
started working on. However, I will personally
insist on :<br>
>>> 1. traceability - currently there is no
traceability in the revised version in the summer<br>
>>> 2. non deletion - do not delete any
content unless you wrote it originally or unless you
announced it beforehand to the group and got no
objections within a few days
<br>
>>> 3. Avoid Adding more material that is
not in the existing versions we had - especially
references - we don't have time for that and that is
not what the editor asked us anyway.
<br>
>>> <br>
>>> I will also ask for fast responses from
all contributors. <br>
>>> <br>
>>> To be practical, I marked the submitted
version and opened the document to those who
requested editing rights in the past. If you want
editing rights, let me know - however, the edits
should be minimal and focus on areas you edited in
the past and be aware that if your edits will not
get approved by everyone, we will revert to the old
version we all accepted. The submitted version was
marked so we can always get back to it.
<br>
>>> <br>
>>> If you want editing rights, let me know
and I will respond within a day - I cannot promise
to be fatter than that these days.
<br>
>>> <br>
>>> Alex, John, Sheriff, you had other
versions you created, I want to merge some of your
changes to the manuscript in this version - here are
my suggestions:<br>
>>> <br>
>>> - Sheriff, I will soften the language
as you requested - this was your main request in the
past, yet I will go over your list of changes and
see what I else can be done without reinventing the
paper<br>
>>> - John - I will 1) merge the
credibility sections , 2) delete the history related
to the working group since it matches with what was
requested, and 3) move the model validation barrier
section away from the table since we did not suggest
a solution there. Hopefully this will make the
paper more appealing to you and you will be willing
to add your name to the list
<br>
>>> - Alex, your changes were made on May
16, 2021 and shared in a way I can see the
differences and trace them back to you - I will try
to add your references and see if I can incorporate
your text changes as much as I can.
<br>
>>> <br>
>>> If the 3 of you are ok with me
migrating your changes, I can start the work to save
time. Yet I want your ok first.
<br>
>>> <br>
>>> I know Eric and Hana were working on
some sections and feel strongly about those -
specifically the stochastic modeling part - I am
open to your changes, please suggest what you feel
strongly about..<br>
>>> <br>
>>> I recall Johnathan Karr wanted to make
some changes, please let me know if there is
anything you feel strongly about - he had a lot of
text in the paper ..<br>
>>> <br>
>>> If I forgot anyone who had major
requests, please remind me. .<br>
>>> <br>
>>> I am trying to avoid a never ending
revisioning cycle. So I am asking you to trust me
and centralize the work in hope I get a better
version by the end of the week..<br>
>>> <br>
>>> Hopefully most of you will be ok with
that.<br>
>>> <br>
>>> Jacob<br>
>>> <br>
>>> <br>
>>> <br>
>>> <br>
>>> ---------- Forwarded message ---------<br>
>>> From: Jacob Barhak <<a
href="mailto:jacob.barhak@gmail.com"
target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">jacob.barhak@gmail.com</a>><br>
>>> Date: Mon, Oct 18, 2021 at 9:34 PM<br>
>>> Subject: Re: Shayn Peirce-Cottler via
Frontiers: Manuscript<br>
>>> To: Peirce-Cottler, Shayn (smp6p) <<a
href="mailto:smp6p@virginia.edu" target="_blank"
moz-do-not-send="true"
class="moz-txt-link-freetext">smp6p@virginia.edu</a>><br>
>>> Cc: Shayn Peirce-Cottler (Via
FrontiersIn) <<a href="mailto:shayn@virginia.edu"
target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">shayn@virginia.edu</a>>,<a
href="mailto:systemsbiology.editorial.office@frontiersin.org"
target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">systemsbiology.editorial.office@frontiersin.org</a>
<<a
href="mailto:systemsbiology.editorial.office@frontiersin.org"
target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">systemsbiology.editorial.office@frontiersin.org</a>>,
Vodovotz, Yoram <<a
href="mailto:vodovotzy@upmc.edu" target="_blank"
moz-do-not-send="true"
class="moz-txt-link-freetext">vodovotzy@upmc.edu</a>><br>
>>> <br>
>>> <br>
>>> Thanks Shayn,<br>
>>> <br>
>>> You will get a revised manuscript
targeted at your journal and get back to you with a
more polished version and satisfies your requests.
