[Population Modeling] Population modeling by examples III collaborative paper

Jacob Barhak jacob.barhak at gmail.com
Sun Jun 18 00:49:24 PDT 2017 

Greetings Collaborative paper authors,

You all contributed slides to the joint presentations aimed at SummerSim
and later to be passed to the dissemination working group.

I was able to assemble a presentation by editing your slides for format.
You can find the draft online at:

https://simtk.org/docman/view.php/962/4656/SummerSim2017PopMod3_Upload_2017_06_18.pptx

Since I made changes in most slides, I would ask that you examine that your
own slide is in ok and fits well with the other slides.

Unless I get an email from you, I will assume you are ok with any changes I
made and with the final product. I mostly changed, format, titles, and
affiliations to be as standard as possible. So please double check me.

Also, if any of you have specific notes they wish to send me to emphasize
during presentation, please let me know by email and I will add those notes
to the notes of the slides in the next version.

So if you have an explanation of a certain image that will help me present,
please send it my way.

Hopefully you will find it in good shape.

           Jacob


On Sun, Jun 4, 2017 at 12:39 PM, Jacob Barhak <jacob.barhak at gmail.com>
wrote:

> Greeting  Collaborative paper authors,
>
> You can find the final submitted version of the collaborative paper in:
>
> https://simtk.org/docman/view.php/962/4654/PopulationModelingByExamples3_
> Submit_2017_06_04.docx
>
> I signed the following copyright form on your behalf:
> http://scs.org/wp-content/uploads/2016/10/AuthorsKitForms-
> TransferOfCopyrightAuthorCert.pdf
>
> The paper will be published by ACM Digital Library and IEEE - the latter
> is new so I know little details, yet I will send you a DOI when I know it.
>
> I would like to remind you to send in your slides. Quite a few of you have
> sent one slide, yet I am still waiting for many more slides - if you have
> not sent one, please do supply your slide as soon as possible to make
> assembly easy.
>
>              Jacob
>
>
>
> On Wed, May 31, 2017 at 1:26 AM, Jacob Barhak <jacob.barhak at gmail.com>
> wrote:
>
>> Greetings Collaborative paper authors,
>>
>> This is a gentle reminder for those who participated in the paper to send
>> one slide for the presentation.
>>
>> Remember this presentation will be circulated beyond SummerSim and online
>> presence. It will be passed to the dissemination working group.
>>
>> It would really help if you can send your slides earlier rather than
>> later.
>>
>>                 Jacob
>>
>>
>>
>> On Fri, May 19, 2017 at 4:23 AM, Jacob Barhak <jacob.barhak at gmail.com>
>> wrote:
>>
>>> Good News Collaborative Paper Authors,
>>>
>>> The paper got accepted for publication. You will find the updated review
>>> here:
>>>
>>> https://groups.google.com/forum/#!topic/public-scientific-re
>>> views/7lr3pCUgZv4
>>>
>>> One reviewer still asks for someone to go over the paper once more for
>>> grammar. I will appreciate a volunteer since I went through it several
>>> times by now and may not see any more grammar issues.
>>>
>>> At this time, we need to start preparing for presentation and I would
>>> ask all contributors to send in one slide to describe their work.
>>>
>>> Can you please send me a presentation with a single Powerpoint slide
>>> representing the work you described in the paper.
>>>
>>> Please use only a single slide using the following template:
>>> https://simtk.org/docman/view.php/962/1893/PopModSlideTempla
>>> te_2015_03_04.pptx
>>>
>>> To reduce traffic, do not send files to the list, instead send a
>>> PowerPoint file directly to me to with the title "SummerSim 2017 Slide"
>>>
>>> Please send slides by 15-June. Yet try not to wait that long - it is only
