stem/index.php - www.eclipse.org/proposals - Git at Google


            
            <?php  																														require_once($_SERVER['DOCUMENT_ROOT'] . "/eclipse.org-common/system/app.class.php");	require_once($_SERVER['DOCUMENT_ROOT'] . "/eclipse.org-common/system/nav.class.php"); 	require_once($_SERVER['DOCUMENT_ROOT'] . "/eclipse.org-common/system/menu.class.php"); 	$App 	= new App();	$Nav	= new Nav();	$Menu 	= new Menu();		include($App->getProjectCommon());    # All on the same line to unclutter the user's desktop'


            $pageTitle 		= "STEM";

            
            $pageKeywords	= "STEM";

            
            $pageAuthor		= "Daniel Ford";


            ob_start();

            
            ?>

            
                <div id="maincontent">

            
            	<div id="midcolumn">


            <h1>STEM, The Spatiotemporal Epidemiological Modeler</h1>

            
            </p>

            
            <?php

            
            include_once($_SERVER['DOCUMENT_ROOT'] . "/projects/fragments/proposal-page-header.php");

            
            generate_header("STEM");

            
            ?>


            <p> This document is a proposal to create a new Eclipse Project under

            
            the <a href="/technology/">Eclipse Technology Project</a> called the

            
            Spatiotemporal Epidemiological Modeler or <a

            
            href="http://www.eclipse.org/ohf/components/stem/">STEM</a>. STEM is

            
            currently a component of the <a

            
            href="http://www.eclipse.org/ohf/">Open Healthcare Framework (OHF)</a>

            
            project, which is also under the

            
            Eclipse

            
            Technology Project.</p>


            <p>This proposal is presented in accordance with the <a

            
            href="/projects/dev_process/proposal-phase.php">Eclipse Development

            
            Process</a> and is written to declare the project's intent and scope

            
            as well as to solicit additional participation and feedback from the

            
            Eclipse community. You are invited to join the project and to provide

            
            feedback using the <a

            
            href="http://www.eclipse.org/newsportal/thread.php?group=eclipse.technology.ohf">

            
            http://www.eclipse.org/newsportal/thread.php?group=eclipse.technology.ohf

            
            </a>newsgroup.</p>


            <h2>Background</h2>


            <p> In the past year (2008), the OHF has seen all of its components,

            
            other than STEM, migrate either to other parts of Eclipse

            
            (e.g., <ahref="http://www.eclipse.org/ohf/components/soda/"> SODA</a>) or to

            
            the external <a href="http://www.openhealthtools.org/"> Open

            
            Healthcare Tools (OHT )</a> organization. This has left STEM as the

            
            only active component in the OHF. . The consensus of the four STEM

            
            committers is that they are very happy with Eclipse and how it is

            
            managed and wish the project to remain with the Foundation. However,

            
            given that the rest of the OHF project has moved, it makes sense to

            
            move STEM out of the OHF and place it directly under the <a

            
            href="/technology/">Eclipse Technology Project</a>. The STEM project

            
            members are looking forward to being a project separate from the OHF

            
            to better establish their "brand" and facilitate communications with

            
            users, contributors and adopters. One of the challenges of being a

            
            component of the OHF is that STEM was mixed in with many different,

            
            completely unrelated, projects; this included sharing a project web

            
            page, newsgroup, developer mailing list and project metadata. This

            
            sharing tended to dilute STEM's effectiveness in communicating with

            
            and developing its community. For instance, the OHF project metadata

            
            is out-of-date and has been for some time; the STEM project has been

            
            unable to correct that issue.

