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<p>Dear Jacob:</p>
<p>Thank you for all your hard work and patience on this paper. I
know you have made a lot of effort to integrate so many differing
ideas and voices.</p>
<p>JAG<br>
</p>
<div class="moz-cite-prefix">On 11/24/2021 9:14 AM, Jacob Barhak
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CAM_y+3R6HbOh5RC2YVG9o3B6Z_4aunhSOHpEMY3m1bZxLFvtQA@mail.gmail.com">
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<div dir="ltr">Thanks James,
<div><br>
</div>
<div>Unless there are any last minute objections, I will submit
the paper this holiday weekend.</div>
<div><br>
</div>
<div>I will update you all on progress.</div>
<div><br>
</div>
<div>Hopefully it will be smooth.</div>
<div><br>
</div>
<div>Happy thanksgiving.</div>
<div><br>
</div>
<div> Jacob</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Wed, Nov 24, 2021 at 8:09
AM Faeder, James R <<a href="mailto:faeder@pitt.edu"
moz-do-not-send="true" class="moz-txt-link-freetext">faeder@pitt.edu</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 style="overflow-wrap: break-word;" lang="EN-US">
<div class="gmail-m_-816442842227439560WordSection1">
<p class="MsoNormal">APPROVE. I apologize for the delay.
These messages were being routed to a folder that I do
not check frequently. I finally found out from a
voicemail message. Thanks everyone for the efforts you
have put into this work and especially Jacob for all of
the work organizing on top of it. Good luck with the
submission and Happy Thanksgiving!</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">Jim</p>
<p class="MsoNormal"> </p>
<div
style="border-right:none;border-bottom:none;border-left:none;border-top:1pt
solid rgb(181,196,223);padding:3pt 0in 0in">
<p class="MsoNormal" style="margin-bottom:12pt"><b><span
style="font-size:12pt;color:black">From:
</span></b><span style="font-size:12pt;color:black">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>Date: </b>Wednesday, November 24, 2021 at 6:47
AM<br>
<b>To: </b>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>>,
Jonathan Karr <<a
href="mailto:jonrkarr@gmail.com" target="_blank"
moz-do-not-send="true"
class="moz-txt-link-freetext">jonrkarr@gmail.com</a>>,
William Waites <<a href="mailto:wwaites@ieee.org"
target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">wwaites@ieee.org</a>>,
Tingting Tang <<a href="mailto:ttang2@sdsu.edu"
target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">ttang2@sdsu.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>>,
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>>,
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>>,
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>>,
Thompson, Robin <<a
href="mailto:Robin.N.Thompson@warwick.ac.uk"
target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">Robin.N.Thompson@warwick.ac.uk</a>><br>
<b>Subject: </b>Re: [Vp-integration-subgroup]
[Vp-reproduce-subgroup] Shayn Peirce-Cottler via
Frontiers: Manuscript</span></p>
</div>
<div>
<p class="MsoNormal">Greetings James Faeder,</p>
<div>
<p class="MsoNormal"> </p>
</div>
<div>
<p class="MsoNormal">You are the last one that needs
to Approve. DISAPPROVE , or ABSTAIN from submission
of the paper. </p>
</div>
<div>
<p class="MsoNormal"> </p>
</div>
<div>
<p class="MsoNormal">I apologize if you already sent a
response yet I have not located any response from
you- it may be my error, yet I need your public
response before I can continue to submit the paper.</p>
</div>
<div>
<p class="MsoNormal"> </p>
</div>
<div>
<p class="MsoNormal">17 of us already
approved submission and you are the last one on my
list.</p>
</div>
<div>
<p class="MsoNormal"> </p>
</div>
<div>
