<div dir="ltr">So Tomas,<div><br></div><div>Before starting editing, to save time it is important that we establish what is going to be edited - I voiced my concern over the large deletions in Johns version more than once - there is a real problem there - many authors may be completely eliminated in the name of style - I don't like it - so John has to decide how he spends his time - first just define what sections you want to contribute in - this will help John comprehend the magnitude of the task - he promised editorial services for two weeks - so before we start wasting time with edits, lets see the entire picture. </div><div><br></div><div>Tomas, what you like may be something I dislike or something I do not care about, and eventually we all have to agree - and there are about 20 of us - this is a legal requirement for copyright transfer. The task here is time consuming and I do not envy John and it is important we all help him realize the task before he spends time on it.</div><div><br></div><div>And please reply to all - there are some contributors that are listed in only one list and some that may not have signed up - they all need to be aware of what we are doing. </div><div><br></div><div>Hopefully you identified the sections you want to contribute to - please state those to move this forward quicker.</div><div><br></div><div> Jacob</div><div><br></div><div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Tue, May 18, 2021 at 9:08 AM Tomas Helikar <<a href="mailto:thelikar2@unl.edu">thelikar2@unl.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>
<p>I suggest we use John's version - the flow has begun to improve
there and he'll be bringing the content over from the submitted
version.</p>
<p>At the top of each of the other version, there should be big red
"DO NOT EDIT THIS VERSION" and a link to John's version that will
be the running draft where our efforts should focus.</p>
<p>Best,<br>
</p>
<div>
<div style="line-height:16px;margin:6px 0px;padding:8px;border-top:1px dotted rgb(174,177,166);border-bottom:1px dotted rgb(174,177,166);font-size:11px;color:grey">
<font size="2.5px;" color="#0049FF">Tomas
Helikar, Ph.D.</font> <br>
Susan J. Rosowski Associate Professor <br>
Department of Biochemistry | University of Nebraska-Lincoln <br>
m: <a href="callto:402-547-8904" style="color:rgb(0,136,204)" target="_blank">402-547-8904</a> | o: <a href="callto:402-472-3530" style="color:rgb(0,136,204)" target="_blank">402-472-3530</a><br>
<a href="http://www.postbox-inc.com" style="border-bottom:1px dotted rgb(170,170,170);color:rgb(0,136,204);text-decoration:none" target="_blank">www.helikarlab.org</a> | <a href="http://helikarlab.org" style="border-bottom:1px dotted rgb(170,170,170);color:rgb(0,136,204);text-decoration:none" target="_blank">cellcollective.org</a><br>
twitter: <a href="http://twitter.com/helikarlab" style="border-bottom:1px dotted rgb(170,170,170);color:rgb(0,136,204);text-decoration:none" target="_blank">@helikarlab</a>, <a href="http://twitter.com/biocollective" style="border-bottom:1px dotted rgb(170,170,170);color:rgb(0,136,204);text-decoration:none" target="_blank">@biocollective</a>
</div>
</div>
<div>On 5/18/21 9:05 AM, Jacob Barhak wrote:<br>
</div>
<blockquote type="cite">
<div>
<font face="sans-serif" color="#FF6347">Non-NU Email</font>
<hr>
</div>
<div dir="ltr">Yes Sheriff,
<div><br>
</div>
<div>You have a good point. Here are the versions of the paper
that I recall.