>>> one slide afterall. I will assemble the presentation and upload it for
>>> your
>>> inspection afterwards.
>>>
>>> The assembled presentation will be presented in SummerSim and eventually
>>> passed to the dissemination working group that will reuse it for teaching,
>>> so please no copyrighted or otherwise restricted material - consider it
>>> creative commons license. We want others to reuse this presentation.
>>>
>>> Try to include only key elements of your work, preferably in graphics.
>>> If you have more than 50 words in the slide,  then it is too long. Better
>>> to have a few pictures and even animation if possible. Remember, my ability
>>> to present your slides is limited, just stick to the very basics. There are
>>> more than 15 of us, so each slide will have less than a minute to be
>>> presented.
>>>
>>> If you must  acknowledge funding, please send exact text in the same
>>> email outside the slide so I can assemble all of these together at the end
>>> of the presentation.
>>>
>>> To get an idea of presentations we had in the past, you can visit:
>>>
>>> https://simtk.org/docman/view.php/962/1897/SpringSim2015PopM
>>> od_Upload_2015_04_10.pptx
>>>
>>> https://simtk.org/docman/view.php/962/1988/PopulationModelli
>>> ngByExamplesII_SummerSim_2016.pdf
>>>
>>> I will really appreciate fast responses here.
>>>
>>>               Jacob
>>>
>>>
>>>
>>> On Thu, May 18, 2017 at 7:56 AM, Jacob Barhak <jacob.barhak at gmail.com>
>>> wrote:
>>>
>>>> Greetings Collaborative paper authors,
>>>>
>>>> A revised version of the paper after second review round was submitted.
>>>> The revised version is available in:
>>>> https://simtk.org/docman/view.php/962/4652/PopulationModelin
>>>> gByExamples3_Submit_2017_05_18.docx
>>>>
>>>> Below is the response for review for the second round:
>>>>
>>>>                Jacob
>>>>
>>>> Second Review Round
>>>>
>>>> ######################################################################
>>>>
>>>> Thomas Woolly
>>>>
>>>> Response: The manuscript has been updated and is much better for it.
>>>> Just to clarify though, my name has an e in Woolley. In terms of the
>>>> rebuttal, I agree that getting everyone together in a digital space is
>>>> difficult as academics are slow to move. However, the authors do seem to
>>>> agree with this general sentiment. Thus, could I ask them to add a sentence
>>>> or two to the discussion section, which specifies the intention of the
>>>> working group to move (slowly) towards a digital platform rather than
>>>> requiring such paper that collates the work. Yours, Thomas
>>>>
>>>>
>>>>
>>>> ####################
>>>>
>>>> RESPONSE:
>>>>
>>>> Apologies for misspelling the name – it was a copy paste error that was
>>>> corrected in the final manuscript.
>>>>
>>>> Thanks for catching it.
>>>>
>>>>
>>>>
>>>> Two sentences were added to the end of the paper indicating that the
>>>> authors started creating sites online on SimTK. In fact, this was a very
>>>> good outcome of the review process. It opens the possibility of more
>>>> centralized mapping of work that will be more accessible that an academic
>>>> paper. Future effort will be directed in this direction – it is beneficial
>>>> to all. If this trend grows the reviewer can claim responsibility for
>>>> starting this – if the reviewer has population modeling colleagues, please
>>>> let them know about this effort. One intention is to disseminate these
>>>> papers with the dissemination working group that just formed under IMAG – a
>>>> centralized web portal would be beneficial.
>>>>
>>>>
>>>>
>>>> ####################
>>>>
>>>>
>>>>
>>>> ######################################################################
>>>>
>>>> Robert Smith?
>>>>
>>>>
>>>>
>>>> Response: I am still uncomfortable with the lack of depth in the Carl
>>>> Asche entry. It's extremely informal, saying things like "Specifically
