[Population Modeling] Population modeling by examples III collaborative paper

Jacob Barhak jacob.barhak at gmail.com
Sun Jun 4 10:39:20 PDT 2017 

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-
>> reviews/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
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>
>>>>
>>>
>>
>
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