<div><br>
</div>
<div>1. The version we all approved - I suggest we use this: <a href="https://urldefense.proofpoint.com/v2/url?u=https-3A__docs.google.com_document_d_1IMEgmdNkx-2DEsnOjGuegpenSIMmKIkK00Lc8Gred3QxM_edit-3Fusp-3Dsharing&d=DwMFaQ&c=Cu5g146wZdoqVuKpTNsYHeFX_rg6kWhlkLF8Eft-wwo&r=ct8WBL42ANwALp5sfmoKGqugGgF8k0-4cJjYaO-gSGg&m=YDnTfj5kBWpXRZrktQP7smDeXePfRkoZxmwhpBzEh8c&s=FanQUPp95Lqx2G9Ojb6SLVQzkZS6mrqBIt_W-zgW8_Q&e=" target="_blank">https://docs.google.com/document/d/1IMEgmdNkx-EsnOjGuegpenSIMmKIkK00Lc8Gred3QxM/edit?usp=sharing</a></div>
<div>2. John Gennari version: <a href="https://urldefense.proofpoint.com/v2/url?u=https-3A__docs.google.com_document_d_1VvyP3YZQdQYjj8DFKOpQ4pn-5F0pdDGgiT_edit-3Fts-3D60a294c2&d=DwMFaQ&c=Cu5g146wZdoqVuKpTNsYHeFX_rg6kWhlkLF8Eft-wwo&r=ct8WBL42ANwALp5sfmoKGqugGgF8k0-4cJjYaO-gSGg&m=YDnTfj5kBWpXRZrktQP7smDeXePfRkoZxmwhpBzEh8c&s=7h_7qlaNYzcnYViiFjrrVhBADdtnSQ8eh_Wg_vxmY4I&e=" target="_blank">https://docs.google.com/document/d/1VvyP3YZQdQYjj8DFKOpQ4pn_0pdDGgiT/edit?ts=60a294c2</a></div>
<div>3. Rahuman Sheriff version: <a href="https://urldefense.proofpoint.com/v2/url?u=https-3A__docs.google.com_document_d_1Ag4ipuybjtthxgV0YjXqYP7AwwNSYcWh_edit&d=DwMFaQ&c=Cu5g146wZdoqVuKpTNsYHeFX_rg6kWhlkLF8Eft-wwo&r=ct8WBL42ANwALp5sfmoKGqugGgF8k0-4cJjYaO-gSGg&m=YDnTfj5kBWpXRZrktQP7smDeXePfRkoZxmwhpBzEh8c&s=yaBZO6lyEXDKmMXfrDPDqy10sDgl0FQgkFFMO3_iShg&e=" target="_blank">https://docs.google.com/document/d/1Ag4ipuybjtthxgV0YjXqYP7AwwNSYcWh/edit</a></div>
<div>4. Alexander Kulesza version <a href="https://urldefense.proofpoint.com/v2/url?u=https-3A__drive.google.com_file_d_1U-5FlTHrV6STXWNT3GiCepvsLk1WdYgzN5_view&d=DwMFaQ&c=Cu5g146wZdoqVuKpTNsYHeFX_rg6kWhlkLF8Eft-wwo&r=ct8WBL42ANwALp5sfmoKGqugGgF8k0-4cJjYaO-gSGg&m=YDnTfj5kBWpXRZrktQP7smDeXePfRkoZxmwhpBzEh8c&s=6gQoAQCH7F2WOy92A0xjfWmCMUjW7onPku8BYcIsY9Y&e=" target="_blank">https://drive.google.com/file/d/1U_lTHrV6STXWNT3GiCepvsLk1WdYgzN5/view</a></div>
<div>5. Original Model Reproducibility, Credibility,
Standardization subgroup version <a href="https://urldefense.proofpoint.com/v2/url?u=https-3A__docs.google.com_document_d_1cqwXAjBWEiJZ1tUBnf66QVHdHd2fKq-5FW0py7t4PNVLo_edit-3Fusp-3Dsharing&d=DwMFaQ&c=Cu5g146wZdoqVuKpTNsYHeFX_rg6kWhlkLF8Eft-wwo&r=ct8WBL42ANwALp5sfmoKGqugGgF8k0-4cJjYaO-gSGg&m=YDnTfj5kBWpXRZrktQP7smDeXePfRkoZxmwhpBzEh8c&s=QH6Rgy4why7ib2YGE2T5AA61L68xDE1K-ySoCdKV9ew&e=" target="_blank">https://docs.google.com/document/d/1cqwXAjBWEiJZ1tUBnf66QVHdHd2fKq_W0py7t4PNVLo/edit?usp=sharing</a></div>
<div>6. Original Integration subgroup version: <a href="https://urldefense.proofpoint.com/v2/url?u=https-3A__docs.google.com_document_d_1voUSrSpv3AZlC1T-2DBLa3W4wzHQ5vEdJCVrBbwMUTDiQ_edit-3Fusp-3Dsharing&d=DwMFaQ&c=Cu5g146wZdoqVuKpTNsYHeFX_rg6kWhlkLF8Eft-wwo&r=ct8WBL42ANwALp5sfmoKGqugGgF8k0-4cJjYaO-gSGg&m=YDnTfj5kBWpXRZrktQP7smDeXePfRkoZxmwhpBzEh8c&s=WPFW1D-ECFULPKl8uijQsNA58J5V7TNynIc9OeqCiBE&e=" target="_blank">https://docs.google.com/document/d/1voUSrSpv3AZlC1T-BLa3W4wzHQ5vEdJCVrBbwMUTDiQ/edit?usp=sharing</a></div>
<div><br>
</div>
<div>The last two versions hold the original discussions
before the merge to the version on top. The history of those
contain most contributions - however it will take hours to
figure out where each text portion is located in the new
version. Yet the new version also includes many
modifications. And I believe Hana has another version of
proofs that were never made public - we did this revision
and proof process before, yet I think she sent me her
version privately. I may be mistaken - it was a long time
ago. </div>
<div><br>
</div>
<div>Hopefully this list will help understand the undertaking
and save time.</div>
<div><br>
</div>
<div> Jacob</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Tue, May 18, 2021 at 8:34
AM Rahuman Sheriff <<a href="mailto:sheriff@ebi.ac.uk" target="_blank">sheriff@ebi.ac.uk</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>Dear John G,