<br>
>>> <br>
>>> It will also allow us to incorporate
newer versions of the text that answer some of your
requests. We really wish to publish it fast, yet we
need more time for the approval process. So your
solution seems correct - I hope you hear back from
us within a month or so.<br>
>>> <br>
>>> Many thanks for the rapid responses.<br>
>>> <br>
>>> Jacob<br>
>>> <br>
>>> <br>
>>> --<br>
>>> Jacob Barhak Ph.D. <br>
>>> Sole Proprietor, Software Developer,
and Computational Disease Modeler<br>
>>> <br>
>>> Jacob Barhak Analytics<br>
>>> 701 Brazos St<br>
>>> Suite 548<br>
>>> Austin TX, 78701<br>
>>> <br>
>>> Email: <a
href="mailto:jacob.barhak@gmail.com"
target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">jacob.barhak@gmail.com</a><br>
>>> <br>
>>> <a
href="https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsites.google.com%2Fview%2Fjacob-barhak%2Fhome&data=04%7C01%7CWinston.Garira%40univen.ac.za%7C4afdd5cc058a498bc11008d9a1da2418%7Cf38ba9d8554c48a2ae4213b1e7f3c797%7C0%7C0%7C637718780727682287%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=gOmUYx5pQzFybacMWUfy9v7oUfcEPnCBBOzOQdICYoU%3D&reserved=0"
target="_blank" moz-do-not-send="true">
https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsites.google.com%2Fview%2Fjacob-barhak%2Fhome&data=04%7C01%7CWinston.Garira%40univen.ac.za%7C4afdd5cc058a498bc11008d9a1da2418%7Cf38ba9d8554c48a2ae4213b1e7f3c797%7C0%7C0%7C637718780727682287%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=gOmUYx5pQzFybacMWUfy9v7oUfcEPnCBBOzOQdICYoU%3D&reserved=0</a><br>
>>> <br>
>>> <br>
>>> <br>
>>> On Mon, Oct 18, 2021 at 7:43 PM
Peirce-Cottler, Shayn (smp6p) <<a
href="mailto:smp6p@virginia.edu" target="_blank"
moz-do-not-send="true"
class="moz-txt-link-freetext">smp6p@virginia.edu</a>>
wrote:<br>
>>> Hi Jacob, <br>
>>> <br>
>>> <br>
>>> Thank you for your detailed reply. I
agree that the issues can be addressed as you have
described below, and that you may need more time to
do so. Hence, I am going to officially reject this
first submission to remove any imposed deadlines,
and I certainly encourage you to make the updates
listed below, and submit a new manuscript at your
earliest convenience.
