[Population Modeling] PopModWkGrpIMAG-news Digest, Vol 28, Issue 3
John Rice
john.rice at noboxes.org
Sat Feb 11 13:43:36 PST 2017
Responding to my self. (Novices so things like that) re: the core and distinguishing features(s) that characterize our intended brand of "population modeling" as special. Thinking maybe it is the science and art for using high performance computational power to generating unique INDIVIDUAL models of synthetic entities with each one defined by a set of characteristics of interest or relevance to a problem being explored by other computational models. The hard part, science or art, is that the validity of the results of a model that draws synthetic entities from a high population of synthetic entities.
Some questions are:
1- Were the right set characteristics used to CREATE each INDIVIDUAL synthetic entity in the population synthetic entities.
2- where the number of characteristics sufficient for the question or phenomenon that the model sampling from the population of synthetic entities is trying to answer and
3- if a small sample were drawn from a population of real entities of interest, and one were drawn from the population of synthetic entities, would the distributions and combinations of the characteristics match (almost). Thus there would be some evidence that the huge easily accessible population of synthetic entities is representative, lhat is it is a valid representation of a population of real entities.
The answers to all 3 questions contribute to determining the Credibility of the modeled population of synthetic entities for their intended use in any other kind of model that uses those entities.
But the "popMod" is done once there is a valid population of synthetic individually modeled entities for use in place of real entities for computation BOI science.
That may
May also help answer a question I seem to remember in this group two years back concerning whether POPMOD was a form of Monticello, or agent based, or ??? modeling. Answer: no. It has nothing to do with the operative model that USED the population, which could be any kind of modeling. The "population" has been modeled when there is a Creditable population of desired size of synthetic entities for convenient controllable use by any other kind of models.
Respects to all
John the Naive.
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 Feb 11, 2017, at 15:00, popmodwkgrpimag-news-request at simtk.org wrote:
>
> Send PopModWkGrpIMAG-news mailing list submissions to
> popmodwkgrpimag-news at simtk.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
> https://simtk.org/mailman/listinfo/popmodwkgrpimag-news
> or, via email, send a message with subject or body 'help' to
> popmodwkgrpimag-news-request at simtk.org
>
> You can reach the person managing the list at
> popmodwkgrpimag-news-owner at simtk.org
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of PopModWkGrpIMAG-news digest..."
>
>
> Today's Topics:
>
> 1. Re: PopModWkGrpIMAG-news Digest, Vol 28, Issue 2 (John Rice)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 10 Feb 2017 23:38:51 -0500
> From: John Rice <john.rice at noboxes.org>
> To: popmodwkgrpimag-news at simtk.org
> Subject: Re: [Population Modeling] PopModWkGrpIMAG-news Digest, Vol
> 28, Issue 2
> Message-ID: <8060FC9C-75FE-412F-B7CA-1B76988A290A at noboxes.org>
> Content-Type: text/plain; charset="utf-8"
>
> Love it!!
>
> Also noted that they call their work individual based modeling which intuitively sounds directly opposite POPMOD. Yet I think it is a better name than PopMod
>
> "We use approach named Individual Based Modelling in which modeler tries
>>
>> to present population of living organisms as being composed of discrete
>> individual organisms."
>
> Computer builds a population of synthetic entities which can then serve a agents in models.
>
> 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 Feb 10, 2017, at 15:00, popmodwkgrpimag-news-request at simtk.org wrote:
>>
>> Send PopModWkGrpIMAG-news mailing list submissions to
>> popmodwkgrpimag-news at simtk.org
>>
>> To subscribe or unsubscribe via the World Wide Web, visit
>> https://simtk.org/mailman/listinfo/popmodwkgrpimag-news
>> or, via email, send a message with subject or body 'help' to
>> popmodwkgrpimag-news-request at simtk.org
>>
>> You can reach the person managing the list at
>> popmodwkgrpimag-news-owner at simtk.org
>>
>> When replying, please edit your Subject line so it is more specific
>> than "Re: Contents of PopModWkGrpIMAG-news digest..."
>>
>>
>> Today's Topics:
>>
>> 1. eVOLUTUS: the simulator of multiscale evolutionary processes
>> tested on Foraminifera (Pawel Topa)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Fri, 10 Feb 2017 10:48:55 +0100
>> From: Pawel Topa <topa at agh.edu.pl>
>> To: popmodwkgrpimag-news at simtk.org
>> Subject: [Population Modeling] eVOLUTUS: the simulator of multiscale
>> evolutionary processes tested on Foraminifera
>> Message-ID: <3d1b47fb-9a73-1559-4485-1c5f0996d7d8 at agh.edu.pl>
>> Content-Type: text/plain; charset="utf-8"; Format="flowed"
>>
>> Dear members of Population Modeling Working Group,
>>
>> let me introduce our project named "eVOLUTUS: the simulator of
>> multiscale evolutionary processes tested on Foraminifera":
>>
>>
>> Our goal is to design a new algorithmic framework for testing and
>> simulating evolutionary principles and their consequences in defined
>> environments at various spatiotemporal scales. Due to biological
>> complexity of organisms and their interactions with the environment, it
>> has never been attempted to design such a numerical framework for the
>> simulation of evolutionary patterns derived from the fossil record of
>> real organisms. As a model organism we will implement Foraminifera,
>> single-celled eukaryotes that occupy marine benthic and pelagic zones
>> throughout the world andhave an extraordinary fossil record throughout
>> the Phanerozoic. This makes them an ideal model often used for testing
>> general evolutionary hypotheses. Recent studies have shown that shell
>> architecture and most prominent morphogenetic trends in shell
>> development distinctly follow molecular phylogenetic patterns.
