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

Wed May 10 10:22:04 PDT 2017

Thanks Jacob. The process for creating an account and project was fairly
easy.

Here is the link: https://simtk.org/projects/ibiosim
This website looks pretty neat but this will probably be used as a wrapper.

Leandro

On Tue, May 9, 2017 at 12:00 AM, Jacob Barhak <jacob.barhak at gmail.com>
wrote:

> 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:
>>>
>>> Send PopModWkGrpIMAG-news mailing list submissions to
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>>>
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>>> When replying, please edit your Subject line so it is more specific
>>> than "Re: Contents of PopModWkGrpIMAG-news digest..."
>>>
>>>
>>> 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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>>> End of PopModWkGrpIMAG-news Digest, Vol 31, Issue 1
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