            
            </p>


            <p> STEM began life as a platform for the collaborative development of

            
            mathematical models that characterize the spread of infectious

            
            diseases in both time and space. STEM was originally developed by <a

            
            href="http://www.research.ibm.com/">IBM Research</a> at its <a

            
            href="http://www.almaden.ibm.com/">Almaden Research Center</a> to be

            
            part of <a

            
            href="http://www-03.ibm.com/press/us/en/pressrelease/19640.wss"> IBM's

            
            Global Pandemic Initiative (GPI)</a>, a working group of global

            
            healthcare "players" (WHO, UN, etc) that IBM formed to help plan for,

            
            and combat, the threat of global pandemic influenza. As part of its

            
            contribution to the GPI, IBM <a

            
            href="http://www-03.ibm.com/industries/government/us/detail/news/G708487G68482D55.html">

            
            donated</a> the source code for STEM to the Eclipse foundation in May

            
            2007. </p>


            <p> STEM enables epidemiologists and other researchers to develop

            
            disease models quickly and collaboratively. STEM includes the basic

            
            data sets that define the political geography, demographic data and

            
            transportation infrastructure for the entire planet, saving the need

            
            for modelers to collect this data on their own. It also includes

            
            configurable "text book" disease models they can use immediately and

            
            extensive editors and wizards that ease model creation. STEM includes

            
            built-in views to visualize the geographic spread of diseases as well

            
            as an interface to <a href="http://earth.google.com/"> Google

            
            Earth</a>. Each disease model is composed of a set of interchangeable

            
            components that supply different aspects of the model, these include

            
            data sets, as well as mathematics. These components can be created by

            
            different researchers and easily shared, thereby fostering cooperation

            
            and collaboration. As a diease modeling system, STEM has an active and

            
            growing community. </p>


            <h2>Technical Scope </h2>


            <p> At its core, STEM is a framework for composing arbitrary graphs

            
            (nodes, edges, labels) from different "parts" and then managing

            
            computations that use the graph as both a source of data and as place

            
            to record state information. One of the main innovations provided by

            
            STEM is that it allows the graph used during a simulation to be

            
            composed from different parts that represent different aspects of the

            
            eventual simulation. For instance, sets of labeled nodes that

            
            represent geographic locations can be combined with sets of labels

            
            that provide population data for those edges for a particular time

            
            period (e.g., 1918). Similarly, different sets of edges can be added

            
            to the graph to incorporate different kinds of relationships, such as

            
            transportation infrastructure or simple physical relationships such as

            
            sharing a common border. Computation is added to the mix through a

            
            similar well defined interface to the graph. These different parts

            
            can be aggregated and saved for reuse in multiple different models.

            
            They can also be exported and distributed to other users. It is this

            
            aggregation and reuse that promotes collaboration as different

            
            components can be created by different parties and easily shared.

            
            </p>


            <p> Having such a general framework enables a variety of other kinds

            
            of applications, not all of which are simulations. It is possible,

            
            for instance, to run STEM in "real-time" where it uses "wall-clock"

            
            time when manipulating the state of the underlying graph and have it

            
            access external data sources as part of that process. Integrating

            
            real-time weather information or other real-time environmental data

            
            into a model in STEM is an example. This ability allows STEM to be

            
            applied to decision support applications that require the integration

            
            of "situational awareness" and analytics; examples would be disaster

            
            planning and response, securities trading and risk management and

            
            logistical planning. The integration of external data sources through

            
            SOA and RSS feeds is a future step being considered for the project.