>>>> busy" as though this were a tossed-out email, rather than an academic work.
>>>> I am sympathetic to the page limit, so just delete this one. Also, the
>>>> reference should be consistent (they're not at present) and different
>>>> authors should be separated by commas.
>>>>
>>>>
>>>>
>>>> One edit: "The order of introduction is arbitrary trying to group by
>>>> common categories as shown in Table 1." I'm not sure I understand this. Is
>>>> it arbitrary or is it trying to group by common categories? I would think
>>>> the latter, so delete the word "arbitrary".
>>>>
>>>> ####################
>>>>
>>>> RESPONSE:
>>>>
>>>> The entry of Carl Asche has been enhanced to present techniques and
>>>> other minor changes were made to fit the text. Since Carl has some
>>>> important work with modeling domain knowledge in diabetes and
>>>> re-hospitalization, it was important to keep his contribution in the paper
>>>> and an effort was made to add depth to it within space limitation. The
>>>> reviewer was probably confused by the misplacement of the reference of
>>>> diabetes survey where hospitalization was mentioned – this was corrected
>>>> and the references were exchanged and made current. The revised text and
>>>> references demonstrate the domain knowledge expertise of the researcher and
>>>> the lab.
>>>>
>>>> Another entry by Dan Yamin was slightly updated by the contributor – so
>>>> now the text better reflect the intentions of the contributor post editing.
>>>>
>>>> Bibliography was inspected and made consistent according to the
>>>> examples in authors kit – in fact reorganization of the bibliography helped
>>>> save some space. With some minor changes in other text, it was possible to
>>>> fit it all in the 12 pages allowed. Other minor changes to the paper were
>>>> made such as the footer in the first page to indicate the conference name.
>>>>
>>>> The order of authors within each category is still arbitrary – yet
>>>> omitting the word “arbitrary” is probably better - the fix was made.
>>>>
>>>> Hopefully the chair and reviewers will accept the paper for publication
>>>> in the current form.
>>>>
>>>> ####################
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> On Fri, May 12, 2017 at 9:07 AM, Jacob Barhak <jacob.barhak at gmail.com>
>>>> wrote:
>>>>
>>>>> Greetings Collaborative paper authors,
>>>>>
>>>>> The reviewers returned response for the response for review.
>>>>>
>>>>> You can find the revised review in the following link:
>>>>>
>>>>> https://groups.google.com/forum/#!topic/public-scientific-re
>>>>> views/7lr3pCUgZv4
>>>>>
>>>>> In a nutshell, the reviewers are asking for some more minor
>>>>> modifications. I will handle those and send the revised version to this
>>>>> list. This gives a last chance to make minor changes. If any author has any
>>>>> important minor changes they wish to make in their text or classification,
>>>>> please let me know by May 15th.
>>>>>
>>>>> And thanks for all those who expressed interest in SimTk projects for
>>>>> your work - I hope more will join to register their projects with the
>>>>> working group page.
>>>>>
>>>>>               Jacob
>>>>>
>>>>>
>>>>>
>>>>> On Mon, May 8, 2017 at 8:19 PM, Jacob Barhak <jacob.barhak at gmail.com>
>>>>> wrote:
>>>>>
>>>>>> Greetings to all collaborative paper authors,
>>>>>>
>>>>>> Following modifications after review, the revised version of the
>>>>>> paper was submitted to SummerSim.
>>>>>>
>>>>>> You can find the revised version in the following link:
>>>>>> https://simtk.org/docman/view.php/962/4649/PopulationModelin
>>>>>> gByExamples3_Submit_2017_05_08.docx
>>>>>>
>>>>>> Below you will find the response to the reviewers.
>>>>>>
>>>>>> Since many changes were made, including many deletions, I will ask
>>>>>> all contributors to look again at their section and let me know if there is