<br>
>>> <br>
>>> <br>
>>> Please let me know if you have any
questions, and thanks again for considering this
journal! I think the topic fits very nicely with the
scope of the journal, and it is certainly an
important topic to our multi-scale modeling
community!<br>
>>> <br>
>>> <br>
>>> -Shayn<br>
>>> <br>
>>> <br>
>>> <br>
>>> Shayn Peirce-Cottler, Ph.D.<br>
>>> <br>
>>> Professor of Biomedical Engineering<br>
>>> <br>
>>> Harrison Distinguished Teaching
Professor<br>
>>> <br>
>>> BME Graduate Program Director<br>
>>> <br>
>>> University of Virginia<br>
>>> <br>
>>> Charlottesville, VA<br>
>>> <br>
>>> <br>
>>> From: Jacob Barhak <<a
href="mailto:jacob.barhak@gmail.com"
target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">jacob.barhak@gmail.com</a>><br>
>>> Date: Monday, October 18, 2021 at 1:57
AM<br>
>>> To: Peirce-Cottler Shayn <<a
href="mailto:shayn@virginia.edu" target="_blank"
moz-do-not-send="true"
class="moz-txt-link-freetext">shayn@virginia.edu</a>><br>
>>> Cc: "<a
href="mailto:systemsbiology.editorial.office@frontiersin.org"
target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">systemsbiology.editorial.office@frontiersin.org</a>"
<<a
href="mailto:systemsbiology.editorial.office@frontiersin.org"
target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">systemsbiology.editorial.office@frontiersin.org</a>>,
"Vodovotz, Yoram" <<a
href="mailto:vodovotzy@upmc.edu" target="_blank"
moz-do-not-send="true"
class="moz-txt-link-freetext">vodovotzy@upmc.edu</a>><br>
>>> Subject: Re: Shayn Peirce-Cottler via
Frontiers: Manuscript<br>
>>> <br>
>>> <br>
>>> Hi Shayn,<br>
>>> <br>
>>> <br>
>>> Thanks for returning the response
quickly. To you comments. <br>
>>> <br>
>>> <br>
>>> 1. This is the list of authors that
agreed to submit this manuscript for review - I
collected their approvals for this version
personally.
<br>
>>> <br>
>>> <br>
>>> • Jonathan Karr, Icahn Institute
for Data Science and Genomic Technology and
Department of Genetics and Genomic Sciences, Icahn
School of Medicine at Mount Sinai USA<br>
>>> • Rahuman Sheriff, The European
Bioinformatics Institute (EMBL-EBI), UK<br>
>>> • James Osborne, School of
Mathematics and Statistics, University of Melbourne,
Australia<br>
>>> • Gilberto Gonzalez Parra,
Mathematics Department, New Mexico Tech, USA<br>
>>> • Eric Forgoston, Department of
Applied Mathematics and Statistics, Montclair State
University, USA<br>
>>> • Ruth Bowness, Department of
Mathematical Sciences, University of Bath, UK<br>
>>> • Yaling Liu, Department of
Mechanical Engineering and Mechanics , Department of
Bioengineering, Lehigh University, USA<br>
>>> • Robin Thompson, Mathematics
Institute & The Zeeman Institute for Systems
Biology and Infectious Disease Epidemiology
Research, University of Warwick, UK<br>
>>> • Winston Garira - Department Of
Mathematics And Applied Mathematics , Modelling
Health and Environmental Linkages Research Group.
University of Venda, South Africa<br>
>>> • Jacob Barhak - Barhak, Jacob,
USA<br>
>>> • John Rice - Independent Retired
Working Group Volunteer, USA<br>
>>> • Marcella Torres, School of Arts
and Sciences, University of Richmond, USA<br>
>>> • Hana M. Dobrovolny , Department
of Physics & Astronomy, Texas Christian
University, Fort Worth, USA<br>
>>> • Tingting Tang, Department of
Mathematics and Statistics in San Diego State
University (SDSU) and SDSU Imperial Valley, USA<br>
>>> • William Waites, Centre for
Mathematical Modelling of Infectious Diseases,
London School of Hygiene and Tropical Medicine, UK<br>
>>> • James Glazier, Biocomplexity
Institute, Indiana University, Bloomington, USA<br>
>>> • James R. Faeder, Department of
Computational and Systems Biology, University of
Pittsburgh, Pittsburgh, USA<br>
>>> <br>
>>> If there is a mismatch of authors in
the submission, it can be easily corrected - we kept
the paper traceable when we constructed it so we can
point to exact texts contributed by each contributor
through their google account and versions kept in
google docs with few exceptions where I personally
added text their wrote and have email conversations
supporting that . I personally collected all those
contributions in google docs when I assembled the
version you see and made sure it is agreed upon by
the contributors. It is important to note that There
was one contributor that asked for more revisions
and did not approve this manuscript, yet allowed
submitting the text without association to it to
avoid delays. The entire conversation was documented
publicly in our mailing list and we got consent from
this contributor to continue and use the text - You
can find the conversation here:
<a
href="https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.simtk.org%2Fpipermail%2Fvp-reproduce-subgroup%2F2021-March%2F000019.html&data=04%7C01%7CWinston.Garira%40univen.ac.za%7C4afdd5cc058a498bc11008d9a1da2418%7Cf38ba9d8554c48a2ae4213b1e7f3c797%7C0%7C0%7C637718780727692287%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=ia5ARWxyBl%2BY%2B11jfwExOLPPxpbhGaqtktpYk1Cyp3c%3D&reserved=0"
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- so there are no copyright issues and the name of
the author is not included in the list above at
their request. Those included in the list have
contributed and approved. If needed, we will correct
the list in the journal to match this list. Please
note that we kept the entire process as transparent
as possible so there will be no issues. If there are
any concerns of authorship, I will be happy to dig
into the history and pull out details.