            
            </p>


            <p> The disease modeling framework, built upon the core, has well

            
            established functionality, but is deliberately designed to be

            
            extensible and has an unlimited capacity to absorb new mathematics and

            
            other aspects of disease models. For the project, however, it aims to

            
            provide a refined, but limited, set of built-in "text book" disease

            
            model mathematics as well as another set of advanced experimental

            
            models that result from project member's own research. </p>


            <p> The incorporation of real-time data sources into STEM is an area

            
            for future development. The scope and breadth of which is uncertain

            
            and likely dependent on the particular application domains used as

            
            examples. </p>


            <p> There are two aspects to STEM, the core for developing simulation

            
            frameworks, and actual simulation frameworks.  The mandates for

            
            developing both of these aspects tend to define and govern their

            
            growth.  The core for simulation frameworks is somewhat organically

            
            constrained as features are only added to it to support the needs of

            
            actual simulation frameworks such as disease modeling.  The base

            
            comprises some nine EMF Ecore models that are used to generate a

            
            significant portion of the core code; no new models are anticipated at

            
            this time.  The remainder of the work on the core is to polish and

            
            refine aspects of the core exposed to users such as model editors,

            
            wizards and other parts of the GUI.  </p>


            <p> STEM is more than a disease modeling system, however, the same

            
            attributes that make a good collaborative system for disease modeling

            
            are the same ones that facilitate other kinds of model development.

            
            To this end, STEM was designed and implemented from its very inception

            
            to be a more versatile platform and framework, with disease modeling

            
            being a very complete example "application."  </p>


            <h2>Organization</h2>


            <h3>Mentors</h3>

            
            <ul>

            
            <li>Ed Merks</li>

            
            <li>Chris Aniszczyk</li>

            
            </ul>


            <h3>Committers</h3>

            
            STEM currently has four existing and active Eclipse Committers.


            <ul>


            <li> <p> Daniel Ford (daford att almaden.ibm.com) </p> <p> Daniel

            
            was the initial Eclipse Committer for STEM. His contributions to the

            
            system include the initial concept of a composable graph framework and

            
            the general architecture and organization of STEM.  He also designed

            
            the UML models that underpin STEM's implementation and is responsible

            
            for their implementation using the Eclipse Modeling Framework (EMF).