>>>>>> any error introduced by mistake. There is still little time to fix small
>>>>>> things, yet no time for any additions or major modifications.
>>>>>>
>>>>>> Hopefully you will all find it in good shape.
>>>>>>
>>>>>>
>>>>>>               Jacob
>>>>>>
>>>>>>
>>>>>> #################################################################
>>>>>>
>>>>>>
>>>>>>
>>>>>> Response to Review for SummerSim 2017 paper #13 – Population Modeling
>>>>>> by Examples III
>>>>>>
>>>>>> The response is embedded within the review text below.
>>>>>>
>>>>>> ############################
>>>>>>
>>>>>>
>>>>>>
>>>>>> This paper is hard to review and I'm not really sure it should be a
>>>>>> paper at all. The paper is an introduction to the work of multiple people,
>>>>>> at different institutions, around the world. I've no doubt this is very
>>>>>> important as it provides a one stop location for someone to pick the right
>>>>>> contact for their questions, problems and collaborations. However, wouldn't
>>>>>> this better suited to being an updateable webpage? Surely, people's
>>>>>> institutions, interests and email addresses will evolve over time, whereas
>>>>>> this article tries to cement the work in time. Equally, having such a
>>>>>> website would allow people to update their own blurbs, which would ensure
>>>>>> accuracy. Stemming from this fact is the problem that I can't review the
>>>>>> science as I am not an expert in the diverse range of subjects that appear.
>>>>>> Thus, all I am left with is discussing the qualities of the written
>>>>>> language. Here the paper falters, with troubling prose throughout. For
>>>>>> example "the Inter Agency Modeling and Analysis Group (IMAG) (IMAG,
>>>>>> Online), that Is composed of government officers, created working group
>>>>>> that can be composed of researches worldwide." However, all of the textual
>>>>>> errors can be fixed after a good proof read. Critically, such errors should
>>>>>> be the responsibility of the journal's copy editor and not the scientific
>>>>>> reviewer. In summary: a useful idea, which is presented in the wrong
>>>>>> medium. Yours, Thomas Woolly
>>>>>>
>>>>>>
>>>>>>
>>>>>> ####################
>>>>>>
>>>>>> RESPONSE:
>>>>>>
>>>>>> Tomas is absolutely correct. It would be great if all modelers will
>>>>>> centralize in one location and create living web pages with links to
>>>>>> possible web pages. However, it is not straightforward possibly because of
>>>>>> academic culture that is still rewarded by publications. Even collecting
>>>>>> this amount of contributions every year takes a lot of effort. So although
>>>>>> not ideal, it may be the best that can be done to help a group with
>>>>>> overlapping interests come together. And I thank the reviewer for
>>>>>> recognizing the importance of bringing this group together. If you check
>>>>>> the previous papers this group produces you will see some evolution. The
>>>>>> first paper just brought a bunch of modelers together. The second paper
>>>>>> actually added a classification, due to a request by a reviewer. After this
>>>>>> review, the folk in the mailing list were asked if they are willing to join
>>>>>> a web portal and create projects. So in the long run the review may
>>>>>> influence researcher to go in that direction. And following this response a
>>>>>> suggestion was posted to our mailing list for folk to join the SimTk model
>>>>>> repository. However, for the mean time I request that the reviewer accepts
>>>>>> the importance of mapping the field and accepts the revised version.
>>>>>>
>>>>>>
>>>>>>
>>>>>> ####################
>>>>>>
>>>>>>
>>>>>>
>>>>>> Second review:
>>>>>>
>>>>>> 1) It is interesting to read about the multiple areas of population
>>>>>> modeling - microscopic and macroscopic scales, theory and computer