<br>
>>> <br>
>>> <br>
>>> <br>
>>> 2. The reason the manuscript was
submitted in this form is to get confirmation on
initial fit and to get some initial feedback. We
were interested in fast review to get the
information quickly out - Also note that we did not
intend this to be a final version - we already have
some modifications in the work that we would like to
introduce where more people contributed , yet we
have not reached agreement on those so we cannot
formally publish them - however, we did reach
agreement on submitting this version for review so
the editor can focus us on what is important to
change to get published with a 3rd Party - enough of
us agreed in a vote that your Journal seems is a
suitable 3rd party and hence the submission. We will
be happy to spend the time to convert the manuscript
to the desired format if you find the content
suitable for the journal. So far your requests are
reasonable and I will convey them to the group
through our mailing list.
<br>
>>> <br>
>>> <br>
>>> 3. Please note that after the list of
authors there is a disclaimer : "The opinion of the
contributors do not reflect the opinions of the
entire working group". Initially this paper started
as an activity requested by the working group leads.
However, by no means it represents all opinions. The
introduction in this version of the paper captures
some of this history of how the manuscript was
created and modified. However, we have other
versions of the manuscript in work where this
history is deleted - If you prefer, we can easily
create a version that detaches from the working
group to eliminate all concerns - this is a
relatively easy fix. However, whatever fix we do, we
will have to approve with all contributors.
<br>
>>> <br>
>>> <br>
>>> 4 The revisions can be done in
reasonable time. However, the process of collecting
approval for all contributors to legally approve the
revised manuscript will take more than 14 days. All
contributors must approve a manuscript for
publication. With this number of authors we will
probably not make it in the time you mentioned -
only the approval process for collecting all
approvals took alone about 3 weeks to approve this
version you see. Hopefully you will understand this
and extend this time period beyond 14 days. <br>
>>> <br>
>>> <br>
>>> In summary: <br>
>>> <br>
>>> Making the fixes you asked for towards
publication is easy - yet getting the approval from
so many people may take us more time than what you
provide. If it is possible to get an extension, it
will be appreciated.
<br>
>>> <br>
>>> <br>
>>> I will add this conversation to our
mailing list so we can start the process of revising
the manuscript. However, if after this email you
have more issues with this paper, Please advise on
the best course of action you see fit so we can
adjust accordingly.
<br>
>>> <br>
>>> <br>
>>> Hopefully we can address your concerns
in time to publish the manuscript in a timely
manner.