            
            Daniel wrote the initial versions of most of the components that

            
            constituted the original STEM contribution, and continues to maintain

            
            a significant number of them today.  Daniel created the initial CQ for

            
            STEM's source code and a second one for STEM's data sets.  He worked

            
            closing with Barb Cochrane on the Eclipse IP process to quickly

            
            "clear" the original STEM source code contribution. He also worked on

            
            the initial part of the (much) longer IP processing of the STEM data

            
            sets (later passing that responsibility to James Kaufman).  Daniel

            
            received his Ph.D. in Computer Science from the University of Waterloo

            
            and is now a Research Staff Member (RSM) at the IBM Almaden Research

            
            Center in San Jose, CA. </p> </li>


            <li><p> James Kaufman (kaufman att almaden.ibm.com) </p><p> James

            
            founded the STEM project with Daniel Ford and was the project's second

            
            Eclipse committer.  James' has a wide range of contributions to the

            
            OHF and the STEM project under Eclipse. He initiated the formation of

            
            the OHF and as the IBM manager of a number of internal IBM Research

            
            Healthcare related projects, pursued the legal and organizational

            
            challenges that lead to their donation to Eclipse to form the initial

            
            OHF code base.  Later, James followed the same path with STEM and

            
            moved it from an internal IBM Research project to an open source

            
            project under Eclipse.  James is also an active and critical

            
            contributor to the STEM code base with primary responsibility in the

            
            development and implementation of mathematical models for the

            
            characterization of disease propagation and the development and

            
            implementation of mathematical tools and for epidemiological data

            
            analysis in STEM.  James also worked closely with the IBM and Eclipse

            
            legal teams to "clear" the STEM contribution to Eclipse. James

            
            received his Ph.D. in Physics from UCSB and is a Manager and Research

            
            Staff Member at the IBM Almaden Research Center in San Jose, CA.</p>

            
            </li>


            <li><p> Stefan Edlund (sedlund att us.ibm.com)</p> <p> Stefan Edlund

            
            is an Eclipse Committer has contributed to STEM since August

            
            2008. Stefan has been working on the logging component in STEM,

            
            dramatically improving its performance. Stefan has also been

            
            contributing to the analytics perspective as well as the mathematics

            
            for STEM disease models. Stefan Edlund is a Senior Software Engineer

            
            at the IBM Almaden Research Center in San Jose, CA.</p> </li>


            <li><p> Yossi Mesika (mesika att il.ibm.com) </p><p> Yossi is an

            
            Eclipse Committer who contributed several new features and

            
            improvements to the STEM project. Yossi worked on the graphical

            
            rendering of the geographical maps within STEM and added some useful

            
            features like presenting graph edges and the use of color

            
            providers. Yossi also used performance testing tools for finding

            
            memory leaks and improving the overall performance of STEM. Yossi is

            
            also the release engineer of STEM and responsible for the automatic

            
            process of generating weekly builds and publishing those in the Web

            
            site. Yossi had also made major contributions to the Eclipse Open

            
            Health Framework (OHF). Yossi is a Research Staff Member at the IBM

            
            Haifa Research Labs in Israel.</p> </li>


            </ul>


            <h3>Collaborations</h3>


            <p> The STEM project is working on the development of its community.

            
            The project is doing well in developing a core set of <b>Committers</b> and

            
            <b>Users</b> (listed below).  The project is working hard on

            
            developing relationships with government, industry and academia.  In

            
            academia, the project is nurturing graduate students in both

            
            Epidemiology and Operations Research to create a natural class of

            
            <b>Adopters</b> to join the project.  </p>


            <ul>


            <li> <p> <a href="http://www.hq.af.mil/"> USAF</a>: STEM currently has

            
            multi-year funding from the United States Air Force for the general

            
            development of the framework as well as for research into specialized

            
            analytics for "reverse engineering" disease model configurations from

            
            incident data. </p></li>


            <li><p> <a href="http://www.uvm.edu/">University of Vermont</a>: STEM

            
            has a successful ongoing collaboration with researchers Dr. Charles

            
            Hulse (Charles.Hulse at uvm.edu) and Joanna Conant (Joanna.Conant at

            
            uvm.edu) at the University of Vermont.  This collaboration has

            
            resulted in one paper with more likely to come in the future.  </p>


            <p> Kaufman, J., Connance, J., Ford, D.A., Kirhata, W., Jones, B.A.,

            
            Douglas, J.V., "Assessing the Accuracy of Spatiotemporal

            
            Epidemiological Models,"  BioSecure 2008, Raleigh, North Carolina,

            
            Dec. 2, 2008.</p> </li>


            <li> <p> <a href="www.jhu.edu">Johns Hopkins</a>: The STEM project

            
            also collaborates with the <a href="http://www.jhsph.edu/">Johns

            
            Hopkins Bloomberg School of Public Health</a>, where we work with

            
            Epidemiology Ph.D., Graduate Student Justin Lesler on the validation

            
            of the mathematics of our disease models. (Full Disclosure: IBM pays

            
            Justin Lessler for this work). </p></li>


            <li><p><a href="www.mit.edu>">MIT</a>: STEM has an ongoing

            
            collaboration with Professor Dick Larson, in the <a

            
            href="http://www.mit.edu/~orc/">Operations Research Department</a> at

            
            MIT for the development of advanced disease models.</p></li>


            <li><p><a href="http://www.mecids.org/index.php"> Middle East

            
            Consortium for Infectious Disease Surveillance</a> (MECIDS): An

            
            organization supported by the <a

            
            href="http://www.nti.org/index.php">Nuclear Threat Initiative</a>

            
            (NTI) and <a href="http://www.sfcg.org/">Search for Common Ground</a>,

            
            which includes the public health departments of <a

            
            href="http://www.health.gov.il/english/"> Israeli<a>, <a

            
            href="http://www.moh.gov.jo/MOH/En/home.php">Jordan</a>, and <a

            
            href="http://www.moh.gov.ps/">Palestinian</a>.  As well as <a

            
            href="http://www.tau.ac.il/index-eng.html"> Tel Aviv University</a>

            
            and <a href="http://www.alquds.edu/index.php"> Al Quds University

            
            </a>.