<div>Many thanks for the update.</div>
<div>I like the new ordering :)</div>
<div><br>
</div>
<div>@Jacob, as you mentioned you have 6 versions, could you
please add the link to those versions in John G document,
so they are all inked.</div>
<div>I give consent to to rephrase my contribution or even
remove part or all of my contribution to the white paper
and present the ideas in other sections if required to
make the paper coherent and flow well.</div>
<div><br>
</div>
<div>The white paper has a great collections of ideas, I
hope we can get it into a good shape soon for submission
and benefit the scientific community.</div>
<div><br>
</div>
<div>Best regards</div>
<div>Sheriff</div>
<div><br>
</div>
<div><br>
<blockquote type="cite">
<div>On 18 May 2021, at 13:28, James Osborne <<a href="mailto:jmosborne@unimelb.edu.au" target="_blank">jmosborne@unimelb.edu.au</a>>
wrote:</div>
<br>
<div>
<div dir="ltr">Sorry I wasn't on the call Yesterday
(it was 1 am for me so not really achievable).
Looking at the emails looks like it was useful.
<div><br>
</div>
<div>Happy to help how I can, in terms of areas as
someone on the multicellular side of life i'm
probably most use on 3 but happy to support
others.</div>
<div><br>
</div>
<div>James </div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Tue, May 18,
2021 at 3:12 PM John Gennari <<a href="mailto:gennari@uw.edu" target="_blank">gennari@uw.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>
<div>
<div style="font-size:12px;text-align:left;font-family:Helvetica,Arial,sans-serif"><strong>
<table style="width:100%;float:left" cellspacing="0" cellpadding="0" border="0">
<tbody>
<tr>
<td style="color:red"><b>External
email: </b>Please exercise
caution</td>
</tr>
</tbody>
</table>
</strong><br>
</div>
<hr>
</div>
<p><br>
</p>
<p>All: About 9 of us had a lively Zoom meeting
today to chat about the manuscript. By the
end, it was a productive meeting, and I'm
hoping that this email will capture some key
outputs from the meeting. I apologize if I
said some things that were a bit
"inflammatory". Obviously 2 years would be
much too long to get this paper out-the door.
<br>
</p>
<p>I saw two outcomes. First, we had some nice
ideas and discussion about re-ordering
(initiated by Tomas Helikar). In the below,
I'm going to propose one possible ordering,
but this is certainly a work-in-progress. The
reason that I think ordering is important is
that it will give us a much better ability to
write a strong concluding section, where we
talk about themes and the larger arc of our
ideas.
<br>
</p>
<p>Second, we agreed that we should nominate
"point persons" who would be in charge of at
least the initial cut of each of the
subsections. As Jacob pointed out, this
information should be easy to get from older
email and history of the development of the
paper. During the zoom meeting, we associated
some co-authors with some sections, but our
coverage wasn't perfect (see challenge #12).
Hopefully people will "stand up" and admit
that some section of text is theirs.
<br>
</p>
<p>So in the below, I include the original title
of the section, a few words about the content
of that section, and then a name (or several
names) of co-authors who will be the "point
person" to make sure that the appropriate
content is included. Obviously, all co-authors
can and should chime in on any part of the
text, but the point person should make sure
that the key ideas are included.
<br>
</p>
<p>The basic ordering idea for the dozen
challenges was to follow the life-cycle of
model development, execution, sharing and
integration, and eventually implementation.
So...
<br>
</p>
<p>*********************************************<br>
</p>
<p><b>(1) "</b><b>Data</b><b> and measurement
definitions</b>". Before you can build a
model, you must have data. So data
availability and measurement standards is the
place to start.