<br>
>>> <br>
>>> <br>
>>> Jacob<br>
>>> <br>
>>> <br>
>>> --<br>
>>> Jacob Barhak Ph.D. <br>
>>> Sole Proprietor, Software Developer,
and Computational Disease Modeler<br>
>>> <br>
>>> Jacob Barhak Analytics<br>
>>> 701 Brazos St<br>
>>> Suite 548<br>
>>> Austin TX, 78701<br>
>>> <br>
>>> Email: <a
href="mailto:jacob.barhak@gmail.com"
target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">jacob.barhak@gmail.com</a><br>
>>> <br>
>>> <a
href="https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsites.google.com%2Fview%2Fjacob-barhak%2Fhome&data=04%7C01%7CWinston.Garira%40univen.ac.za%7C4afdd5cc058a498bc11008d9a1da2418%7Cf38ba9d8554c48a2ae4213b1e7f3c797%7C0%7C0%7C637718780727692287%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=Ce1AaYV56fay8a5ng%2FtH8OhrVLjo9344eynKrsKrx5I%3D&reserved=0"
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>>> <br>
>>> <br>
>>> <br>
>>> On Sun, Oct 17, 2021 at 9:56 AM Shayn
Peirce-Cottler (Via FrontiersIn) <<a
href="mailto:noreply@frontiersin.org"
target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">noreply@frontiersin.org</a>>
wrote:<br>
>>> <br>
>>> Dear Jacob, <br>
>>> <br>
>>> Thank you for your manuscript
submission. I cannot send it out for review in its
current form because I have a few concerns, but if
you can address the following issues, I will
certainly reconsider a revised manuscript if the
following are adequately addressed:<br>
>>> <br>
>>> 1. The author list that is on the first
page differs from the author list that was provided
at the time of submission.
<br>
>>> <br>
>>> 2. The manuscript needs to be submitted
using the official Frontiers template.<br>
>>> <br>
>>> 3. The manuscript states that it
represents the views of a number of special interest
and working groups, and the authors should provide
assurances that they have the authority and approval
to speak on behalf of the working groups that are
listed.<br>
>>> <br>
>>> 4. There are places throughout the
manuscript, and most frequently in the second half,
where information is provided as bulleted talking
points without context. Those sections should be
revised into paragraphs of text or summarized in a
table (or figure).<br>
>>> <br>
>>> If you wish to submit a revised
manuscript, the journal provides a 14-day time
window for you to do so. Please let me know if you
have any questions.
<br>
>>> <br>
>>> Thank you,<br>
>>> Shayn<br>
>>> <br>
>>> <br>
>>> ---------------------------------<br>
>>> <br>
>>> Manuscript title: Model Integration in
Computational Biology: The Role of Reproducibility,
Credibility and Utility<br>
>>> Manuscript ID: 793932<br>
>>> Authors: Marcella Torres, Jacob Barhak,
Ruth Bowness, Hana Maria Dobrovolny, James Faeder,
Eric Forgoston, Winston Garira, Yaling Liu, James
Osborne, Gilberto Gonzalez Parra, John Rice, Rahuman
Sheriff, Tingting Tang, Robin Thompson, William
Waites
<br>
>>> Date submitted: 12 Oct 2021 <br>
>>> Edited by: Shayn Peirce-Cottler<br>
>>> <br>
>>> <br>
>>> Research Topic: Insights in Systems
Biology: Multiscale Mechanistic Modeling 2021<br>
>>> Review forum direct access link: <a
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> -- <br>
> James A. Glazier, PhD<br>
> Professor of Intelligent Systems Engineering,
Adjunct Professor of Physics<br>
> Director, Biocomplexity Institute<br>
> Indiana University, Bloomington<br>
> (812) 391-2159 (cell)<br>
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</blockquote>
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<br clear="all">
<div><br>
</div>
-- <br>
<div dir="ltr" class="gmail_signature">
<div dir="ltr">-- ------------------
<div>Yaling Liu, Professor </div>
<div>Department of Bioengineering, Director of Graduate
Studies<br>
</div>
<div>Department of Mechanical Engineering and Mechanics </div>
<div>Lehigh University </div>
<div><a href="http://www.lehigh.edu/~yal310" target="_blank"
moz-do-not-send="true">www.lehigh.edu/~yal310</a><br>
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</div>
</blockquote>
<pre class="moz-signature" cols="72">--
James A. Glazier, PhD
Professor of Intelligent Systems Engineering, Adjunct Professor of Physics
Director, Biocomplexity Institute
Indiana University, Bloomington
(812) 391-2159 (cell)</pre>
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