[Population Modeling] Population modeling by examples III collaborative paper
Jacob Barhak
jacob.barhak at gmail.com
Thu May 18 05:56:31 PDT 2017
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/PopulationModelingByExamples3_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-reviews/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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