<p class="MsoNormal">I tried to contact your
department in the last few days and left voice
messages to your administrators since I could not
locate your direct phone. </p>
</div>
<div>
<p class="MsoNormal"> </p>
</div>
<div>
<p class="MsoNormal">I will really appreciate it if
someone can contact you and make sure you get this
message.</p>
</div>
<div>
<p class="MsoNormal"> </p>
</div>
<div>
<p class="MsoNormal">I really hope we get an answer so
I can process the paper by thanksgiving weekend.</p>
</div>
<div>
<p class="MsoNormal"> </p>
</div>
<div>
<p class="MsoNormal"> Jacob</p>
</div>
<div>
<p class="MsoNormal"> </p>
</div>
<div>
<p class="MsoNormal"> </p>
</div>
</div>
<p class="MsoNormal"> </p>
<div>
<div>
<p class="MsoNormal">On Fri, Nov 19, 2021 at 12:22 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:</p>
</div>
<blockquote
style="border-top:none;border-right:none;border-bottom:none;border-left:1pt
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6pt;margin-left:4.8pt;margin-right:0in">
<div>
<p class="MsoNormal">Thanks John, Hi James Faedar, </p>
<div>
<p class="MsoNormal"> </p>
</div>
<div>
<p class="MsoNormal">John, with your approval
below we only need James Faedar to respond so I
can proceed. </p>
</div>
<div>
<p class="MsoNormal"> </p>
</div>
<div>
<p class="MsoNormal">Can someone contact him
to make sure he saw this correspondence? He
should receive these messages, yet if someone is
in contact with him regularly, please ask him to
respond so we can move on.</p>
</div>
<div>
<p class="MsoNormal"> </p>
</div>
<div>
<p class="MsoNormal">One last thing before
submission. If there is anyone who thinks this
paper should not be published, I would ask them
to write to this mailing list publicly - if
there is any error or omission that anyone
thinks is important, we want to know about it
before submitting the article. This request is
public and not targeted at the authors - if
there is something we missed, we want to know it
before submission.</p>
</div>
<div>
<p class="MsoNormal"> </p>
</div>
<div>
<p class="MsoNormal">Hopefully James Feedar will
respond quickly and there will be no public
objection and we can get this paper published
quickly.</p>
</div>
<div>
<p class="MsoNormal"> </p>
</div>
<div>
<p class="MsoNormal"> Jacob</p>
</div>
<div>
<p class="MsoNormal"> </p>
</div>
<div>
<p class="MsoNormal"> </p>
</div>
</div>
<p class="MsoNormal"> </p>
<div>
<div>
<p class="MsoNormal">On Thu, Nov 18, 2021 at 4:34
PM 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>>
wrote:</p>
</div>
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<div>
<p class="MsoNormal" style="margin-bottom:12pt">I
approve submission.</p>
<div>
<p class="MsoNormal">Typed with two thumbs on
my iPhone. (757) 318-0671</p>
<div>
<p class="MsoNormal"> </p>
</div>
<div>
<div>
<p class="MsoNormal">“Upon this gifted
age, in its dark hour,</p>
</div>
<div>
<p class="MsoNormal">Rains from the sky a
meteoric shower</p>
</div>
<div>
<p class="MsoNormal">Of facts . . . they
lie unquestioned, uncombined.</p>
</div>
<div>
<p class="MsoNormal">Wisdom enough to
leech us of our ill</p>
</div>
<div>
<p class="MsoNormal">Is daily spun; but
there exists no loom</p>
</div>
<div>
<p class="MsoNormal">To weave it into
fabric.”</p>
</div>
<div>
<p class="MsoNormal"> </p>
</div>
<div>
<p class="MsoNormal">–Edna St. Vincent
Millay,</p>
</div>
<div>
<p class="MsoNormal"> </p>
</div>
<div>
<p class="MsoNormal"> </p>
</div>
</div>
</div>
<div>
<p class="MsoNormal"
style="margin-bottom:12pt"><br>
On Nov 17, 2021, at 22:04, 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:</p>
</div>
<div>
<p class="MsoNormal"></p>
<div>
<p class="MsoNormal">Hi James Faedar, Hi
John Rice,</p>
<div>
<p class="MsoNormal"> </p>
