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Home » Archived » OHF » Using Stem to simulate dengue fever: two questions/problems
Using Stem to simulate dengue fever: two questions/problems [message #580026] Sun, 15 July 2007 22:17
Nicoletta De Maio is currently offline Nicoletta De Maio
Messages: 8
Registered: July 2009
Junior Member
Hi

I was told to post the following e-mail conversation to the newsgroup, so
there you go.

My original questions were:
----Quote----
Hello

I'm working in the bioinformatics group at NITD (Novartis Institute for
tropical Diseases) in Singapore and we're looking at using Stem to
simulate dengue fever epidemics. I'm the person assigned to evaluating
Stem to see if it may be useful to us.

I've collected as much of the documentation as I could find and it gave me
a pretty good understanding of the structure of a scenario, and of what's
available and what's not. But now I'm running into some practical problems.

First of all, I'd like to use the available geographic information for
Singapore rather than try and cobble something together myself. According
to the Models tab in the Designer View there is such a model (SGP (0,1,2)
Full infrastructure). But how do I get it into my project? I've created a
Scenario in the appropriate subfolder in the Project viewer and attached
the model to that. But I'm not able to copy it to the models folder within
my own project, at least not within the Designer view. (I haven't tried to
do it 'by hand', i.e. moving files around outside the running application,
by the way. I'm not sure that's wise...)

I need to do this because I'm planning to attach the Infector to the
scenario, but the Disease decorator to the model, or parts of it.

Which brings me to the next problem. I've used the wizard to create an
infector and dropped it in the Decorators folder of my project - but when
I try to do the same thing with a disease the dialog window will accept
all of my input before issuing an error message and do nothing when I
click 'finish'. The message name/description is simply the name of the
package 'org.eclipse.ohf.stem.ui'; there is no indication of what Stem
thinks happened. The stack trace is a bit long so here's the beginning of
it:

java.lang.reflect.InvocationTargetException
at
org.eclipse.jface.operation.ModalContext.runInCurrentThread( ModalContext.java:381)
at org.eclipse.jface.operation.ModalContext.run(ModalContext.ja va:313)
at org.eclipse.jface.wizard.WizardDialog.run(WizardDialog.java: 934)
at
org.eclipse.ohf.stem.ui.wizards.NewIdentifiableWizard.perfor mFinish(NewIdentifiableWizard.java:146)
at
org.eclipse.jface.wizard.WizardDialog.finishPressed(WizardDi alog.java:742)
at
org.eclipse.jface.wizard.WizardDialog.buttonPressed(WizardDi alog.java:373)
at org.eclipse.jface.dialogs.Dialog$2.widgetSelected(Dialog.jav a:616)
at
org.eclipse.swt.widgets.TypedListener.handleEvent(TypedListe ner.java:227)
at org.eclipse.swt.widgets.EventTable.sendEvent(EventTable.java :66)
at org.eclipse.swt.widgets.Widget.sendEvent(Widget.java:1101)
at org.eclipse.swt.widgets.Display.runDeferredEvents(Display.ja va:3320)
at org.eclipse.swt.widgets.Display.readAndDispatch(Display.java :2972)
at org.eclipse.jface.window.Window.runEventLoop(Window.java:820 )
at org.eclipse.jface.window.Window.open(Window.java:796)
at
org.eclipse.ohf.stem.ui.wizards.NewIdentifiableWizard$NewIde ntifiableWizardAction.run(NewIdentifiableWizard.java:1043)
at
org.eclipse.ohf.stem.ui.wizards.NewDiseaseWizard$NewAction.r un(NewDiseaseWizard.java:161)
at org.eclipse.ui.internal.PluginAction.runWithEvent(PluginActi on.java:256)
---<snip>---

(Still with me? Oh, good...:) )
I can't really make head or tail of it - do you have ideas what might be
going wrong? Oh, and I'm running Stem off the jarfile, not from within
eclipse.

So - the point of this e-mail. I'd appreciate any pointers or instructions
on how to solve either problem. I'm more than happy to provide further
information if necessary - just drop me a line. I'd really like to get
this off the ground (especially because so much geographical data is
already there) but it seems I have to get past the planning stage first!

By the way, feel free to forward all or part of this to someone else if
I've contacted the wrong developer. In that case - sorry to have bothered
you, it was not my intention to get on anyone's nerves. In any case:
thanks!

:-) Nicoletta De Maio

----Quote----

And here's Dan Ford's reply:
----Quote----
Nicoletta,
thanks for your note, you contacted the right person. I'm on
vacation right now with limited connectivity so I'll give a short reply
now and try to follow up with you next week when I return home. I also
you like to point you to the project newsgroup, it would be great for the
project to capture your questions and my answers for all to see. If you
want to post this response in the newsgroup that would be great.
http://www.eclipse.org/newsgroups/

1) with the current milestone release, 0.2.0M1, you cannot copy the
internal built-in models to user defined projects. I believe there is a
bug open on this issue, but a reference to will have to wait until next
week. This will be corrected, it just was one of the things we cut from
this release. You should, however, be able to drag it into a Model or
Scenario that you create with a wizard and it should work. The only
reason you would drag a copy to your own project would be to modify the
underlying model. The built-in version cannot be changed as other models
may refer to it and would not expect it to be different in any way.

There is a tutorial to be written that describes much of what you want to
accomplish, basically what you need to do is create a hierarchy of models
using the wizard and compose the hierarchy by dragging a child model on to
its parent. Try creating your lowest-level model and dragging a disease
model (one of the built in ones or one you create using the disease
wizard) into it. Then drag the built-in Singapore model and dropping it
there as well. Save that model. Create another model and in its editor
drag the built-in "Aggregating SEIR Disease Model" (decorator) to it.
This will aggregate values in the geographic hierarchy as well as
propagate population members along transportation links. Also, drag and
drop the first model you created to the new model's open editor to make it
a child. Save the second model. Create your Scenario using the Wizard,
and drag the second model you created to the Scenario in its editor and
drop it. Do the same with the Infector and the Sequencer you want to use.
Save it.

Double click on the new Scenario and if all is well, it will run.

2) The exception is a bug, could you open a bug report please. This will
help you follow its progress and help us track down and fix the problem.
Have a look at http://wiki.eclipse.org/Bug_Reporting_FAQ and if you have
any problems just send me a note.

3) I have some experience modeling Dengue fever. In the first version of
STEM (the eclipse version is the second), I implemented the model outlined
in:

Cummings DAT, Irizarry RA, Huang NE, Endy TP, Nisalak A, Ungchusak K,
Burke DS (2004) Travelling waves in the occurrence of dengue haemorrhagic
fever in Thailand. Nature 427 (6972): 344-347.

This model required a more sophisticated disease model than simple SEIR as
it segments the population by the sequence of serotypes that they have
been infected with. Unfortunately, that model is not yet implemented in
the new version of STEM.

Best Regards

Dan Ford
IBM Almaden
----Quote----

Hope this is useful to anyone besides myself.

:-) Nicoletta
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