>>>>>> simulation, implications of the modeling results to mathematical modelling
>>>>>> and computer simulation and the areas of biology that are under study.
>>>>>>
>>>>>> ####################
>>>>>>
>>>>>> RESPONSE:
>>>>>>
>>>>>> The reviewer is interested. This is encouraging.
>>>>>>
>>>>>> ####################
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> 2) I suggest that each section start with one clear sentence that
>>>>>> states how their contributors work is related to population modelling. This
>>>>>> was not always clear from the outset.
>>>>>>
>>>>>> ####################
>>>>>>
>>>>>> RESPONSE:
>>>>>>
>>>>>> The paper was revised to include a description sentence for each
>>>>>> entry. This is a good idea.
>>>>>>
>>>>>> ####################
>>>>>>
>>>>>>
>>>>>>
>>>>>> 3) There are several grammar issues. In particular, the tense of the
>>>>>> first sentence is not always the same. The result is that the document
>>>>>> doesn't flow very well.
>>>>>>
>>>>>> ####################
>>>>>>
>>>>>> RESPONSE:
>>>>>>
>>>>>> Yes, the reviewer is correct. This was improved. The text was
>>>>>> originally adapted from multiple contributions that the authors sent to the
>>>>>> mailing list – there was no binding format with regards to the text and the
>>>>>> editor tried to change only what is absolutely needed change to avoid
>>>>>> planting wrong intention during modifications – sometimes authors choose
>>>>>> certain format on purpose. Several correction passes were made and
>>>>>> hopefully the reviewer will be content with the result.
>>>>>>
>>>>>> ####################
>>>>>>
>>>>>>
>>>>>>
>>>>>> 4) I like the table. I suggest that the table be introduced before
>>>>>> the descriptions, providing a Table of Contents type map of the material
>>>>>> that follows.
>>>>>>
>>>>>> ####################
>>>>>>
>>>>>> RESPONSE:
>>>>>>
>>>>>> This is a good idea and the paper was rewritten to reflect this.
>>>>>>
>>>>>> ####################
>>>>>>
>>>>>>
>>>>>>
>>>>>> 5) Perhaps the order of the contributors could be modified to a more
>>>>>> logical sequence. For example, by main area of research focus. If this is
>>>>>> not possible to do, then perhaps alphabetical order would be okay.
>>>>>>
>>>>>> Jane Heffernan York University
>>>>>>
>>>>>>
>>>>>>
>>>>>> ####################
>>>>>>
>>>>>> RESPONSE:
>>>>>>
>>>>>> This change was made to make the map show clusters – the order now is
>>>>>> such that the map is visually pleasing with the most prevalent category of
>>>>>> public health first. Thanks for the suggestion.
>>>>>>
>>>>>> ####################
>>>>>>
>>>>>>
>>>>>>
>>>>>> Third review:
>>>>>>
>>>>>> Although this is an overview of the field, it should still strive to
>>>>>> have academic depth. Publicising the work of contributors is nice, but the
>>>>>> entries should also be informative. This is not always true. In particular,
>>>>>> I suggest either deleting or significantly expanding the entry from Carl
>>>>>> Asche, which adds almost nothing. Overall, it should be streamlined and
>>>>>> sentences written out in full.
>>>>>>
>>>>>> Robert Smith? The University of Ottawa
>>>>>>
>>>>>>
>>>>>>
>>>>>> ####################
>>>>>>
>>>>>> RESPONSE:
>>>>>>
>>>>>> Carl Asche sent some more text that was added, yet adding more text
>>>>>> was a challenge since the paper size limit is 12 pages. So multiple changes
>>>>>> were made to accommodate the reviews – hopefully the revised version is
>>>>>> found in better shape.
>>>>>>
>>>>>> ####################
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Fri, Apr 28, 2017 at 9:58 AM, Jacob Barhak <jacob.barhak at gmail.com
>>>>>> > wrote:
>>>>>>
>>>>>>> Greetings to all collaborative paper authors,
>>>>>>>
>>>>>>> The review for our paper came back and is available on:
>>>>>>>
>>>>>>> https://groups.google.com/forum/#!topic/public-scientific-re
