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Public Health Disease Simulation Framework (STEM) Proposal [message #16978]

Mon, 24 April 2006 17:20

Daniel Ford

Messages: 148
Registered: July 2009
Location: New York

Senior Member

Name: Public Health Disease Simulation Framework (STEM)

Scope: To develop an integrated set of tools and data sets for developing
simulations that model the spatial and temporal spread of infectious disease
(e.g., Avian Influenza, Foot-and-Mouth Disease, etc.) The set will include
the following contents and capabilities:

* The ability to compose disease models from components via eclipse plug-ins

* Geographic data and population figures for UN Administration levels 0, 1,
& 2 (e.g., Country, Province/State, County/Municipality)

* Data definitions for all major cities, airports, road ways, rail-roads
etc. in the world

* Graphical editors for simulations, data sets, etc.

* Library of basic SEIR and SIR disease models

* Support for report generation (e.g., BIRT)

* Meta-data (Dublin core) for all components

* Visualization of the geographic spread of disease.

* Example code for dynamic model components (e.g., weather, bird migration)

* Documentation

* Multilingual support

Component Lead:

Daniel Ford, IBM Research

Stakeholders

- Contributors

IBM Research

Interested Universities

Interested Government Labs

Interested Corporate Research Groups

- Reviewers

Justin Lessler, Johns Hopkins Bloomberg School of Public Health

- Customers

IBM

Interested Universities

Interested Government Labs

Interested Corporate Research Groups

Government National centers for disease control

Government departments of agriculture

Disaster planning and response organizations

World health organizations

Corporate Agribusiness

NGO's

- Other committers (other than component lead)

TBD

Deliverables /Projected milestones

The first version of the basic framework described above in the late 2006
timeframe. Likely there would be two language versions (English, Spanish).
The definitions for detailed geographic features such as roadways would
likely be incomplete for some if not many countries.

External dependencies and relationships

* General Eclipse platform

* EMF for code generation

* BIRT for report generation

* GEF for some visualizations

* Open source geographic data sets

Relevant standards and their status (availability and SMM status)

* Dublin Core for component meta-data

* Various geographic/spatial standards

* Standard Geographic naming conventions (e.g., "Getty Thesaurus of
Geographic Names")

Issues

* Ease of use: The potential user base has a wide range of skill levels. The
more advanced users will be comfortable with extending the framework by
developing code in Java and creating eclipse plug-ins. However, the majority
of the users will not have such skills. Much attention will be needed to
address this imbalance. Perhaps various types of "Wizards" can be developed
to make the system more accessible.

* Multilingual support: This does not include just the software, but also
the meta-data for the data sets. There could be quite a bit of meta-data and
keeping it all translated in all supported languages could be a challenge.

Report message to a moderator

Re: Public Health Disease Simulation Framework (STEM) Proposal [message #17007 is a reply to message #16978]

Tue, 25 April 2006 22:57

Eclipse User

Originally posted by: grahame.jivamedical.com

Hi Dan

looks good. Why the name STEM?

This will go up for a vote by the committers
shortly

Grahame

Daniel Ford wrote:
> Name: Public Health Disease Simulation Framework (STEM)
>
> Scope: To develop an integrated set of tools and data sets for developing
> simulations that model the spatial and temporal spread of infectious disease
> (e.g., Avian Influenza, Foot-and-Mouth Disease, etc.) The set will include
> the following contents and capabilities:
>
> * The ability to compose disease models from components via eclipse plug-ins
>
> * Geographic data and population figures for UN Administration levels 0, 1,
> & 2 (e.g., Country, Province/State, County/Municipality)
>
> * Data definitions for all major cities, airports, road ways, rail-roads
> etc. in the world
>
> * Graphical editors for simulations, data sets, etc.
>
> * Library of basic SEIR and SIR disease models
>
> * Support for report generation (e.g., BIRT)
>
> * Meta-data (Dublin core) for all components
>
> * Visualization of the geographic spread of disease.
>
> * Example code for dynamic model components (e.g., weather, bird migration)
>
> * Documentation
>
> * Multilingual support
>
> Component Lead:
>
> Daniel Ford, IBM Research
>
> Stakeholders
>
> - Contributors
>
> IBM Research
>
> Interested Universities
>
> Interested Government Labs
>
> Interested Corporate Research Groups
>
> - Reviewers
>
> Justin Lessler, Johns Hopkins Bloomberg School of Public Health
>
> - Customers
>
> IBM
>
> Interested Universities
>
> Interested Government Labs
>
> Interested Corporate Research Groups
>
> Government National centers for disease control
>
> Government departments of agriculture
>
> Disaster planning and response organizations
>
> World health organizations
>
> Corporate Agribusiness
>
> NGO's
>
>
> - Other committers (other than component lead)
>
> TBD
>
> Deliverables /Projected milestones
>
> The first version of the basic framework described above in the late 2006
> timeframe. Likely there would be two language versions (English, Spanish).
> The definitions for detailed geographic features such as roadways would
> likely be incomplete for some if not many countries.
>
> External dependencies and relationships
>
> * General Eclipse platform
>
> * EMF for code generation
>
> * BIRT for report generation
>
> * GEF for some visualizations
>
> * Open source geographic data sets
>
> Relevant standards and their status (availability and SMM status)
>
> * Dublin Core for component meta-data
>
> * Various geographic/spatial standards
>
> * Standard Geographic naming conventions (e.g., "Getty Thesaurus of
> Geographic Names")
>
>
>
> Issues
>
> * Ease of use: The potential user base has a wide range of skill levels. The
> more advanced users will be comfortable with extending the framework by
> developing code in Java and creating eclipse plug-ins. However, the majority
> of the users will not have such skills. Much attention will be needed to
> address this imbalance. Perhaps various types of "Wizards" can be developed
> to make the system more accessible.
>
> * Multilingual support: This does not include just the software, but also
> the meta-data for the data sets. There could be quite a bit of meta-data and
> keeping it all translated in all supported languages could be a challenge.
>
>