</div>
<div>
<p class="MsoNormal">Please check the
manuscript and declare by REPLY ALL if
you APPROVE, DISAPPROVE or ABSTAIN.</p>
</div>
<div>
<p class="MsoNormal"> </p>
</div>
<div>
<p class="MsoNormal">James, if you
responded and I did not get the email, I
apologize - there are some
communication hiccups occasionally. Yet
I need your public approval to proceed
and use your name.</p>
</div>
<div>
<p class="MsoNormal"> </p>
</div>
<div>
<p class="MsoNormal">John, I know you
allowed us to send the paper, yet you
need to be specific and declare if you
want to be included as an Author or just
moved to acknowledgements. You did have
a major contribution, so I hope you will
APPROVE. </p>
</div>
<div>
<p class="MsoNormal"> </p>
</div>
<div>
<p class="MsoNormal">Once I have your
answer I can proceed. Hopefully you will
both APPROVE quickly.</p>
</div>
<div>
<p class="MsoNormal"> </p>
</div>
<div>
<p class="MsoNormal"> Jacob</p>
</div>
</div>
<p class="MsoNormal"> </p>
<div>
<div>
<p class="MsoNormal">On Wed, Nov 17, 2021
at 3:02 PM 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:</p>
</div>
<blockquote
style="border-top:none;border-right:none;border-bottom:none;border-left:1pt
solid rgb(204,204,204);padding:0in 0in 0in
6pt;margin-left:4.8pt;margin-right:0in">
<div>
<p><span
style="font-size:10pt;font-family:Verdana,sans-serif">Hi
Jacob and all,</span></p>
<p><span
style="font-size:10pt;font-family:Verdana,sans-serif">I
approve the submission of the
manuscript. </span></p>
<p><span
style="font-size:10pt;font-family:Verdana,sans-serif">Please
update the citation Tiwari et 2020
Preprint to </span></p>
<p><span
style="font-size:10pt;font-family:Verdana,sans-serif">Tiwari
K, Kananathan S, Roberts MG, Meyer
JP, Sharif Shohan MU, Xavier A,
Maire M, Zyoud A, Men J, Ng S,
Nguyen TVN, Glont M, Hermjakob H,
Malik-Sheriff RS. Reproducibility in
systems biology modelling. Mol Syst
Biol. 2021 Feb;17(2):e9982. doi:
10.15252/msb.20209982. PMID:
33620773; PMCID: PMC7901289.</span></p>
<p><span
style="font-size:10pt;font-family:Verdana,sans-serif">Also
my name and affiliation below</span></p>
<p><span
style="font-size:10pt;font-family:Verdana,sans-serif">Rahuman
S. <u>
Malik Sheriff</u></span></p>
<p><span
style="font-size:10pt;font-family:Verdana,sans-serif">European
Molecular Biology Laboratory,
European Bioinformatics Institute
(EMBL-EBI), Wellcome Genome Campus,
Hinxton, Cambridge, UK</span></p>
<p><span
style="font-size:10pt;font-family:Verdana,sans-serif"> </span></p>
<p><span
style="font-size:10pt;font-family:Verdana,sans-serif">Thanks
for pushing this work forward</span></p>
<p><span
style="font-size:10pt;font-family:Verdana,sans-serif">Best
regards</span></p>
<p><span
style="font-size:10pt;font-family:Verdana,sans-serif">Sheriff</span></p>
<p><span
style="font-size:10pt;font-family:Verdana,sans-serif"> </span></p>
<p
id="gmail-m_-816442842227439560gmail-m_-1664506982640354478gmail-m_2983802147113687999gmail-m_3056082822452168104gmail-m_5776642796092585345reply-intro"><span
style="font-size:10pt;font-family:Verdana,sans-serif">On 2021-11-17
18:58, Jonathan Karr wrote:</span></p>
<blockquote
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5pt;margin-left:0in;margin-right:0in">
<div
id="gmail-m_-816442842227439560gmail-m_-1664506982640354478gmail-m_2983802147113687999gmail-m_3056082822452168104gmail-m_5776642796092585345replybody1">
<div>
<p class="MsoNormal"><span
style="font-size:10pt;font-family:Verdana,sans-serif">Hi
Jacob,
</span></p>
<div>
<p class="MsoNormal"><span
style="font-size:10pt;font-family:Verdana,sans-serif"> </span></p>
</div>
<div>
<p class="MsoNormal"><span
style="font-size:10pt;font-family:Verdana,sans-serif">Thank
you again for spearheading