>>>>>>> views/7lr3pCUgZv4
>>>>>>>
>>>>>>> Generally the comments were editorial and grammar related. I will
>>>>>>> prepare a response. Yet I will suggest that all authors take a look.  If
>>>>>>> you want to make changes in your text, please send me your revised text in
>>>>>>> the next week until May 6th. I will appreciate help with reviewing grammar
>>>>>>> of the final version if anyone can volunteer time in a week.
>>>>>>>
>>>>>>> Also, I am interested in the response of the first reviewer Thomas
>>>>>>> Woolly. How many of you are open to creating a free SimTK user
>>>>>>> account and adding your project there so we can create a live paper as
>>>>>>> requested?
>>>>>>>
>>>>>>> The reviewer has a good idea.  Hopefully we can at least partially
>>>>>>> accommodate it.
>>>>>>>
>>>>>>>            Jacob
>>>>>>>
>>>>>>>
>>>>>>> On Apr 18, 2017 12:27 AM, "Jacob Barhak" <jacob.barhak at gmail.com>
>>>>>>> wrote:
>>>>>>>
>>>>>>>> Greeting to all collaborative paper authors,
>>>>>>>>
>>>>>>>> Some of you sent some comments and we had one more entry, so I was
>>>>>>>> able to revised the version before submission. You can find the submitted
>>>>>>>> version in:
>>>>>>>> https://simtk.org/docman/view.php/962/4645/PopulationModelin
>>>>>>>> gByExamples3_Submit_2017_04_17.docx
>>>>>>>>
>>>>>>>> The paper will now go to review and I will get back to you once it
>>>>>>>> is received. - again many thanks for those who contributed.
>>>>>>>>
>>>>>>>>              Jacob
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> On Sun, Apr 16, 2017 at 6:33 AM, Jacob Barhak <
>>>>>>>> jacob.barhak at gmail.com> wrote:
>>>>>>>>
>>>>>>>>> Greetings population modelers,
>>>>>>>>>
>>>>>>>>> With many of you submitting introductions about their work, it was
>>>>>>>>> possible to assemble a third review paper that originated from this group.
>>>>>>>>>
>>>>>>>>> The paper was edited from introductions by the following
>>>>>>>>> contributors.
>>>>>>>>>
>>>>>>>>> Bishal Paudel
>>>>>>>>> Carl Asche
>>>>>>>>> Vivek Balaraman
>>>>>>>>> Michael Thomas
>>>>>>>>> Nathan Geffen
>>>>>>>>> Pawel Topa
>>>>>>>>> Katherine Ogurtsova
>>>>>>>>> Jeff Shrager
>>>>>>>>> Christopher Fonnesbeck
>>>>>>>>> Resit Akcakaya
>>>>>>>>> Matthias Templ
>>>>>>>>> Amit Huppert
>>>>>>>>> Marco Ajelli
>>>>>>>>> Dan Yamin
>>>>>>>>> Leandro Watanabe
>>>>>>>>> Ram Pendyala
>>>>>>>>>
>>>>>>>>> If your name is not on the list and you contributed an
>>>>>>>>> introduction, please contact me - I did my best to assemble all those who
>>>>>>>>> contributed introductions publicly, yet if any changes are needed, now is
>>>>>>>>> the time to correct me.
>>>>>>>>>
>>>>>>>>> For those listed above, please have a look at the paper and if any
>>>>>>>>> fixes are needed, please let me know. I had to cut text and references to
>>>>>>>>> fit space and maintain format - so please double check me. Especially check
>>>>>>>>> your own section and your line in the table that maps the work. Do check I
>>>>>>>>> spelled your name correctly and affiliation is correct.
>>>>>>>>>
>>>>>>>>> The draft paper can be located at the following link:
>>>>>>>>> https://simtk.org/docman/view.php/962/4644/PopulationModelin
>>>>>>>>> gByExamples3_Upload_2017_04_16.docx
>>>>>>>>>
>>>>>>>>> I plan to submit the paper to SummerSim tomorrow April 17th for
>>>>>>>>> review. If anyone sees anything critical before then, let me know in the
>>>>>>>>> next day - otherwise there will be time to make changes as reviews come
>>>>>>>>> back.
>>>>>>>>>
>>>>>>>>> Again, thanks for all those who took the time to contribute.
>>>>>>>>>
>>>>>>>>>                Jacob
>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://simtk.org/pipermail/popmodwkgrpimag-news/attachments/20170618/f361462f/attachment-0001.html>

More information about the PopModWkGrpIMAG-news mailing list