Report message to a moderator

Re: Public Health Disease Simulation Framework (STEM) Proposal [message #17036 is a reply to message #17007]

Mon, 01 May 2006 15:08

Daniel Ford

Messages: 148
Registered: July 2009
Location: New York

Senior Member

Grahame,
sorry, I should have been more explicit. We just use the acronym STEM
all the time that it has become 2nd nature. STEM stands for
"Spatio-Temporal Epidemiological Modeler", meaning that it is an
epidemiological "moder" in both space and time. I like to think that the
"E" in STEM stands for "Event" which would imply that it is more general
system, which it is.

Dan

"Grahame Grieve" <grahame@jivamedical.com> wrote in message
news:e2m9in$s6m$1@utils.eclipse.org...
> Hi Dan
>
> looks good. Why the name STEM?
>
> This will go up for a vote by the committers
> shortly
>
> Grahame
>
> Daniel Ford wrote:
>> Name: Public Health Disease Simulation Framework (STEM)
>>
>> Scope: To develop an integrated set of tools and data sets for developing
>> simulations that model the spatial and temporal spread of infectious
>> disease (e.g., Avian Influenza, Foot-and-Mouth Disease, etc.) The set
>> will include the following contents and capabilities:
>>
>> * The ability to compose disease models from components via eclipse
>> plug-ins
>>
>> * Geographic data and population figures for UN Administration levels 0,
>> 1, & 2 (e.g., Country, Province/State, County/Municipality)
>>
>> * Data definitions for all major cities, airports, road ways, rail-roads
>> etc. in the world
>>
>> * Graphical editors for simulations, data sets, etc.
>>
>> * Library of basic SEIR and SIR disease models
>>
>> * Support for report generation (e.g., BIRT)
>>
>> * Meta-data (Dublin core) for all components
>>
>> * Visualization of the geographic spread of disease.
>>
>> * Example code for dynamic model components (e.g., weather, bird
>> migration)
>>
>> * Documentation
>>
>> * Multilingual support
>>
>> Component Lead:
>>
>> Daniel Ford, IBM Research
>>
>> Stakeholders
>>
>> - Contributors
>>
>> IBM Research
>>
>> Interested Universities
>>
>> Interested Government Labs
>>
>> Interested Corporate Research Groups
>>
>> - Reviewers
>>
>> Justin Lessler, Johns Hopkins Bloomberg School of Public Health
>>
>> - Customers
>>
>> IBM
>>
>> Interested Universities
>>
>> Interested Government Labs
>>
>> Interested Corporate Research Groups
>>
>> Government National centers for disease control
>>
>> Government departments of agriculture
>>
>> Disaster planning and response organizations
>>
>> World health organizations
>>
>> Corporate Agribusiness
>>
>> NGO's
>>
>>
>> - Other committers (other than component lead)
>>
>> TBD
>>
>> Deliverables /Projected milestones
>>
>> The first version of the basic framework described above in the late 2006
>> timeframe. Likely there would be two language versions (English,
>> Spanish). The definitions for detailed geographic features such as
>> roadways would likely be incomplete for some if not many countries.
>>
>> External dependencies and relationships
>>
>> * General Eclipse platform
>>
>> * EMF for code generation
>>
>> * BIRT for report generation
>>
>> * GEF for some visualizations
>>
>> * Open source geographic data sets
>>
>> Relevant standards and their status (availability and SMM status)
>>
>> * Dublin Core for component meta-data
>>
>> * Various geographic/spatial standards
>>
>> * Standard Geographic naming conventions (e.g., "Getty Thesaurus of
>> Geographic Names")
>>
>>
>>
>> Issues
>>
>> * Ease of use: The potential user base has a wide range of skill levels.
>> The more advanced users will be comfortable with extending the framework
>> by developing code in Java and creating eclipse plug-ins. However, the
>> majority of the users will not have such skills. Much attention will be
>> needed to address this imbalance. Perhaps various types of "Wizards" can
>> be developed to make the system more accessible.
>>
>> * Multilingual support: This does not include just the software, but also
>> the meta-data for the data sets. There could be quite a bit of meta-data
>> and keeping it all translated in all supported languages could be a
>> challenge.
>>