this effort.</span></p>
<div>
<p class="MsoNormal"><span
style="font-size:10pt;font-family:Verdana,sans-serif"> </span></p>
</div>
<div>
<p class="MsoNormal"><span
style="font-size:10pt;font-family:Verdana,sans-serif">I
approve the submission. I
think the paper organizes
a variety of important
issues toward more
credible models, and the
content is sound.</span></p>
<div>
<p class="MsoNormal"><span
style="font-size:10pt;font-family:Verdana,sans-serif"> </span></p>
</div>
<div>
<p class="MsoNormal"><span
style="font-size:10pt;font-family:Verdana,sans-serif">My
affiliation is
Department of Genetics
and Genomic Sciences,
Icahn School of Medicine
at Mount Sinai, New
York, NY, USA.</span></p>
</div>
<div>
<p class="MsoNormal"><span
style="font-size:10pt;font-family:Verdana,sans-serif"> </span></p>
</div>
<div>
<p class="MsoNormal"><span
style="font-size:10pt;font-family:Verdana,sans-serif">As
others have mentioned, I
think the paper would be
more impactful with
further editing to make
the paper easier to
read:</span></p>
</div>
<div>
<ul type="disc">
<li class="MsoNormal">
<span
style="font-size:10pt;font-family:Verdana,sans-serif">More
clearly articulate the
goals/motivation for
more credible models</span></li>
<li class="MsoNormal">
<span
style="font-size:10pt;font-family:Verdana,sans-serif">Be
more concise and
focused</span></li>
<li class="MsoNormal">
<span
style="font-size:10pt;font-family:Verdana,sans-serif">Remove
redundancies by
grouping related text</span></li>
<li class="MsoNormal">
<span
style="font-size:10pt;font-family:Verdana,sans-serif">Fill
in the gaps in logic
in the introduction
with more transitions,
less extraneous
information, and/or a
brief outline.</span></li>
<li class="MsoNormal">
<span
style="font-size:10pt;font-family:Verdana,sans-serif">Change
the title of the
"Utility of models"
section to something
like "Challenges with
using multiscale
models" (James'
suggestion)</span></li>
<li class="MsoNormal">
<span
style="font-size:10pt;font-family:Verdana,sans-serif">Order
the "Utility of
models" subsections to
be easier to follow,
perhaps from model
construction through
to reuse</span></li>
<li class="MsoNormal">
<span
style="font-size:10pt;font-family:Verdana,sans-serif">Rephrase
the titles of the
"Utility of models"
subsections to focus
on opportunities for
improvement rather
than current problems</span></li>
</ul>
</div>
<div>
<p class="MsoNormal"><span
style="font-size:10pt;font-family:Verdana,sans-serif">Regards,</span></p>
</div>
<div>
<p class="MsoNormal"><span
style="font-size:10pt;font-family:Verdana,sans-serif">Jonathan</span></p>
</div>
</div>
</div>
</div>
<p class="MsoNormal"><span
style="font-size:10pt;font-family:Verdana,sans-serif"> </span></p>
<div>
<div>
<p class="MsoNormal"><span
style="font-size:10pt;font-family:Verdana,sans-serif">On
Wed, Nov 10, 2021 at 11:25
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:</span></p>
</div>
<blockquote
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<div>
<p class="MsoNormal"><span
style="font-size:10pt;font-family:Verdana,sans-serif">Thanks
to all contributors who
answered,
</span></p>
<div>
<p class="MsoNormal"><span
style="font-size:10pt;font-family:Verdana,sans-serif"> </span></p>
</div>
<div>
<p class="MsoNormal"><span
style="font-size:10pt;font-family:Verdana,sans-serif">Most
contributors approved by
now.</span></p>
</div>
<div>
<p class="MsoNormal"><span
style="font-size:10pt;font-family:Verdana,sans-serif"> </span></p>
</div>
<div>
<p class="MsoNormal"><span
style="font-size:10pt;font-family:Verdana,sans-serif">James
and Wiliam, I am not
sure how many more
revisions there will be
for this publication. I
did not add several
important references of
my own in this revision.
