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Malaria [message #529691] Mon, 26 April 2010 18:49 Go to next message
Werner Keil is currently offline Werner Keil
Messages: 1083
Registered: July 2009
Senior Member
I know, Matthias among others suggested disease models for animal- or food
transmitted diseases.
It may not be directly addressable by STEM 1, but this White House call to
fight Malaria at least should be of interest for many people dealing with
infectious diseases:
http://www.whitehouse.gov/blog/2010/04/23/us-expands-anti-ma laria-effort-progress-takes-hold

Werner
Re: Malaria [message #529755 is a reply to message #529691] Tue, 27 April 2010 06:43 Go to previous messageGo to next message
Arik Kershenbaum is currently offline Arik Kershenbaum
Messages: 13
Registered: January 2010
Location: Israel
Junior Member
Much as I'd like to start doing zoonosis work in STEM, I'm not sure that malaria is the disease to start with. Since it's so widely endemic, changes and variations in incidence are more to do with varying prevalence and differences in mosquito ecology, rather than flow of infection. We wouldn't be leveraging the ability of STEM to model movement of infected individuals. WNV is possibly a more promising first step.

Having said that, we certainly could use STEM (even if not to its full capability) to model the effect of anti-malarial drugs. I've never looked at the innoculator code; how comprehensive is the support for medical intervention? Can we model a fixed rate of innoculation (or oral medication) in a particular region for example?

Another interesting direction we could take the example of malaria, is to look at the effect of movement of infected individuals (e.g. urbanisation), assuming that vector ecology is locally constant. I think we would need two things for this. (1) The ability to maintain a fixed incidence/prevalence in certain administrative regions, representing the endemic rural areas, and (2) variable transmission in different administrative regions, representing differences in vector ecology in rural and urban areas. That way, we could see under what conditions an influx from the villages to the cities of carriers of the parasite would lead to endemic establishment of the disease in urban areas.

I suspect that neither of these two features is supported; am I correct?


==============
Arik Kershenbaum
Prof Blaustein's laboratory
Department of Evolutionary and Environmental Biology
University of Haifa
http://research.haifa.ac.il/~leon/html/Arik_Page.htm
Re: Malaria [message #530171 is a reply to message #529755] Wed, 28 April 2010 17:38 Go to previous messageGo to next message
Werner Keil is currently offline Werner Keil
Messages: 1083
Registered: July 2009
Senior Member
Thanks for the input.

If you have any of it for a (theoretical or actual) AIDS model, feel free
to let me know as soon as you can.

If any of you feel entitled as co-authors for the material beside Jamie,
please also don't hesitate to tell me.

Werner
Re: Malaria [message #530175 is a reply to message #529755] Wed, 28 April 2010 18:12 Go to previous messageGo to next message
Stefan Edlund is currently offline Stefan Edlund
Messages: 127
Registered: July 2009
Location: IBM
Senior Member
To try and answer some of Arik's questions:

I've never looked at the innoculator code; how comprehensive is the support for medical intervention? Can we model a fixed rate of innoculation (or oral medication) in a particular region for example?

The code you are referring to is the Trigger code in STEM. It's the ability to say after a condition is true, modify some aspect of the simulation. Right now, it's not as advanced as we would like it to be. A group in India used STEM to invoke an inoculator after a certain time had progressed in the simulation, and that's about all we can do right now. The inoculation only happens once, so for instance at day 20, x % of the population is vaccinated. It would probably be more useful to use a daily rate instead.

Another interesting direction we could take the example of malaria, is to look at the effect of movement of infected individuals (e.g. urbanisation), assuming that vector ecology is locally constant. I think we would need two things for this. (1) The ability to maintain a fixed incidence/prevalence in certain administrative regions, representing the endemic rural areas, and (2) variable transmission in different administrative regions, representing differences in vector ecology in rural and urban areas. That way, we could see under what conditions an influx from the villages to the cities of carriers of the parasite would lead to endemic establishment of the disease in urban areas.

I suspect that neither of these two features is supported; am I correct?

This is a good suggestion. I think we can handle movement of people between rural and urban areas simply by allowing the fraction between the two vary between simulations and exploring the effect (like we do for other parameters today). On the other hand, if you want to model movement taking place within a single simulation, we need to improve the migration code in STEM. We do have the concept of migration edges, but they are not really being used currently.
Re: Malaria [message #548406 is a reply to message #529691] Wed, 21 July 2010 17:26 Go to previous messageGo to next message
Werner Keil is currently offline Werner Keil
Messages: 1083
Registered: July 2009
Senior Member
This is probably something smaller, but maybe worth keeping an eye on for
early 2011:
http://www.embl.de/training/courses_conferences/conference/2 010/BMP10-01/index.html

It says to be anual, and likely to be in Germany every year or at least
Europe.

