index.php - gerrit/www.eclipse.org/stem - 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();

            
            $theme = "Nova";

            
            include ($App->getProjectCommon()); // All on the same line to unclutter the user's desktop'

            
            require_once ($_SERVER['DOCUMENT_ROOT'] . "/stem/functions.php");


            // *****************************************************************************

            
            //

            
            // template.php

            
            //

            
            // Author: Yossi Mesika

            
            // Date: 2009-07-19

            
            //

            
            // Description: Main web page for STEM

            
            //

            
            //

            
            // ****************************************************************************


            //

            
            // Begin: page-specific settings. Change these.

            
            $pageTitle = "STEM";

            
            $pageKeywords = "STEM";

            
            $pageAuthor = "James Kaufman, Stefan Edlund, Yossi Mesika";


            // Add page-specific Nav bars here

            
            // Format is Link text, link URL (can be http://www.someothersite.com/), target (_self, _blank), level (1, 2 or 3)

            
            // $Nav->addNavSeparator("My Page Links", "downloads.php");

            
            // $Nav->addCustomNav("My Link", "mypage.php", "_self", 3);

            
            // $Nav->addCustomNav("Google", "http://www.google.com/", "_blank", 3);


            // End: page-specific settings

            
            //


            // Paste your HTML content between the EOHTML markers!

            
            ob_start();

            
            ?>


            <style>

            
            h1 {text-align:center;}

            
            .container {

            
                width: 90%;

            
            }

            
            </style>


            <div id="maincontent" style="width:95%" >

            
            	<div id="midcolumn" style="width:70%">


            		<h1>The Spatiotemporal Epidemiological Modeler (STEM) Project</h1>


            		<div class="homeitem3col">

            
            			<a id ="about"></a>

            
            			<h3>About STEM</h3>

            
            			<div style="padding: 3px;">

            
            				<img alt="STEM Banner" src="/stem/images/STEM_SPLASH5_300.gif"

            
            					style="float: right; width: 300px;; height: 172px" />

            
            				<p>The Spatiotemporal Epidemiological Modeler (STEM) tool is

            
            					designed to help scientists and public health officials create and

            
            					use spatial and temporal models of emerging infectious diseases.

            
            					These models can aid in understanding and potentially preventing

            
            					the spread of such diseases.</p>

            
            				<p>Policymakers responsible for strategies to contain disease and

            
            					prevent epidemics need an accurate understanding of disease

            
            					dynamics and the likely outcomes of preventive actions. In an

            
            					increasingly connected world with extremely efficient global

            
            					transportation links, the vectors of infection can be quite

            
            					complex. STEM facilitates the development of advanced mathematical

            
            					models, the creation of flexible models involving multiple

            
            					populations (species) and interactions between diseases, and a

            
            					better understanding of epidemiology.</p>

            
            				<p>STEM is designed to make it easy for developers and researchers

            
            					to plug in their choice of models. It comes with a large number of

            
            					existing compartment models and a new model building framework that

            
            					allows users to rapidly extend existing models or to create

            
            					entirely new models. The model building framework provides a simple

            
            					graphical users interface and automatically generates all of the

            
            					model code and hot injects the code into STEM at runtime. In many

            
            					cases, no knowledge of Eclipse or Java is required. The STEM code

            
            					generator even allows users to build models affected by changes in

            
            					climate data.</p>

            
            				<p>

            
            					Any STEM model can be run either stochastically or

            
            					deterministically - simply by switching between solver plugins.

            
            					Users can choose between many different numerical solvers of

            
            					ordinary differential equations (including finite difference,

            
            					Runge-Kutta, 4 solvers from The Apache Commons Mathematics Library,

            
            					and Stochastic). The stochastic solver computes integer

            
            					(individual) based transitions picking randomly from a binomial

            
            					distribution (also from Apach Math). Simulation results can be

            
            					output with a choice of pluggable loggers, including delimiting

            
            					files, video loggers, and map loggers. STEM can be used to study

            
            					quite complex models (for example a model of Dengue Fever with 51

            
            					differential equations) and can run global scale simulations. <a

            
            						href="http://wiki.eclipse.org/index.php/STEM">Click here</a> for

            
            					the complete STEM documentation.