            </p></li>


            <li><p> <a href="http://www.publichealth.pitt.edu/"> University of

            
            Pittsburgh Graduate School of Public Health</a> and <a

            
            href="http://www.medschool.pitt.edu/"> School of Medicine</a>,

            
            Prof. Burce Lee</p></li>


            </ul>


            <h2>Tentative Plan </h2><p>


            2009-06 V0.4: Base release for Disease modeling

            
            2009-12 V0.5: Non-disease modeling example application

            
            2010-06 V0.6: Integrated situational awareness and analytics


                  </div>

            
              </div>

            
            <?php

            
            	$html = ob_get_contents();

            
            	ob_end_clean();


            	# Generate the web page

            
            	$App->generatePage($theme, $Menu, $Nav, $pageAuthor, $pageKeywords, $pageTitle, $html);

            
            ?>
	<?php require_once($_SERVER['DOCUMENT_ROOT'] . "/eclipse.org-common/system/app.class.php"); require_once($_SERVER['DOCUMENT_ROOT'] . "/eclipse.org-common/system/nav.class.php"); require_once($_SERVER['DOCUMENT_ROOT'] . "/eclipse.org-common/system/menu.class.php"); $App = new App(); $Nav = new Nav(); $Menu = new Menu(); include($App->getProjectCommon()); # All on the same line to unclutter the user's desktop'

	$pageTitle = "STEM";
	$pageKeywords = "STEM";
	$pageAuthor = "Daniel Ford";

	ob_start();
	?>
	<div id="maincontent">
	<div id="midcolumn">

	<h1>STEM, The Spatiotemporal Epidemiological Modeler</h1>
	</p>
	<?php
	include_once($_SERVER['DOCUMENT_ROOT'] . "/projects/fragments/proposal-page-header.php");
	generate_header("STEM");
	?>




	<p> This document is a proposal to create a new Eclipse Project under
	the <a href="/technology/">Eclipse Technology Project</a> called the
	Spatiotemporal Epidemiological Modeler or <a
	href="http://www.eclipse.org/ohf/components/stem/">STEM</a>. STEM is
	currently a component of the <a
	href="http://www.eclipse.org/ohf/">Open Healthcare Framework (OHF)</a>
	project, which is also under the
	Eclipse
	Technology Project.</p>

	<p>This proposal is presented in accordance with the <a
	href="/projects/dev_process/proposal-phase.php">Eclipse Development
	Process</a> and is written to declare the project's intent and scope
	as well as to solicit additional participation and feedback from the
	Eclipse community. You are invited to join the project and to provide
	feedback using the <a
	href="http://www.eclipse.org/newsportal/thread.php?group=eclipse.technology.ohf">
	http://www.eclipse.org/newsportal/thread.php?group=eclipse.technology.ohf
	</a>newsgroup.</p>

	<h2>Background</h2>

	<p> In the past year (2008), the OHF has seen all of its components,
	other than STEM, migrate either to other parts of Eclipse
	(e.g., <ahref="http://www.eclipse.org/ohf/components/soda/"> SODA</a>) or to
	the external <a href="http://www.openhealthtools.org/"> Open
	Healthcare Tools (OHT )</a> organization. This has left STEM as the
	only active component in the OHF. . The consensus of the four STEM
	committers is that they are very happy with Eclipse and how it is
	managed and wish the project to remain with the Foundation. However,
	given that the rest of the OHF project has moved, it makes sense to
	move STEM out of the OHF and place it directly under the <a
	href="/technology/">Eclipse Technology Project</a>. The STEM project
	members are looking forward to being a project separate from the OHF
	to better establish their "brand" and facilitate communications with
	users, contributors and adopters. One of the challenges of being a
	component of the OHF is that STEM was mixed in with many different,
	completely unrelated, projects; this included sharing a project web
	page, newsgroup, developer mailing list and project metadata. This
	sharing tended to dilute STEM's effectiveness in communicating with
	and developing its community. For instance, the OHF project metadata
	is out-of-date and has been for some time; the STEM project has been
	unable to correct that issue.
	</p>


