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STEM pneumonic plague simulation [message #1272982]

Wed, 19 March 2014 08:24

$fabrizio d\'amico is currently offline$ fabrizio d\'amico

Messages: 5
Registered: March 2014

Junior Member

Dear all,
i'm a new user of STEM.

I'm attending a PhD course and part of my work is focused on the simulation of spread of a yersinia pestis aerosol in a bioterrorist attack.
I'm working on a SEIR model for the disease, but I have some questions:

- the rates related to changes of compartmentals have to vary between 0 and 1?
- is there any place where these data can be consulted for pneumonic plague?

Fabrizio

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Re: STEM pneumonic plague simulation [message #1278663 is a reply to message #1272982]

Thu, 27 March 2014 17:10

Stefan Edlund

Messages: 27
Registered: July 2009

Junior Member

Hi Frabrizio,

here's some answers.

1. No, the unit of the rate parameters in a disease model is 1/(time period), where time period is 1 day by default. As an example, if recovery rate is set at 0.1, infected individuals are expected to ill for 10 days. Our wiki has some more information about compartment modeling in general: https://wiki.eclipse.org/Introduction_to_Compartment_Models

2. If by data sources you mean literature estimates on parameters values for pneumonic plague, here a good resource we found: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2870621/

Best Regards,
/ Stefan

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Re: STEM pneumonic plague simulation [message #1279482 is a reply to message #1278663]

Fri, 28 March 2014 20:42

$fabrizio d\'amico is currently offline$ fabrizio d\'amico

Messages: 5
Registered: March 2014

Junior Member

Dear Stefan,
thank you so much.
I examined the paper that you suggested and other papers... I found the value only of R0. Is it correct to derive the beta (transmission rate) from the R0 formula?
Thank you so much!

fabrizio

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Re: STEM pneumonic plague simulation [message #1279490 is a reply to message #1279482]

Fri, 28 March 2014 20:53

Stefan Edlund

Messages: 27
Registered: July 2009

Junior Member

Right, for an SEIR model R0 is transmissionRate/recoveryRate, so given R0 and recovery rate you can compute transmission rate.

Regards,
/ Stefan

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Re: STEM pneumonic plague simulation [message #1279491 is a reply to message #1279490]

Fri, 28 March 2014 20:55

Stefan Edlund

Messages: 27
Registered: July 2009

Junior Member

By the way, are you using STEM in your PhD course?

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Re: STEM pneumonic plague simulation [message #1279496 is a reply to message #1279491]

Fri, 28 March 2014 21:01

$fabrizio d\'amico is currently offline$ fabrizio d\'amico

Messages: 5
Registered: March 2014

Junior Member

I'm using STEM and other software in order to demonstrate the importance of stand off detection of biological agents released for a bioterrorist attack. I'm working on some simulations that show how is important an early detection of the threat

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Re: STEM pneumonic plague simulation [message #1279951 is a reply to message #1279491]

Sat, 29 March 2014 14:31

$fabrizio d\'amico is currently offline$ fabrizio d\'amico

Messages: 5
Registered: March 2014

Junior Member

I have another question.
How I can record my epidemiological data in order to use them in the analysis tool???

thanks

fabrizio

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Re: STEM pneumonic plague simulation [message #1283529 is a reply to message #1279951]

Thu, 03 April 2014 14:23

James Kaufman

Messages: 240
Registered: July 2009

Senior Member

Fabrizio,
Please see the following documentation on logging in STEM
https://wiki.eclipse.org/STEM_Loggers

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Re: STEM pneumonic plague simulation [message #1306090 is a reply to message #1283529]

Sun, 20 April 2014 20:47

$fabrizio d\'amico is currently offline$ fabrizio d\'amico

Messages: 5
Registered: March 2014

Junior Member

Dear James,
thank you.
I need to understand some other things...
1. the correct values of mortality and birth rates (here we speack about the first one). I consulted some statistical data about the mortality rate in lazio (Italy). The value is 9.4. This value represents the number of deaths that occurs every 1000 people for one year... so it means that in a population of 1000 people, every year, 9.4 statistically dead.
The question is if this value (0.0094) is the one that has to be inserted in the population model form. Or not?
2. disease mortality rate: all the others epidemiological rates are expressed as (1/number of days in a particular epidemiological state). Is the same for the disease mortality rate? If a person affected by pneumonic plague dead after 3 days from the onset of symptoms, the disease mortality rate will be 1/3=0.33?

Many thanks!

fabrizio

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