The Malaria network organizing it could be valuable contacts to exchange
experience regarding Malaria models or data.

Werner
Re: Malaria [message #550973 is a reply to message #529755] Wed, 04 August 2010 17:50 Go to previous messageGo to next message
James Kaufman is currently offline James Kaufman
Messages: 165
Registered: July 2009
Senior Member
Hi Arik,
I was thinking more in terms of a STEM demo that implemented Ronald Ross equations for Malaria (like from Anderson and May) just to show how one might approach zoonosis. The advantage being that the demo only has to show two populations; a (toy) model of Mosquitos and of Humans.
Re: Malaria [message #552403 is a reply to message #529691] Thu, 12 August 2010 06:26 Go to previous messageGo to next message
steph  is currently offline steph
Messages: 7
Registered: August 2010
Junior Member
Im a college student and I wanted to do a malaria simulation on my country using STEM.

cant I do it using two populations?

this paper (A VECTOR-HOST MODEL FOR EPIDEMICS)
was one of the firsts ive read(i dont understand it completely though)


http://www.stanford.edu/~irinak/Math420FinalPaper.pdf
Re: Malaria [message #552869 is a reply to message #552403] Fri, 13 August 2010 22:40 Go to previous messageGo to next message
James Kaufman is currently offline James Kaufman
Messages: 165
Registered: July 2009
Senior Member
Steph,
This sounds like a great idea. We are just now discussing the best way to implement a first Malaria model. Would you like to join a phone call on it? We have a toll free number for the group call next Weds at 10AM PDT. Please let us know.
Best Regards,
Jamie and Stefan
Re: Malaria [message #552959 is a reply to message #552869] Sun, 15 August 2010 07:23 Go to previous messageGo to next message
Arik Kershenbaum is currently offline Arik Kershenbaum
Messages: 13
Registered: January 2010
Location: Israel
Junior Member
I looked at the new implementation of multipopulation dieases and I'm pleased to say it seems to work easily and well. I made a couple of toy models using the lattice layout.

Now we really need to think about how to implement our full malaria model. I believe that the first challenge is to get some good estimates of the paramters for the disease model. I'm going to make a start on that now. Also, we'll need ecological parameters about mosquito densities etc. Then we can start putting the model to work on real geographical graphs.

This is going to be quite a big project and I think if there are college students like Steph who want to get involved, that could be very useful. What country is it you wanted to model?

Arik


==============
Arik Kershenbaum
Prof Blaustein's laboratory
Department of Evolutionary and Environmental Biology
University of Haifa
http://research.haifa.ac.il/~leon/html/Arik_Page.htm
Re: Malaria [message #552962 is a reply to message #529691] Sun, 15 August 2010 08:10 Go to previous messageGo to next message
steph  is currently offline steph
Messages: 7
Registered: August 2010
Junior Member
Philippines.

This is a college SP and using STEM is a proposal. I'm still not sure if it will be approved of.

It doesn't have to be grand. There aren't very many vector host model simulations available. Modeling would be the focus of the work. Its interesting because most simulations involve human contact. This is something different.

by the way, when you say creating a model, do you mean
creating one as a 'user of STEM' or as a 'programmer of STEM'?

[Updated on: Mon, 16 August 2010 05:46]

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Re: Malaria [message #553016 is a reply to message #552869] Mon, 16 August 2010 06:09 Go to previous messageGo to next message
steph  is currently offline steph
Messages: 7
Registered: August 2010
Junior Member
I don't know if I can be of any help, after all Ive only just seen STEM this Friday. I haven't explored it yet. Also, I have a class on Wed.

This is very interesting, though I admit that my work doesn't have to be Malaria, I'm just interested in Vector Host Model and ways in representing the disease transfer.

Also, I'm not sure if ill be allowed to do it(the work) in STEM. But like what Mr. Kershenbaum said, modeling of the disease transfer can be done in a multitude of ways, In fact, Networking(or something like it) has been used before but that is with same species transfer (usually STD's).


I just think that essentially, it has to be done with two populations and finding a way to connect them(like connecting layers in GIS).
Re: Malaria [message #554336 is a reply to message #552962] Sat, 21 August 2010 19:13 Go to previous message
Werner Keil is currently offline Werner Keil
Messages: 1083
Registered: July 2009
Senior Member
Thanks for the updates. Glad my thread was eagerly followed from so many
parts of the world.