>>
>> We use approach named Individual Based Modelling in which modeler tries
>> to present population of living organisms as being composed of discrete
>> individual organisms. The model that uses IBM in natural way can be
>> implemented using Agent-based Modeling computational paradigm. In order
>> to model evolutionary processes we use the well known genetic operators:
>> mutation and crossing over which are applied to the virtual genome
>> consisted of parameters that govern agent (foraminifers) behavior.
>> Selection is simply made by adaptation to environmental conditions in
>> virtual habitat.
>>
>> References:
>> 1) Pawe? Topa, ?ukasz Faber, Jaros?aw Tyszka, Maciej Komosinski,
>> Modelling ecology and evolution of Foraminifera in the agent-oriented
>> distributed platform, Journal of Computational Science, Volume 18,
>> January 2017, Pages 69-84, ISSN 1877-7503,
>> http://dx.doi.org/10.1016/j.jocs.2016.07.009.
>> (//www.sciencedirect.com/science/article/pii/S1877750316301168)
>> Abstract: Abstract
>> We present a new software platform called eVolutus for simulating
>> evolution of living organisms. We choose Foraminifera as model organisms
>> that represent a group of single-cellular, mainly marine, organisms that
>> construct well fossilisable protective shells. They have lived on Earth
>> for more than 540 million years and have left an extraordinary fossil
>> record that is excellent for testing palaeoecological and evolutionary
>> hypotheses. We use the AgE platform, which is a lightweight
>> agent-oriented platform supporting distributed computation. The paper
>> presents the general architecture of this modelling environment as well
>> as more detailed descriptions of the implemented rules and applied
>> solutions. The utility of this software is demonstrated by presenting
>> the configuration and results of sample experiments.
>> Keywords: Agent-based modelling; Artificial Life; Multi-agent systems;
>> Foraminifera
>>
>> 2) Maciej Komosinski, Agnieszka Mensfelt, Jaros?aw Tyszka, Jan Gole?,
>> Multi-agent simulation of benthic foraminifera response to annual
>> variability of feeding fluxes, Journal of Computational Science,
>> Available online 3 October 2016, ISSN 1877-7503,
>> http://dx.doi.org/10.1016/j.jocs.2016.09.009.
>> (//www.sciencedirect.com/science/article/pii/S1877750316301715)
>> Abstract: Abstract
>> In this work we describe a novel simulation model of foraminifera and
>> their microhabitat. The simulations reported here are focused on the
>> response of foraminiferal populations to environmental feeding fluxes.
>> The experiments allowed to calibrate the model and to simulate realistic
>> population patterns known from culture experiments, as well as from
>> oceanographic and paleoecologic studies. Variability of annual food flux
>> has a direct impact on productivity of foraminifera: population sizes
>> closely follow the intensity of constant and seasonal food fluxes in
>> both scenarios. This correlation between the food influx and population
>> size is interpreted as the consequence of changing the carrying capacity
>> of the system. Seasonal pulses of particulate organic matter enhance the
>> population size which is represented by a higher number of fossilized
>> shells. Our model offers a flexible experimental design to run
>> sophisticated in silico experiments. This approach reveals a novel
>> methodology for testing sensitivity of fossil and recent foraminiferal
>> assemblages to environmental changes. Furthermore, it facilitates
>> predictive applications for monitoring studies based on simulation of
>> various scenarios.
>> Keywords: Foraminifera; Simulation; Population dynamics; Life cycles;
>> Seasonality
>>
>>> 2. Categorize your modeling approach by research area. Keywords we
>>> used in the past are:
>>> Managing disease spread
>>> Resource planning and allocation
>>> Predicting drug effects
>>> Risk assessment
>>> Ecosystem management
>>> Testing theory
>>> Epidemiology and public health
>> Individual based modeling.
>>
>>
>>>
>>> 3. Add keywords for computational methods you used. Examples include
>>> Agent Based Models, differential equations, Monte-Carlo simulation,
>>> yet there are many more options that you can find in: Table 1 in:
>>> https://simtk.org/docman/view.php/962/1963/SummerSim_2016_PopMod_Submit_2016_05_15_Robert_Smith.pdf
>> * Agent Based Modeling
>> * Evolutionary Computations
>>
>>
>> Kind regards
>>
>> Pawe? Topa
>> Jarek Tyszka
>> Maciek Komosinski
>> -------------- next part --------------
>> An HTML attachment was scrubbed...
>> URL: <https://simtk.org/pipermail/popmodwkgrpimag-news/attachments/20170210/3c16b663/attachment-0001.html>
>>
>> ------------------------------
>>
>> Subject: Digest Footer
>>
>> _______________________________________________
>> PopModWkGrpIMAG-news mailing list
>> PopModWkGrpIMAG-news at simtk.org
>> https://simtk.org/mailman/listinfo/popmodwkgrpimag-news
>>
>>
>> ------------------------------
>>
>> End of PopModWkGrpIMAG-news Digest, Vol 28, Issue 2
>> ***************************************************
>>
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: <https://simtk.org/pipermail/popmodwkgrpimag-news/attachments/20170210/d11a906d/attachment-0001.html>
>
> ------------------------------
>
> Subject: Digest Footer
>
> _______________________________________________
> PopModWkGrpIMAG-news mailing list
> PopModWkGrpIMAG-news at simtk.org
> https://simtk.org/mailman/listinfo/popmodwkgrpimag-news
>
>
> ------------------------------
>
> End of PopModWkGrpIMAG-news Digest, Vol 28, Issue 3
> ***************************************************
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://simtk.org/pipermail/popmodwkgrpimag-news/attachments/20170211/f0efc099/attachment-0001.html>
More information about the PopModWkGrpIMAG-news
mailing list