<br>
</p>
<p><b>People: </b>Hana D, Jacob B<br>
</p>
<p><b>(2) "</b><b>The variety of modeling
languages</b>" This is about the choice of
modeling languages, such as using SBML,
CellML, or Matlab. As I said on the phone
call, this is sort of about "syntax"--how do
you write down your model?
<br>
</p>
<p><b>People:</b> John G, Jon K, Rahuman S.</p>
<p><b>(3) "</b><b>The variety of modeling
paradigms and scales"</b><b> </b>Separately
from modeling syntax, we must acknowledge
modeling paradigms with very different
semantics. Some clear examples are PDEs versus
ODEs versus rule-based systems (and obviously
one can combine these). Certainly semantics
might impact syntax (the prior challenge), in
that certain modeling language might be
appropriate only for some paradigms.</p>
<p>People: James G, Eric F (?) <br>
</p>
<p><b>(4) "</b><b>Units standardization</b>" A
common reason that models are not reproducible
are errors in units, or misunderstanding about
units, or simply a lack of information about
units.
<br>
</p>
<p>People: Jacob B, Hana D</p>
<p><b>(5) "</b><b>A lack of annotations in
models</b>". Once researchers publish
models, they must annotate the model so that
others can understand it. Quality annotation
is essential for both search and
reproducibility.
<br>
</p>
<p>People: John G.</p>
<p><b>(6) "</b><b>Models are hard to locate"</b>
If your goal is to reproduce, understand and
possibly reuse or integrate some other model,
one must first find that model. This requires
annotation (prior section) and repositories
(Physiome Model Repository, BioModels) and
search platforms (ModeleXchange). <br>
</p>
<p>People: Jon K, John G.</p>
<p><b>(7) "</b><b>Common platforms to execute
models" </b>A model is pretty worthless as
a static object. For folk to understand and
reproduce models they must be executable.
Alas, there is no single or consistent way of
executing a model -- and of course, this
interacts direction with section #2 and #3,
above: Execution platforms are usually only
for one modeling paradigm, and often for one
modeling language. The BioSimulators work goes
here.</p>
<p>People: Jon K. <br>
</p>
<p><b>(8) "</b><b>Credibility </b><b>and
validity of models</b>" Once a model is
published, how do folk know it is right? Model
validation is a big topic and challenge.
Credibility follows (in part) from validation,
but also requires transparency and
reproducibility, etc. <br>
</p>
<p>People: John Rice, Jon K, Jacob B</p>
<p><b>(9) "</b><b>Environments to adapt and
integrate models</b>" As I see it, one of
the end-targets for this manuscript is to
better enable model integration, to build
better models. There are many challenges with
the task of integrating two (or more) models.
(One that has recently been discussed is that
even if model A and model B are valid and
correct, there is no guarantee that the
combined model A+B is correct. I liked what
William Waites and Katherine Morse posted on
this subject.) This section is where SBML-comp
and SemGen environments can be mentioned.</p>
<p>People: John G.</p>
<p>(<b>10) "Challenges for stochastic models" </b>Special
challenges specific to stochaistic modeling.
An obvious point to mention is repeatability
-- stochastic models don't necessarily give
the same results with the same inputs.
<br>
</p>
<p>People: James G., Eric F<br>
</p>
<p><b>(11) "Licensing barriers" </b>Issues
around "open source" and CC0 licensing.
<br>
</p>
<p>People: Jacob B<br>
</p>
<p><b>(12) "Barriers to model implementations
and applications"</b> (I might suggest this
be re-phrased for better clarity). What this
section should discuss are challenges is
getting a community to actually use models for
"real-world" applications or decision making.
This is more of a cultural/societal challenge,
and thus seems like a nice big-picture way to
end.
<br>
</p>
<p><b>People: ?? </b>I don't have any names
here...<br>
</p>
<p>*********************************************</p>
<p>We didn't really talk much about it in the
Zoom meeting, but there have been ideas tossed
around about a "baker's dozen", i.e., adding a
13th challenge. We could also potentially
merge some of the above.
<br>
</p>
<p class="MsoNormal">The "point persons" listed
above is obviously a subset of co-authors.