These links are not directly technically related, but if those trying to use
STEM in better predicting and fightint it may find sources of data or even
funding through some of those:
http://www.malariaenvoy.com/
and related pages like
http://www.facebook.com/MalariaEnvoy?v=app_7146470109&re f=ts
http://www.rbm.who.int/

It seems most of these initiatives are either about medication or mosquito
nets, but similar to Flu, if those "weapons" can be applied smart and
effectively instead of "cluster-bombing" entire countries with nets where
none are needed then, I guess that's where prediction helpers like STEM can
be quite handy ;-)

HTH,
Werner
Re: Malaria [message #563459 is a reply to message #529691] Tue, 27 April 2010 06:43 Go to previous message
Arik Kershenbaum is currently offline Arik Kershenbaum
Messages: 13
Registered: January 2010
Location: Israel
Junior Member
Much as I'd like to start doing zoonosis work in STEM, I'm not sure that malaria is the disease to start with. Since it's so widely endemic, changes and variations in incidence are more to do with varying prevalence and differences in mosquito ecology, rather than flow of infection. We wouldn't be leveraging the ability of STEM to model movement of infected individuals. WNV is possibly a more promising first step.

Having said that, we certainly could use STEM (even if not to its full capability) to model the effect of anti-malarial drugs. I've never looked at the innoculator code; how comprehensive is the support for medical intervention? Can we model a fixed rate of innoculation (or oral medication) in a particular region for example?

Another interesting direction we could take the example of malaria, is to look at the effect of movement of infected individuals (e.g. urbanisation), assuming that vector ecology is locally constant. I think we would need two things for this. (1) The ability to maintain a fixed incidence/prevalence in certain administrative regions, representing the endemic rural areas, and (2) variable transmission in different administrative regions, representing differences in vector ecology in rural and urban areas. That way, we could see under what conditions an influx from the villages to the cities of carriers of the parasite would lead to endemic establishment of the disease in urban areas.

I suspect that neither of these two features is supported; am I correct?
--

==============
Arik Kershenbaum
Prof Blaustein's laboratory
Department of Evolutionary and Environmental Biology
University of Haifa
http://research.haifa.ac.il/~leon/html/Arik_Page.htm


==============
Arik Kershenbaum
Prof Blaustein's laboratory
Department of Evolutionary and Environmental Biology
University of Haifa
http://research.haifa.ac.il/~leon/html/Arik_Page.htm
Re: Malaria [message #563530 is a reply to message #563459] Wed, 28 April 2010 17:38 Go to previous message
Werner Keil is currently offline Werner Keil
Messages: 1083
Registered: July 2009
Senior Member
Thanks for the input.

If you have any of it for a (theoretical or actual) AIDS model, feel free
to let me know as soon as you can.

If any of you feel entitled as co-authors for the material beside Jamie,
please also don't hesitate to tell me.

Werner
Re: Malaria [message #563552 is a reply to message #563459] Wed, 28 April 2010 18:12 Go to previous message
Stefan Edlund is currently offline Stefan Edlund
Messages: 127
Registered: July 2009
Location: IBM
Senior Member
To try and answer some of Arik's questions:

I've never looked at the innoculator code; how comprehensive is the support for medical intervention? Can we model a fixed rate of innoculation (or oral medication) in a particular region for example?

The code you are referring to is the Trigger code in STEM. It's the ability to say after a condition is true, modify some aspect of the simulation. Right now, it's not as advanced as we would like it to be. A group in India used STEM to invoke an inoculator after a certain time had progressed in the simulation, and that's about all we can do right now. The inoculation only happens once, so for instance at day 20, x % of the population is vaccinated. It would probably be more useful to use a daily rate instead.

Another interesting direction we could take the example of malaria, is to look at the effect of movement of infected individuals (e.g. urbanisation), assuming that vector ecology is locally constant. I think we would need two things for this. (1) The ability to maintain a fixed incidence/prevalence in certain administrative regions, representing the endemic rural areas, and (2) variable transmission in different administrative regions, representing differences in vector ecology in rural and urban areas. That way, we could see under what conditions an influx from the villages to the cities of carriers of the parasite would lead to endemic establishment of the disease in urban areas.

I suspect that neither of these two features is supported; am I correct?

This is a good suggestion. I think we can handle movement of people between rural and urban areas simply by allowing the fraction between the two vary between simulations and exploring the effect (like we do for other parameters today). On the other hand, if you want to model movement taking place within a single simulation, we need to improve the migration code in STEM. We do have the concept of migration edges, but they are not really being used currently.
Re: Malaria [message #564461 is a reply to message #529691] Wed, 21 July 2010 17:26 Go to previous message
Werner Keil is currently offline Werner Keil
Messages: 1083
Registered: July 2009
Senior Member
This is probably something smaller, but maybe worth keeping an eye on for
early 2011:
http://www.embl.de/training/courses_conferences/conference/2 010/BMP10-01/index.html

It says to be anual, and likely to be in Germany every year or at least
Europe.

The Malaria network organizing it could be valuable contacts to exchange
experience regarding Malaria models or data.

