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STEM New Feature Requests Discussion [message #43642] Wed, 09 July 2008 17:17 Go to next message
James Kaufman is currently offline James Kaufman
Messages: 158
Registered: July 2009
Senior Member
Let's add our discussion of new STEM feature requests here
STEM Should also Run as a web application [message #43679 is a reply to message #43642] Wed, 09 July 2008 17:25 Go to previous messageGo to next message
James Kaufman is currently offline James Kaufman
Messages: 158
Registered: July 2009
Senior Member
STEM should also run as a web application. Please put your ideas on the
best way to do this hear under this item.
Need to automate system builds and posting of the latest STEM executable [message #43710 is a reply to message #43642] Wed, 09 July 2008 17:26 Go to previous messageGo to next message
James Kaufman is currently offline James Kaufman
Messages: 158
Registered: July 2009
Senior Member
The STEM build process should be automated so the Eclipse Website
every night gets the latest STEM executable
Caching Scenarios [message #43755 is a reply to message #43642] Wed, 09 July 2008 17:28 Go to previous messageGo to next message
Eclipse User
Originally posted by: ymesika.gmail.com

Running a US scenario takes some times due to access to disk for reading
the data. It could be great if the data would be cached so that running
the scenario again wouldn't require re-reading the data from the file
system.

Such feature should be toggled from the preferences so that those who
don't wish to use it will simply turn caching off.
Re: STEM New Feature Requests Discussion [message #43778 is a reply to message #43642] Wed, 09 July 2008 17:30 Go to previous messageGo to next message
Jo Conant is currently offline Jo Conant
Messages: 6
Registered: July 2009
Junior Member
Triggered events. Essentially, I'd like to take a look at how to set up
an event to occur at a specific time or given a specific circumstance.
For example, creating a few infectors that would be triggered at a certain
time period.

Perhaps this could also be used to create interventions. For example,
after a specific amount of time or number of people infected, public
policy decisions such as closing roads, vaccinating people, etc could be
implemented.
Re: STEM Should also Run as a web application [message #43810 is a reply to message #43679] Wed, 09 July 2008 17:49 Go to previous messageGo to next message
Matthew Davis
Messages: 269
Registered: July 2009
Senior Member
Hi Jamie, what kinds of parallelism factors are in STEM? Is it a
candidate for Map/Reduce? It would really neat to see if there is a use
case for "cloud computing" in its computations. And, if you wanted to
make it a "software as a service" application for mass consumption,
perhaps even beyond the epidemiology, "the cloud" would be a great way
to host the computationally-intensive service.

As for how to do it as a Web app, a smartly done Google Maps interface
would really enhance the usability in my opinion. I'm not sure you can
duplicate the polygon renderings in the application's main visualizer in
Google Maps due to the browser's resource uses, but you could still do
some really interesting views merging the BIRT reports with municipality
markers in Google Maps. There are a ton of "mashup" uses IMO.

-Matt


James Kaufman wrote:
> STEM should also run as a web application. Please put your ideas on the
> best way to do this hear under this item.
>
Re: STEM Should also Run as a web application [message #43840 is a reply to message #43810] Wed, 09 July 2008 18:17 Go to previous messageGo to next message
James Kaufman is currently offline James Kaufman
Messages: 158
Registered: July 2009
Senior Member
Hi Matt,
Thank you for the GREAT comment.

Regarding parallelism, in the most general case (of a spatio-temporal
EVENT modeler) I think the answer is "it depends". It depends on how
connected your graph is. In the case of STEM today and the way we have
implemented air travel, the application should be able to make great use
of parallelism. The world naturally can be divided (for example) by
contents with relatively few edges than need to be communicated between
servers. This lowers the messaging overhead and simplifies partitioning
and distribution of the problem.

Regarding the google maps interface idea, this is a good suggestion. We
don't need to render the internal polygons in STEM but we do need an
association between IDs and locations on the graph. It's fairly easy for
us to plug in other viewers. I think the more difficult part of running on
the server is giving users an intuitive interface with the functionality
they need to "compose" a problem the way they currently do with the STEM
Eclipse rich client app.