Report message to a moderator

Re: Public Health Disease Simulation Framework (STEM) Proposal [message #17065 is a reply to message #17036]

Tue, 16 May 2006 02:45

Daniel Ford

Messages: 148
Registered: July 2009
Location: New York

Senior Member

IBM announced the Global Pandemic Initiative (GPI) today. This initiative
includes STEM. You can read about it here
http://www.siliconvalley.com/mld/siliconvalley/14583722.htm or in many other
news sources (e.g. WSJ), do a google search on "IBM pandemic" and you'll get
the latest hits.

Dan

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Re: Public Health Disease Simulation Framework (STEM) Proposal [message #568255 is a reply to message #16978]

Tue, 25 April 2006 22:57

Grahame Grieve

Messages: 76
Registered: July 2009

Member

Hi Dan

looks good. Why the name STEM?

This will go up for a vote by the committers
shortly

Grahame

Daniel Ford wrote:
> Name: Public Health Disease Simulation Framework (STEM)
>
> Scope: To develop an integrated set of tools and data sets for developing
> simulations that model the spatial and temporal spread of infectious disease
> (e.g., Avian Influenza, Foot-and-Mouth Disease, etc.) The set will include
> the following contents and capabilities:
>
> * The ability to compose disease models from components via eclipse plug-ins
>
> * Geographic data and population figures for UN Administration levels 0, 1,
> & 2 (e.g., Country, Province/State, County/Municipality)
>
> * Data definitions for all major cities, airports, road ways, rail-roads
> etc. in the world
>
> * Graphical editors for simulations, data sets, etc.
>
> * Library of basic SEIR and SIR disease models
>
> * Support for report generation (e.g., BIRT)
>
> * Meta-data (Dublin core) for all components
>
> * Visualization of the geographic spread of disease.
>
> * Example code for dynamic model components (e.g., weather, bird migration)
>
> * Documentation
>
> * Multilingual support
>
> Component Lead:
>
> Daniel Ford, IBM Research
>
> Stakeholders
>
> - Contributors
>
> IBM Research
>
> Interested Universities
>
> Interested Government Labs
>
> Interested Corporate Research Groups
>
> - Reviewers
>
> Justin Lessler, Johns Hopkins Bloomberg School of Public Health
>
> - Customers
>
> IBM
>
> Interested Universities
>
> Interested Government Labs
>
> Interested Corporate Research Groups
>
> Government National centers for disease control
>
> Government departments of agriculture
>
> Disaster planning and response organizations
>
> World health organizations
>
> Corporate Agribusiness
>
> NGO's
>
>
> - Other committers (other than component lead)
>
> TBD
>
> Deliverables /Projected milestones
>
> The first version of the basic framework described above in the late 2006
> timeframe. Likely there would be two language versions (English, Spanish).
> The definitions for detailed geographic features such as roadways would
> likely be incomplete for some if not many countries.
>
> External dependencies and relationships
>
> * General Eclipse platform
>
> * EMF for code generation
>
> * BIRT for report generation
>
> * GEF for some visualizations
>
> * Open source geographic data sets
>
> Relevant standards and their status (availability and SMM status)
>
> * Dublin Core for component meta-data
>
> * Various geographic/spatial standards
>
> * Standard Geographic naming conventions (e.g., "Getty Thesaurus of
> Geographic Names")
>
>
>
> Issues
>
> * Ease of use: The potential user base has a wide range of skill levels. The
> more advanced users will be comfortable with extending the framework by
> developing code in Java and creating eclipse plug-ins. However, the majority
> of the users will not have such skills. Much attention will be needed to
> address this imbalance. Perhaps various types of "Wizards" can be developed
> to make the system more accessible.
>
> * Multilingual support: This does not include just the software, but also
> the meta-data for the data sets. There could be quite a bit of meta-data and
> keeping it all translated in all supported languages could be a challenge.
>
>

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