[Population Modeling] PopModWkGrpIMAG-news Digest, Vol 31, Issue 1

Mon May 8 23:00:38 PDT 2017

Thanks Leandro,

The idea the reviewer suggested of creating a live document is pretty
simple to follow if enough of us create SimTk projects. It should not take
more than 20 minutes to create a portal for your project in SimTK.

I suggested SimTk since I know it is easy to create a project there and
that it provides many tools to support a project if you want to have
advanced capabilities.

The process to create a project in SimTK is simple and free:
1) Create an account at : https://simtk.org/account/register.php
2) From your account create a project page with description and submit it
3) Wait until approval
4) Modify your project with multimedia, and sections such as mailing list,
wiki, etc.

When you create such a project, let me know about the link and I will make
sure that the Population modeling working group site contains a link to the
project. There is no need to wait for anyone - if every population modeler
creates a site on their own, I can just collect the links to the project
sites. If you already have a project site, you can create a SimTK wrapper
to gain additional visibility.

By the way, once you have a project in SimTK, your project will be listed
in other modeling directories so you get increased visibility.

Hopefully more of the collaborators in this paper will choose to do so.

              Jacob

On Mon, May 8, 2017 at 11:20 PM, Leandro Watanabe <leandrohw at gmail.com>
wrote:

> Thanks for all the work Jacob and all.
>
> If the idea of publishing softwares on a website moves forward, I would be
> happy to share information about our tool.
>
> Leandro
>
> On Mon, May 8, 2017 at 7:44 PM, John Rice <john.rice at noboxes.org> wrote:
>
>> Nice work Jacob and all!   It does remain and interesting way to
>> communicate to the work of a community which may not yet be ready to box
>> itself into a textual definition of its approach to modeling.
>>
>> John
>>
>> Typed with two thumbs on my iPhone.  (757) 318-0671
>>
>> “The biggest risk you run in life is having fifteen people sitting
>> around a table all agreeing with everything you say.  If that’s the
>> environment you work in, you’re going to blow up one day.”
>>
>>     - Ken Langone, Founder of Home Depot
>>
>>
>>
>>
>>
>> On May 8, 2017, at 21:19, popmodwkgrpimag-news-request at simtk.org wrote:
>>
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>>
>> Today's Topics:
>>
>>   1. Re: Population modeling by examples III    collaborative paper
>>      (Jacob Barhak)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Mon, 8 May 2017 20:19:22 -0500
>> From: Jacob Barhak <jacob.barhak at gmail.com>
>> To: "popmodwkgrpimag-news at simtk.org" <popmodwkgrpimag-news at simtk.org>
>> Subject: Re: [Population Modeling] Population modeling by examples III
>>    collaborative paper
>> Message-ID:
>>    <CAM_y+3Rj3wxL_M0MOV8JgXav8=GDOVPw9wD+ttpkHpi_idmggA at mail.gmail.com>
>> Content-Type: text/plain; charset="utf-8"
>>
>> 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-reviews/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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