One idea, maybe we can divide STEM so users can download the designer
perspective and run that locally. Once they have created their own
scenario we could send the scenario (and xml file) to the instance of STEM
running on the server. Since we now have full import/export functionality
working, users can already email and share their own custom scenarios
(graphs and diseases they have created). If the simulation perspective
could run on the server we can simply send it the scenario to run through
a web interface. I agree the preferred visualization might change over
time. If we can make a single instance of STEM work server side we could
then thing about how to add the parallelism...
Re: STEM Should also Run as a web application [message #43869 is a reply to message #43810] Fri, 11 July 2008 13:33 Go to previous messageGo to next message
Daniel Ford is currently offline Daniel Ford
Messages: 138
Registered: July 2009
Location: New York
Senior Member
Matt,
for the kinds of simulations we've been working on, mostly disease
spread in sub-global regions (e.g, North America, Asia, etc.) modelled at
administration level 2, we haven't really run out of horsepower quite yet so
going to a parrallel computing model might be a bit premature. These types
of models create graphs with on the order of 10000 nodes and simuliar
magnitude labels. Such models tend to run well on a single laptop. However,
for much bigger models representing finer detail (millions of nodes in the
representational graph) it might be the only way to make them work. I
expect disease models wouldn't really need quite that level of detail, but
if you were doing some kind of situational awareness application coupled
with integrated simulations for decision support then we'd need the power.

Something to think about or investigate is how we could leverage the fact
that all of STEM's modeling code is generated by EMF. One can provide their
own JET templates to the EMF code generator, so could we, for instance,
fiddle with the JET templates so that they generate code that would work
directly with something like Hadoop?

--
Daniel Ford
IBM Almaden Research Center
San Jose, CA
Re: Need to automate system builds and posting of the latest STEM executable [message #43901 is a reply to message #43710] Fri, 11 July 2008 13:35 Go to previous messageGo to next message
Daniel Ford is currently offline Daniel Ford
Messages: 138
Registered: July 2009
Location: New York
Senior Member
Lack of automation in the build process is the biggest failing of the
project I think. It's not like there isn't any, it just isn't something
that really works yet. It's not like we don't know it is good for us.

--
Daniel Ford
IBM Almaden Research Center
San Jose, CA
"James Kaufman" <kaufman@almaden.ibm.com> wrote in message
news:3424615de3cc43d618d3c131b9a386a8$1@www.eclipse.org...
> The STEM build process should be automated so the Eclipse Website
> every night gets the latest STEM executable
>
Re: Caching Scenarios [message #43929 is a reply to message #43755] Fri, 11 July 2008 13:38 Go to previous messageGo to next message
Daniel Ford is currently offline Daniel Ford
Messages: 138
Registered: July 2009
Location: New York
Senior Member
There's a bug for this already

https://bugs.eclipse.org/bugs/show_bug.cgi?id=177769

--
Daniel Ford
IBM Almaden Research Center
San Jose, CA
Re: STEM New Feature Requests Discussion [message #43958 is a reply to message #43778] Fri, 11 July 2008 13:46 Go to previous messageGo to next message
Daniel Ford is currently offline Daniel Ford
Messages: 138
Registered: July 2009
Location: New York
Senior Member
I've opened a bug for this and have a UML model for implementation.

https://bugs.eclipse.org/bugs/show_bug.cgi?id=240489

--
Daniel Ford
IBM Almaden Research Center
San Jose, CA
Data output/analysis [message #45057 is a reply to message #43642] Tue, 05 August 2008 21:29 Go to previous messageGo to next message
Jo Conant is currently offline Jo Conant
Messages: 6
Registered: July 2009
Junior Member
I would like to see an analysis perspective built into STEM that outputs
some common epidemic measures, as well as other data not included in the
CSV files. Here's my wishlist:

Data output:
1. Single CSV file. It be nice to be able to have a single CSV file for
the whole area of interest, instead of having one for each location within
the area (e.g. a single file for the state of Vermont instead of having
one for each town in VT). This would allow users to make more
broad/general analysis.

2. New cases of infection. I'd like to be able to see how many new cases
of infection occur per timeframe (e.g. each day), as opposed to just
knowing how many people are in the infected state on a given day. (As
stated in #1, it'd be nice to have this data for an individual location as
well as for the entire area of interest.) Perhaps this can be
incorporated into the CSV logger? This would allow users to determine
incidence in addition to prevalence.

Data analysis:
3. Attack rate. "New cases" data for the entire area of interest (#2) can
be used to determine the illness attack rate, which is the number of new
cases / number of people at risk during the outbreak period. Attack rate
is a common measure reported in epidemiological research.