Frankly I wanted to keep
reference changes to a
minimum and kept it
as close as possible to
the origin . However, we
are transferring the
paper to the publisher
under CC license, so it
will not be hard to
create another derived
version with all sorts
of additions and
modifications in the
future where people can
edit it as they see fit
and add whatever
references they want -
so after it gets
published you can
continue working on
other versions as you
see fit. For now I ask
we focus on publishing
this version alone and I
really hope the editors
will not put us through
another revision round
since it makes no sense
at this point - any
change is
not substantial compared
to what we have already
and any delay is more
damaging than
productive.</span></p>
</div>
<div>
<p class="MsoNormal"><span
style="font-size:10pt;font-family:Verdana,sans-serif"> </span></p>
</div>
<div>
<p class="MsoNormal"><span
style="font-size:10pt;font-family:Verdana,sans-serif">To
be productive I ask that
the following people who
did not answer so far
take the time to
APPROVE, DISAPPROVE, or
ABSTAIN.:</span></p>
</div>
<div>
<p class="MsoNormal"><span
style="font-size:10pt;font-family:Verdana,sans-serif">Robin
Thompson</span></p>
</div>
<div>
<p class="MsoNormal"><span
style="font-size:10pt;font-family:Verdana,sans-serif">James
R. Faeder</span></p>
</div>
<div>
<p class="MsoNormal"><span
style="font-size:10pt;font-family:Verdana,sans-serif">Jonathan
Karr<br>
Rahuman Sheriff</span></p>
</div>
<div>
<p class="MsoNormal"><span
style="font-size:10pt;font-family:Verdana,sans-serif">John
Rice</span></p>
</div>
<div>
<p class="MsoNormal"><span
style="font-size:10pt;font-family:Verdana,sans-serif"> </span></p>
</div>
<div>
<div>
<p class="MsoNormal"><span
style="font-size:10pt;font-family:Verdana,sans-serif">John Rice - thanks
for your support, yet
you will have to be
specific: You can
either choose APPROVE
or ABSTAIN - both of
these options will
move the paper
forwards. APPROVE will
add your name to the
list of authors with
all responsibilities
and privileges listed
or implied , ABSTAIN
will put you in
acknowledgements
without any
obligation. So John,
please choose if you
want your name on the
paper or not in this
specific version - any
decision you make will
be ok. </span></p>
</div>
<div>
<p class="MsoNormal"><span
style="font-size:10pt;font-family:Verdana,sans-serif"> </span></p>
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<div>
<p class="MsoNormal"><span
style="font-size:10pt;font-family:Verdana,sans-serif">I hope we can
father all support
quickly so I can move
forward and submit the
paper.</span></p>
</div>
</div>
<div>
<p class="MsoNormal"><span
style="font-size:10pt;font-family:Verdana,sans-serif"> </span></p>
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<p class="MsoNormal"><span
style="font-size:10pt;font-family:Verdana,sans-serif">
Jacob</span></p>
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<p class="MsoNormal"><span
style="font-size:10pt;font-family:Verdana,sans-serif"> </span></p>
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</div>
<p class="MsoNormal"><span
style="font-size:10pt;font-family:Verdana,sans-serif"> </span></p>
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<div>
<p class="MsoNormal"><span
style="font-size:10pt;font-family:Verdana,sans-serif">On
Tue, Nov 9, 2021 at 5:46
AM William Waites <<a
href="mailto:wwaites@ieee.org" target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">wwaites@ieee.org</a>>
wrote:</span></p>
</div>
<blockquote
style="border-top:none;border-right:none;border-bottom:none;border-left:1pt
solid
rgb(204,204,204);padding:0in
0in 0in
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<p class="MsoNormal"><span
style="font-size:10pt;font-family:Verdana,sans-serif">I'm
just chasing down
references for use in
another context and I
notice that the Ke et al
paper is still a
pre-print after more
than a year. There is no
problem in my opinion
citing preprints but it
is suspect in this case:
there's been a ton of
work on SARS-CoV-2
infectiousness, why
didn't this get
published? Probably not
best to rely on it as an
example of practice.
Perhaps to fix on
revision.<br>
<br>
-w<br>
<br>
_______________________________________________<br>
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</blockquote>
</div>
</blockquote>
</div>
</div>
</blockquote>
<p><span
style="font-size:10pt;font-family:Verdana,sans-serif"> </span></p>
</div>
</blockquote>
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</blockquote>
</div>
</blockquote>
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</blockquote>
</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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