	<p> STEM began life as a platform for the collaborative development of
	mathematical models that characterize the spread of infectious
	diseases in both time and space. STEM was originally developed by <a
	href="http://www.research.ibm.com/">IBM Research</a> at its <a
	href="http://www.almaden.ibm.com/">Almaden Research Center</a> to be
	part of <a
	href="http://www-03.ibm.com/press/us/en/pressrelease/19640.wss"> IBM's
	Global Pandemic Initiative (GPI)</a>, a working group of global
	healthcare "players" (WHO, UN, etc) that IBM formed to help plan for,
	and combat, the threat of global pandemic influenza. As part of its
	contribution to the GPI, IBM <a
	href="http://www-03.ibm.com/industries/government/us/detail/news/G708487G68482D55.html">
	donated</a> the source code for STEM to the Eclipse foundation in May
	2007. </p>

	<p> STEM enables epidemiologists and other researchers to develop
	disease models quickly and collaboratively. STEM includes the basic
	data sets that define the political geography, demographic data and
	transportation infrastructure for the entire planet, saving the need
	for modelers to collect this data on their own. It also includes
	configurable "text book" disease models they can use immediately and
	extensive editors and wizards that ease model creation. STEM includes
	built-in views to visualize the geographic spread of diseases as well
	as an interface to <a href="http://earth.google.com/"> Google
	Earth</a>. Each disease model is composed of a set of interchangeable
	components that supply different aspects of the model, these include
	data sets, as well as mathematics. These components can be created by
	different researchers and easily shared, thereby fostering cooperation
	and collaboration. As a diease modeling system, STEM has an active and
	growing community. </p>

	<h2>Technical Scope </h2>

	<p> At its core, STEM is a framework for composing arbitrary graphs
	(nodes, edges, labels) from different "parts" and then managing
	computations that use the graph as both a source of data and as place
	to record state information. One of the main innovations provided by
	STEM is that it allows the graph used during a simulation to be
	composed from different parts that represent different aspects of the
	eventual simulation. For instance, sets of labeled nodes that
	represent geographic locations can be combined with sets of labels
	that provide population data for those edges for a particular time
	period (e.g., 1918). Similarly, different sets of edges can be added
	to the graph to incorporate different kinds of relationships, such as
	transportation infrastructure or simple physical relationships such as
	sharing a common border. Computation is added to the mix through a
	similar well defined interface to the graph. These different parts
	can be aggregated and saved for reuse in multiple different models.
	They can also be exported and distributed to other users. It is this
	aggregation and reuse that promotes collaboration as different
	components can be created by different parties and easily shared.
	</p>

	<p> Having such a general framework enables a variety of other kinds
	of applications, not all of which are simulations. It is possible,
	for instance, to run STEM in "real-time" where it uses "wall-clock"
	time when manipulating the state of the underlying graph and have it
	access external data sources as part of that process. Integrating
	real-time weather information or other real-time environmental data
	into a model in STEM is an example. This ability allows STEM to be
	applied to decision support applications that require the integration
	of "situational awareness" and analytics; examples would be disaster
	planning and response, securities trading and risk management and
	logistical planning. The integration of external data sources through
	SOA and RSS feeds is a future step being considered for the project.
	</p>

	<p> The disease modeling framework, built upon the core, has well
	established functionality, but is deliberately designed to be
	extensible and has an unlimited capacity to absorb new mathematics and
	other aspects of disease models. For the project, however, it aims to
	provide a refined, but limited, set of built-in "text book" disease
	model mathematics as well as another set of advanced experimental
	models that result from project member's own research. </p>

	<p> The incorporation of real-time data sources into STEM is an area
	for future development. The scope and breadth of which is uncertain
	and likely dependent on the particular application domains used as
	examples. </p>