That's fine and appropriate. Just for
transparency, I follow what I think is pretty
standard policy for authorship issues, and
nicely summarized by the<span style="font-family:Helvetica,sans-serif">
International Committee of Medical Journal
Editors (ICMJE); see 2019 updated document
at
</span><a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__www.icmje.org_icmje-2Drecommendations.pdf&d=DwMFaQ&c=Cu5g146wZdoqVuKpTNsYHeFX_rg6kWhlkLF8Eft-wwo&r=ct8WBL42ANwALp5sfmoKGqugGgF8k0-4cJjYaO-gSGg&m=YDnTfj5kBWpXRZrktQP7smDeXePfRkoZxmwhpBzEh8c&s=l29d3A9PItAUv4N0WkCuREqes9tSKSW7sk5GDEo6VBA&e=" target="_blank">http://www.icmje.org/icmje-recommendations.pdf</a>
(Or see, below my signature, a summary of the
key points of this document).
<br>
</p>
<p class="MsoNormal">Finally, I've made the
document editable by all at <a href="https://urldefense.proofpoint.com/v2/url?u=https-3A__docs.google.com_document_d_1VvyP3YZQdQYjj8DFKOpQ4pn-5F0pdDGgiT_edit-3Fts-3D60a294c2&d=DwMFaQ&c=Cu5g146wZdoqVuKpTNsYHeFX_rg6kWhlkLF8Eft-wwo&r=ct8WBL42ANwALp5sfmoKGqugGgF8k0-4cJjYaO-gSGg&m=YDnTfj5kBWpXRZrktQP7smDeXePfRkoZxmwhpBzEh8c&s=7h_7qlaNYzcnYViiFjrrVhBADdtnSQ8eh_Wg_vxmY4I&e=" target="_blank">
https://docs.google.com/document/d/1VvyP3YZQdQYjj8DFKOpQ4pn_0pdDGgiT/edit?ts=60a294c2</a>
<br>
<span style="font-family:Helvetica,sans-serif"></span></p>
<div><br>
</div>
<p>-John G.<br>
==========================================================================<br>
Associate Professor & Graduate Program
Director <a href="mailto:gennari@uw.edu" target="_blank">
<gennari@uw.edu></a><br>
Dep't of Biomedical Informatics
and telephone:206-616-6641<br>
Medical Education, box
358047 <br>
University of Washington<br>
Seattle, WA 98109-4714 <a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__faculty.washington.edu_gennari_&d=DwMFaQ&c=Cu5g146wZdoqVuKpTNsYHeFX_rg6kWhlkLF8Eft-wwo&r=ct8WBL42ANwALp5sfmoKGqugGgF8k0-4cJjYaO-gSGg&m=YDnTfj5kBWpXRZrktQP7smDeXePfRkoZxmwhpBzEh8c&s=7h8T10a2oOTChEmXp5dGxDnAIghmjMroKsXSfcbIH9Y&e=" target="_blank">
http://faculty.washington.edu/gennari/</a><br>
==========================================================================<br>
<br>
</p>
<div><br>
</div>
<p class="MsoNormal" style="margin-left:0.25in"><span style="font-size:10pt;line-height:107%;font-family:Helvetica,sans-serif">The
ICMJE recommends that authorship be based on
the following 4 criteria:
</span></p>
<p style="margin-left:0.75in">
<span style="font-size:10pt;line-height:107%;font-family:Helvetica,sans-serif"><span>1.<span>
</span></span></span><span style="font-size:10pt;line-height:107%;font-family:Helvetica,sans-serif">Substantial
contributions to the conception or design of
the work; or the acquisition, analysis, or
interpretation of data for the work; AND</span></p>
<p style="margin-left:0.75in">
<span style="font-size:10pt;line-height:107%;font-family:Helvetica,sans-serif"><span>2.<span>
</span></span></span><span style="font-size:10pt;line-height:107%;font-family:Helvetica,sans-serif">Drafting
the work or revising it critically for
important intellectual content; AND
</span></p>
<p style="margin-left:0.75in">
<span style="font-size:10pt;line-height:107%;font-family:Helvetica,sans-serif"><span>3.<span>
</span></span></span><span style="font-size:10pt;line-height:107%;font-family:Helvetica,sans-serif">Final
approval of the version to be published; AND
</span></p>
<p style="margin-left:0.75in">
<span style="font-size:10pt;line-height:107%;font-family:Helvetica,sans-serif"><span>4.<span>
</span></span></span><span style="font-size:10pt;line-height:107%;font-family:Helvetica,sans-serif">Agreement
to be accountable for all aspects of the
work in ensuring that questions related to
the accuracy or integrity of any part of the
work are appropriately investigated and
resolved.</span></p>
<p style="margin-left:0.75in">
<span style="font-size:10pt;line-height:107%;font-family:Helvetica,sans-serif"><br>
</span></p>
<div><br>
</div>
<p><br>
</p>
</div>
</blockquote>
</div>
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