4. Epidemic curve. Use the "new cases" data for the entire area of
interest (again, #2) to create an epidemic curve, which is a graph that
plots the number of new cases per date of onset. Doing so would allow the
user to determine the peak of the epidemic/outbreak (the day that has the
most number of new cases).
Replay simulation with incidence data [message #48417 is a reply to message #43642] Fri, 26 September 2008 11:16 Go to previous message
Jo Conant is currently offline Jo Conant
Messages: 6
Registered: July 2009
Junior Member
The new Epidemic view in the Analysis Perspective is a wonderful addition
to STEM. It would be great to be able to view the simulation (map of
disease spread) and incidence and death data all on the same screen (part
of Epidemic view?), with the ability to scroll through the scenario and
see how the peaks and valleys on the incidence and deaths graphs correlate
to geographic locations of infections. I imagine being able to move a
toggle under the map back and forth and watching the map change in
correlation with a line crossing the charts that correspond to the time on
the map.
STEM Should also Run as a web application [message #585828 is a reply to message #43642] Wed, 09 July 2008 17:25 Go to previous message
James Kaufman is currently offline James Kaufman
Messages: 158
Registered: July 2009
Senior Member
STEM should also run as a web application. Please put your ideas on the
best way to do this hear under this item.
Need to automate system builds and posting of the latest STEM executable [message #585837 is a reply to message #43642] Wed, 09 July 2008 17:26 Go to previous message
James Kaufman is currently offline James Kaufman
Messages: 158
Registered: July 2009
Senior Member
The STEM build process should be automated so the Eclipse Website
every night gets the latest STEM executable
Caching Scenarios [message #585851 is a reply to message #43642] Wed, 09 July 2008 17:28 Go to previous message
Yossi Mesika is currently offline Yossi Mesika
Messages: 13
Registered: July 2009
Junior Member
Running a US scenario takes some times due to access to disk for reading
the data. It could be great if the data would be cached so that running
the scenario again wouldn't require re-reading the data from the file
system.

Such feature should be toggled from the preferences so that those who
don't wish to use it will simply turn caching off.
Re: STEM New Feature Requests Discussion [message #585862 is a reply to message #43642] Wed, 09 July 2008 17:30 Go to previous message
Jo Conant is currently offline Jo Conant
Messages: 6
Registered: July 2009
Junior Member
Triggered events. Essentially, I'd like to take a look at how to set up
an event to occur at a specific time or given a specific circumstance.
For example, creating a few infectors that would be triggered at a certain
time period.

Perhaps this could also be used to create interventions. For example,
after a specific amount of time or number of people infected, public
policy decisions such as closing roads, vaccinating people, etc could be
implemented.
Re: STEM Should also Run as a web application [message #585868 is a reply to message #43679] Wed, 09 July 2008 17:49 Go to previous message
Matthew Davis
Messages: 269
Registered: July 2009
Senior Member
Hi Jamie, what kinds of parallelism factors are in STEM? Is it a
candidate for Map/Reduce? It would really neat to see if there is a use
case for "cloud computing" in its computations. And, if you wanted to
make it a "software as a service" application for mass consumption,
perhaps even beyond the epidemiology, "the cloud" would be a great way
to host the computationally-intensive service.

As for how to do it as a Web app, a smartly done Google Maps interface
would really enhance the usability in my opinion. I'm not sure you can
duplicate the polygon renderings in the application's main visualizer in
Google Maps due to the browser's resource uses, but you could still do
some really interesting views merging the BIRT reports with municipality
markers in Google Maps. There are a ton of "mashup" uses IMO.

-Matt


James Kaufman wrote:
> STEM should also run as a web application. Please put your ideas on the
> best way to do this hear under this item.
>
Re: STEM Should also Run as a web application [message #585879 is a reply to message #43810] Wed, 09 July 2008 18:17 Go to previous message
James Kaufman is currently offline James Kaufman
Messages: 158
Registered: July 2009
Senior Member
Hi Matt,
Thank you for the GREAT comment.

Regarding parallelism, in the most general case (of a spatio-temporal
EVENT modeler) I think the answer is "it depends". It depends on how
connected your graph is. In the case of STEM today and the way we have
implemented air travel, the application should be able to make great use
of parallelism. The world naturally can be divided (for example) by
contents with relatively few edges than need to be communicated between
servers. This lowers the messaging overhead and simplifies partitioning
and distribution of the problem.

Regarding the google maps interface idea, this is a good suggestion. We
don't need to render the internal polygons in STEM but we do need an
association between IDs and locations on the graph. It's fairly easy for
us to plug in other viewers. I think the more difficult part of running on
the server is giving users an intuitive interface with the functionality
they need to "compose" a problem the way they currently do with the STEM
Eclipse rich client app.

One idea, maybe we can divide STEM so users can download the designer
perspective and run that locally. Once they have created their own
scenario we could send the scenario (and xml file) to the instance of STEM
running on the server. Since we now have full import/export functionality
working, users can already email and share their own custom scenarios
(graphs and diseases they have created). If the simulation perspective
could run on the server we can simply send it the scenario to run through
a web interface. I agree the preferred visualization might change over
time. If we can make a single instance of STEM work server side we could
then thing about how to add the parallelism...
Re: STEM Should also Run as a web application [message #585895 is a reply to message #43810] Fri, 11 July 2008 13:33 Go to previous message
Daniel Ford is currently offline Daniel Ford
Messages: 138
Registered: July 2009
Location: New York
Senior Member
Matt,
for the kinds of simulations we've been working on, mostly disease
spread in sub-global regions (e.g, North America, Asia, etc.) modelled at
administration level 2, we haven't really run out of horsepower quite yet so
going to a parrallel computing model might be a bit premature. These types
of models create graphs with on the order of 10000 nodes and simuliar
magnitude labels. Such models tend to run well on a single laptop. However,
for much bigger models representing finer detail (millions of nodes in the
representational graph) it might be the only way to make them work. I
expect disease models wouldn't really need quite that level of detail, but
if you were doing some kind of situational awareness application coupled
with integrated simulations for decision support then we'd need the power.