	<p> There are two aspects to STEM, the core for developing simulation
	frameworks, and actual simulation frameworks. The mandates for
	developing both of these aspects tend to define and govern their
	growth. The core for simulation frameworks is somewhat organically
	constrained as features are only added to it to support the needs of
	actual simulation frameworks such as disease modeling. The base
	comprises some nine EMF Ecore models that are used to generate a
	significant portion of the core code; no new models are anticipated at
	this time. The remainder of the work on the core is to polish and
	refine aspects of the core exposed to users such as model editors,
	wizards and other parts of the GUI. </p>


	<p> STEM is more than a disease modeling system, however, the same
	attributes that make a good collaborative system for disease modeling
	are the same ones that facilitate other kinds of model development.
	To this end, STEM was designed and implemented from its very inception
	to be a more versatile platform and framework, with disease modeling
	being a very complete example "application." </p>

	<h2>Organization</h2>

	<h3>Mentors</h3>
	<ul>
	<li>Ed Merks</li>
	<li>Chris Aniszczyk</li>
	</ul>


	<h3>Committers</h3>
	STEM currently has four existing and active Eclipse Committers.

	<ul>

	<li> <p> Daniel Ford (daford att almaden.ibm.com) </p> <p> Daniel
	was the initial Eclipse Committer for STEM. His contributions to the
	system include the initial concept of a composable graph framework and
	the general architecture and organization of STEM. He also designed
	the UML models that underpin STEM's implementation and is responsible
	for their implementation using the Eclipse Modeling Framework (EMF).
	Daniel wrote the initial versions of most of the components that
	constituted the original STEM contribution, and continues to maintain
	a significant number of them today. Daniel created the initial CQ for
	STEM's source code and a second one for STEM's data sets. He worked
	closing with Barb Cochrane on the Eclipse IP process to quickly
	"clear" the original STEM source code contribution. He also worked on
	the initial part of the (much) longer IP processing of the STEM data
	sets (later passing that responsibility to James Kaufman). Daniel
	received his Ph.D. in Computer Science from the University of Waterloo
	and is now a Research Staff Member (RSM) at the IBM Almaden Research
	Center in San Jose, CA. </p> </li>

	<li><p> James Kaufman (kaufman att almaden.ibm.com) </p><p> James
	founded the STEM project with Daniel Ford and was the project's second
	Eclipse committer. James' has a wide range of contributions to the
	OHF and the STEM project under Eclipse. He initiated the formation of
	the OHF and as the IBM manager of a number of internal IBM Research
	Healthcare related projects, pursued the legal and organizational
	challenges that lead to their donation to Eclipse to form the initial
	OHF code base. Later, James followed the same path with STEM and
	moved it from an internal IBM Research project to an open source
	project under Eclipse. James is also an active and critical
	contributor to the STEM code base with primary responsibility in the
	development and implementation of mathematical models for the
	characterization of disease propagation and the development and
	implementation of mathematical tools and for epidemiological data
	analysis in STEM. James also worked closely with the IBM and Eclipse
	legal teams to "clear" the STEM contribution to Eclipse. James
	received his Ph.D. in Physics from UCSB and is a Manager and Research
	Staff Member at the IBM Almaden Research Center in San Jose, CA.</p>
	</li>

	<li><p> Stefan Edlund (sedlund att us.ibm.com)</p> <p> Stefan Edlund
	is an Eclipse Committer has contributed to STEM since August
	2008. Stefan has been working on the logging component in STEM,
	dramatically improving its performance. Stefan has also been
	contributing to the analytics perspective as well as the mathematics
	for STEM disease models. Stefan Edlund is a Senior Software Engineer
	at the IBM Almaden Research Center in San Jose, CA.</p> </li>

	<li><p> Yossi Mesika (mesika att il.ibm.com) </p><p> Yossi is an
	Eclipse Committer who contributed several new features and
	improvements to the STEM project. Yossi worked on the graphical
	rendering of the geographical maps within STEM and added some useful
	features like presenting graph edges and the use of color
	providers. Yossi also used performance testing tools for finding
	memory leaks and improving the overall performance of STEM. Yossi is
	also the release engineer of STEM and responsible for the automatic
	process of generating weekly builds and publishing those in the Web
	site. Yossi had also made major contributions to the Eclipse Open
	Health Framework (OHF). Yossi is a Research Staff Member at the IBM
	Haifa Research Labs in Israel.</p> </li>