Werner
Re: Malaria [message #564556 is a reply to message #563459] Wed, 04 August 2010 17:50 Go to previous message
James Kaufman is currently offline James Kaufman
Messages: 165
Registered: July 2009
Senior Member
Hi Arik,
I was thinking more in terms of a STEM demo that implemented Ronald Ross equations for Malaria (like from Anderson and May) just to show how one might approach zoonosis. The advantage being that the demo only has to show two populations; a (toy) model of Mosquitos and of Humans.
Re: Malaria [message #564610 is a reply to message #529691] Thu, 12 August 2010 06:26 Go to previous message
steph  is currently offline steph
Messages: 7
Registered: August 2010
Junior Member
Im a college student and I wanted to do a malaria simulation on my country using STEM.

cant I do it using two populations?

this paper (A VECTOR-HOST MODEL FOR EPIDEMICS)
was one of the firsts ive read(i dont understand it completely though)


http://www.stanford.edu/~irinak/Math420FinalPaper.pdf
Re: Malaria [message #564639 is a reply to message #564610] Fri, 13 August 2010 22:40 Go to previous message
James Kaufman is currently offline James Kaufman
Messages: 165
Registered: July 2009
Senior Member
Steph,
This sounds like a great idea. We are just now discussing the best way to implement a first Malaria model. Would you like to join a phone call on it? We have a toll free number for the group call next Weds at 10AM PDT. Please let us know.
Best Regards,
Jamie and Stefan
Re: Malaria [message #564658 is a reply to message #564639] Sun, 15 August 2010 07:23 Go to previous message
Arik Kershenbaum is currently offline Arik Kershenbaum
Messages: 13
Registered: January 2010
Location: Israel
Junior Member
I looked at the new implementation of multipopulation dieases and I'm pleased to say it seems to work easily and well. I made a couple of toy models using the lattice layout.

Now we really need to think about how to implement our full malaria model. I believe that the first challenge is to get some good estimates of the paramters for the disease model. I'm going to make a start on that now. Also, we'll need ecological parameters about mosquito densities etc. Then we can start putting the model to work on real geographical graphs.

This is going to be quite a big project and I think if there are college students like Steph who want to get involved, that could be very useful. What country is it you wanted to model?

Arik
--

==============
Arik Kershenbaum
Prof Blaustein's laboratory
Department of Evolutionary and Environmental Biology
University of Haifa
http://research.haifa.ac.il/~leon/html/Arik_Page.htm


==============
Arik Kershenbaum
Prof Blaustein's laboratory
Department of Evolutionary and Environmental Biology
University of Haifa
http://research.haifa.ac.il/~leon/html/Arik_Page.htm
Re: Malaria [message #564676 is a reply to message #529691] Sun, 15 August 2010 08:10 Go to previous message
steph  is currently offline steph
Messages: 7
Registered: August 2010
Junior Member
Philippines.

This is a college SP and using STEM is a proposal. I'm still not sure if it will be approved of.

It doesn't have to be grand. There aren't very many vector host model simulations available. Modeling would be the focus of the work. Its interesting because most simulations involve human contact. This is something different.
Re: Malaria [message #564696 is a reply to message #564639] Mon, 16 August 2010 06:09 Go to previous message
steph  is currently offline steph
Messages: 7
Registered: August 2010
Junior Member
I don't know if I can be of any help, after all Ive only just seen STEM this Friday. I haven't explored it yet. Also, I have a class on Wed.

This is very interesting, though I admit that my work doesn't have to be Malaria, I'm just interested in Vector Host Model and ways in representing the disease transfer.

Also, I'm not sure if ill be allowed to do it(the work) in STEM. But like what Mr. Kershenbaum said, modeling of the disease transfer can be done in a multitude of ways, In fact, Networking(or something like it) has been used before but that is with same species transfer (usually STD's).


I just think that essentially, it has to be done with two populations and finding a way to connect them(like connecting layers in GIS).
Re: Malaria [message #564790 is a reply to message #564676] Sat, 21 August 2010 19:13 Go to previous message
Werner Keil is currently offline Werner Keil
Messages: 1083
Registered: July 2009
Senior Member
Thanks for the updates. Glad my thread was eagerly followed from so many
parts of the world.

These links are not directly technically related, but if those trying to use
STEM in better predicting and fightint it may find sources of data or even
funding through some of those:
http://www.malariaenvoy.com/
and related pages like
http://www.facebook.com/MalariaEnvoy?v=app_7146470109&re f=ts
http://www.rbm.who.int/

It seems most of these initiatives are either about medication or mosquito
nets, but similar to Flu, if those "weapons" can be applied smart and
effectively instead of "cluster-bombing" entire countries with nets where
none are needed then, I guess that's where prediction helpers like STEM can
be quite handy ;-)

HTH,
Werner
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