Something to think about or investigate is how we could leverage the fact
that all of STEM's modeling code is generated by EMF. One can provide their
own JET templates to the EMF code generator, so could we, for instance,
fiddle with the JET templates so that they generate code that would work
directly with something like Hadoop?

--
Daniel Ford
IBM Almaden Research Center
San Jose, CA
Re: Need to automate system builds and posting of the latest STEM executable [message #585904 is a reply to message #43710] Fri, 11 July 2008 13:35 Go to previous message
Daniel Ford is currently offline Daniel Ford
Messages: 138
Registered: July 2009
Location: New York
Senior Member
Lack of automation in the build process is the biggest failing of the
project I think. It's not like there isn't any, it just isn't something
that really works yet. It's not like we don't know it is good for us.

--
Daniel Ford
IBM Almaden Research Center
San Jose, CA
"James Kaufman" <kaufman@almaden.ibm.com> wrote in message
news:3424615de3cc43d618d3c131b9a386a8$1@www.eclipse.org...
> The STEM build process should be automated so the Eclipse Website
> every night gets the latest STEM executable
>
Re: Caching Scenarios [message #585918 is a reply to message #43755] Fri, 11 July 2008 13:38 Go to previous message
Daniel Ford is currently offline Daniel Ford
Messages: 138
Registered: July 2009
Location: New York
Senior Member
There's a bug for this already

https://bugs.eclipse.org/bugs/show_bug.cgi?id=177769

--
Daniel Ford
IBM Almaden Research Center
San Jose, CA
Re: STEM New Feature Requests Discussion [message #585933 is a reply to message #43778] Fri, 11 July 2008 13:46 Go to previous message
Daniel Ford is currently offline Daniel Ford
Messages: 138
Registered: July 2009
Location: New York
Senior Member
I've opened a bug for this and have a UML model for implementation.

https://bugs.eclipse.org/bugs/show_bug.cgi?id=240489

--
Daniel Ford
IBM Almaden Research Center
San Jose, CA
Data output/analysis [message #586446 is a reply to message #43642] Tue, 05 August 2008 21:29 Go to previous message
Jo Conant is currently offline Jo Conant
Messages: 6
Registered: July 2009
Junior Member
I would like to see an analysis perspective built into STEM that outputs
some common epidemic measures, as well as other data not included in the
CSV files. Here's my wishlist:

Data output:
1. Single CSV file. It be nice to be able to have a single CSV file for
the whole area of interest, instead of having one for each location within
the area (e.g. a single file for the state of Vermont instead of having
one for each town in VT). This would allow users to make more
broad/general analysis.

2. New cases of infection. I'd like to be able to see how many new cases
of infection occur per timeframe (e.g. each day), as opposed to just
knowing how many people are in the infected state on a given day. (As
stated in #1, it'd be nice to have this data for an individual location as
well as for the entire area of interest.) Perhaps this can be
incorporated into the CSV logger? This would allow users to determine
incidence in addition to prevalence.

Data analysis:
3. Attack rate. "New cases" data for the entire area of interest (#2) can
be used to determine the illness attack rate, which is the number of new
cases / number of people at risk during the outbreak period. Attack rate
is a common measure reported in epidemiological research.

4. Epidemic curve. Use the "new cases" data for the entire area of
interest (again, #2) to create an epidemic curve, which is a graph that
plots the number of new cases per date of onset. Doing so would allow the
user to determine the peak of the epidemic/outbreak (the day that has the
most number of new cases).
Replay simulation with incidence data [message #587759 is a reply to message #43642] Fri, 26 September 2008 11:16 Go to previous message
Jo Conant is currently offline Jo Conant
Messages: 6
Registered: July 2009
Junior Member
The new Epidemic view in the Analysis Perspective is a wonderful addition
to STEM. It would be great to be able to view the simulation (map of
disease spread) and incidence and death data all on the same screen (part
of Epidemic view?), with the ability to scroll through the scenario and
see how the peaks and valleys on the incidence and deaths graphs correlate
to geographic locations of infections. I imagine being able to move a
toggle under the map back and forth and watching the map change in
correlation with a line crossing the charts that correspond to the time on
the map.
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