	</ul>


	<h3>Collaborations</h3>

	<p> The STEM project is working on the development of its community.
	The project is doing well in developing a core set of <b>Committers</b> and
	<b>Users</b> (listed below). The project is working hard on
	developing relationships with government, industry and academia. In
	academia, the project is nurturing graduate students in both
	Epidemiology and Operations Research to create a natural class of
	<b>Adopters</b> to join the project. </p>

	<ul>

	<li> <p> <a href="http://www.hq.af.mil/"> USAF</a>: STEM currently has
	multi-year funding from the United States Air Force for the general
	development of the framework as well as for research into specialized
	analytics for "reverse engineering" disease model configurations from
	incident data. </p></li>

	<li><p> <a href="http://www.uvm.edu/">University of Vermont</a>: STEM
	has a successful ongoing collaboration with researchers Dr. Charles
	Hulse (Charles.Hulse at uvm.edu) and Joanna Conant (Joanna.Conant at
	uvm.edu) at the University of Vermont. This collaboration has
	resulted in one paper with more likely to come in the future. </p>

	<p> Kaufman, J., Connance, J., Ford, D.A., Kirhata, W., Jones, B.A.,
	Douglas, J.V., "Assessing the Accuracy of Spatiotemporal
	Epidemiological Models," BioSecure 2008, Raleigh, North Carolina,
	Dec. 2, 2008.</p> </li>

	<li> <p> <a href="www.jhu.edu">Johns Hopkins</a>: The STEM project
	also collaborates with the <a href="http://www.jhsph.edu/">Johns
	Hopkins Bloomberg School of Public Health</a>, where we work with
	Epidemiology Ph.D., Graduate Student Justin Lesler on the validation
	of the mathematics of our disease models. (Full Disclosure: IBM pays
	Justin Lessler for this work). </p></li>

	<li><p><a href="www.mit.edu>">MIT</a>: STEM has an ongoing
	collaboration with Professor Dick Larson, in the <a
	href="http://www.mit.edu/~orc/">Operations Research Department</a> at
	MIT for the development of advanced disease models.</p></li>

	<li><p><a href="http://www.mecids.org/index.php"> Middle East
	Consortium for Infectious Disease Surveillance</a> (MECIDS): An
	organization supported by the <a
	href="http://www.nti.org/index.php">Nuclear Threat Initiative</a>
	(NTI) and <a href="http://www.sfcg.org/">Search for Common Ground</a>,
	which includes the public health departments of <a
	href="http://www.health.gov.il/english/"> Israeli<a>, <a
	href="http://www.moh.gov.jo/MOH/En/home.php">Jordan</a>, and <a
	href="http://www.moh.gov.ps/">Palestinian</a>. As well as <a
	href="http://www.tau.ac.il/index-eng.html"> Tel Aviv University</a>
	and <a href="http://www.alquds.edu/index.php"> Al Quds University
	</a>.

	</p></li>

	<li><p> <a href="http://www.publichealth.pitt.edu/"> University of
	Pittsburgh Graduate School of Public Health</a> and <a
	href="http://www.medschool.pitt.edu/"> School of Medicine</a>,
	Prof. Burce Lee</p></li>

	</ul>

	<h2>Tentative Plan </h2><p>

	2009-06 V0.4: Base release for Disease modeling
	2009-12 V0.5: Non-disease modeling example application
	2010-06 V0.6: Integrated situational awareness and analytics





	</div>
	</div>
	<?php
	$html = ob_get_contents();
	ob_end_clean();

	# Generate the web page
	$App->generatePage($theme, $Menu, $Nav, $pageAuthor, $pageKeywords, $pageTitle, $html);
	?>