[Population Modeling] Soliciting contributions for a population modeling paper

[Jacob Barhak]

Thanks to Olaf and Sergey for contributing,

I encourage others in the list to contribute, here is my own contribution
to the paper:

The Reference Model of disease progression predicts disease burden
including outcomes and costs in diabetic populations. It validates
combinations of disease models and hypotheses against clinical trial
results. Baseline populations from the trials are modeled from publicly
available statistics. Populations are generated using Monte Carlo
techniques. Population generation from public summary data avoids
restritictions associated with individual patient data, and therefore
allows access to more modeling data. The MIcro Simulation Tool (MIST) is
developed to support such population modeling capabilities. This free
software tool uses Evolutionary Computation and High Performance Computing.
MIST runs over the cloud!

J. Barhak, The Reference Model  for Disease Progression uses MIST to find
data fitness.  PyData Silicon Valley 2014:
Presentation: http://sites.google.com/site/jacobbarhak/home/PyData_S
V_2014_Upload_2014_05_02.pptx

Video: https://www.youtube.com/watch?v=vyvxiljc5vA

Barhak, A. Garrett, Population Generation from
Statistics Using Genetic Algorithms with MIST +
INSPYRED. MODSIM World 2014, VA.
Paper:
http://sites.google.com/site/jacobbarhak/home/MODSIM2014_MIST_INSPYRED_Paper_Submit_2014_03_10.pdf
Presentation:
http://sites.google.com/site/jacobbarhak/home/MODSIM_World_2014_Submit_2014_04_11.pptx
On Dec 9, 2014 8:18 PM, "Sergey Nuzhdin" <snuzhdin at usc.edu> wrote:

>  Dear Colleagues,
>
> we have a couple of activities for ‘population modeling’, but i think the
> below is most relevant for this group.
>
> Yours
>
> Sergey
>
> In societies – both animal and human – many individuals interact with one
> another. These social interactions can affect group size and composition,
> and conversely, group size and composition can affect social interactions
> among individuals. Individuals within societies differ in important ways
> from one another; for example in their likelihood of associating with, or
> attacking other individuals; and if they are attacked themselves, they may
> differ in how they adjust their own behavior based on that experience. All
> this suggests that differences among individuals in mean levels of behavior
> and behavioral plasticity must affect, and be affected by, higher level
> properties of groups and societies. However, untangling the effects of
> individual differences in behavior and behavioral plasticity on the social
> and spatial patterns of groups and societies is refractory to current
> modeling and analytic tools. Feedbacks between behavior at the level of
> individuals and behavior at the level of groups and societies must be
> understood in order to predict the behaviors and their key health outcomes
> at each of these levels.
>
> Foley, B. R., J. B. Saltz, S. V. Nuzhdin and P. Marjoram. 2015. A novel
> Bayesian approach to modelling Social Niche Construction uncovers cryptic
> behavioural mechanisms of group formation in *D. melanogaster. Amer.
> Naturalist* (*accepted pending revision*).
>
> Saltz, J. B. and S. V. Nuzhdin. 2014. The (overlooked) role of niche
> construction in genetics. *Trends Evol. Ecol.* 29: 8-14. Ardekani, S., A.
> Biyani, J. Dalton, J. Saltz, M. Arbeitman, J. Tower, S. Nuzhdin and S.
> Tavare. 2013. Three dimensional tracking and behavior monitoring of
> multiple fruit flies. *J. R. Soc. Lond. Interface* 10: 20120547.
>
>
>
>
>
> *From:* popmodwkgrpimag-news-bounces at simtk.org [mailto:
> popmodwkgrpimag-news-bounces at simtk.org] *On Behalf Of *Dammann, Olaf
> *Sent:* Tuesday, December 09, 2014 8:51 AM
> *To:* Jacob Barhak; popmodwkgrpimag-news at simtk.org
> *Subject:* RE: [Population Modeling] Soliciting contributions for a
> population modeling paper
>
>
>
> Dear Jacob & All,
>
> Grand idea! See attached for our 2 cents.
>
> Best wishes,
>
> Olaf & Ben
>
>
>
> *From:* Jacob Barhak [mailto:jacob.barhak at gmail.com
> <jacob.barhak at gmail.com>]
> *Sent:* Monday, December 08, 2014 9:28 PM
> *To:* popmodwkgrpimag-news at simtk.org
> *Subject:* [Population Modeling] Soliciting contributions for a
> population modeling paper
>
>
>
> Greetings all population modeling members,
>
> Sergey and I discussed writing a population modeling paper. In the IMAG
> meeting we tried to define population modeling by a set of terms you can
> find in the IMAG site,  yet definition by example may be better.
>
> Therefore we are soliciting contributions from all list members. The idea
> would be to define this group by collecting examples of work from each
> member.
>
> To this end,  I would ask for everyone receiving this post to reply to it
> with one paragraph about what they do within population modeling. And
> please add at least one reference to own work.
>
> I volunteer to assemble the paragraphs and references into a paper and
> submit it to one of the SCS conferences using the names of all contributors
> who post to the list. You are  welcome to invite coleagues to join this
> thread or suggest another target venue to the paper.
>
> I look forward to read your introductions to your own work.
>
>          Jacob
>
> --
> Jacob Barhak Ph.D.
> http://sites.google.com/site/jacobbarhak/
>
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