            
            				</p>

            
            				<p>

            
            					<a href="./intro.php"> more.... </a>

            
            				</p>

            
            			</div>

            
            		</div>


            		<div class="homeitem3col">

            
            			<a id="status"></a>

            
            			<h3>Project Status</h3>

            
            			<div style="padding: 3px;">

            
            				<p>

            
            					<b><a href="downloads.php">Download latest build today</a> </b>

            
            				</p>

            
            			</div>

            
            		</div>


            		<div class="homeitem3col">

            
            			<a id="gettingstarted" /></a>

            
            			<h3>Getting Started</h3>

            
            			<div style="padding: 3px;">

            
            				<p>


            				<ul>

            
            					<li><a href="downloads.php">Download STEM!</a> (available for

            
            						Windows, Linux and Mac)</li>

            
            					<li><a href="http://wiki.eclipse.org/Installation_Guide"

            
            						title="Installation Guide">Installation Guide</a></li>

            
            					<li><a href="http://wiki.eclipse.org/STEM_FAQ">FAQ</a></li>

            
            				</ul>

            
            			</div>

            
            		</div>


            		<div class="homeitem3col">

            
            			<a id="resources" /></a>

            
            			<h3>Resources</h3>

            
            			<div style="padding: 3px;">

            
            				<p>STEM Project Resources</p>

            
            				<ul>

            
            					<li><a

            
            						href="https://bugs.eclipse.org/bugs/buglist.cgi?query_format=advanced&short_desc_type=allwordssubstr&short_desc=&classification=Technology&product=STEM&long_desc_type=allwordssubstr&long_desc=&bug_file_loc_type=allwordssubstr&bug_file_loc=&status_whiteboard_type=allwordssubstr&status_whiteboard=&keywords_type=allwords&keywords=&emailtype1=substring&email1=&emailtype2=substring&email2=&bugidtype=include&bug_id=&votes=&chfieldfrom=&chfieldto=Now&chfieldvalue=&cmdtype=doit&order=Reuse+same+sort+as+last+time&field0-0-0=noop&type0-0-0=noop&value0-0-0=">Existing

            
            							STEM Bugs</a> on <a href="https://bugs.eclipse.org/bugs/">Bugzilla</a>.<br />

            
            						<a href="https://bugs.eclipse.org/bugs/enter_bug.cgi?product=STEM">Submit

            
            							a new bug</a></li>

            
            					<li><a href="http://wiki.eclipse.org/Welcome_STEM_Developers">Developers

            
            							Documentation</a> Guide</li>

            
            					<li><a

            
            						href="http://www.eclipse.org/newsportal/thread.php?group=eclipse.stem">Newsgroup</a>

            
            						(See <a href="http://www.eclipse.org/newsgroups/">About the

            
            							newsgroups</a> if you have access problems)</li>

            
            					<li><a href="http://wiki.eclipse.org/index.php/STEM">Wiki</a></li>

            
            					<li><a href="https://wiki.eclipse.org/STEM_Eclipse_Setup">Access

            
            							the STEM source code</a></li>

            
            					<li><a href="http://www.eclipse.org">Main Eclipse Foundation

            
            							website</a></li>

            
            					<li><a href="http://www.eclipse.org/legal/privacy.php">Privacy

            
            							policy</a></li>

            
            					<li><a href="http://www.eclipse.org/legal/termsofuse.php">Website

            
            							terms of use</a></li>

            
            					<li><a href="http://www.eclipse.org/legal/copyright.php">Copyright

            
            							agent</a></li>

            
            					<li><a href="http://www.eclipse.org/legal">Legal</a></li>


            				</ul>

            
            			</div>

            
            		</div>

            
            	</div>


                <div id="rightcolumn" style="width:30%">

            
                	<div class="sideitem">

            
                		<h6>News</h6>

            
                			<?php getRssFeed('http://www.eclipse.org/forums/rdf.php?mode=m&l=1&basic=1&frm=72&n=5', $_SERVER['DOCUMENT_ROOT'] . '/stem/data/rss_cache.xml'); ?>

            
                			<br> <i><a href="http://www.eclipse.org/forums/index.php?t=thread&frm_id=72">more...</a></i>


                	</div>

            
                	<div class="sideitem">

            
                		<h6>Videos and presentations</h6>

            
                			<?php getData('/stem/data/videos.xml', 10); ?>

            
                		</div>

            
                	<div class="sideitem">

            
                		<h6>Downloadable Scenarios</h6>

            
                			<?php getData('/stem/data/scenarios.xml', 4, 'images/icon-save.gif'); ?>

            
                			<br /> <a href="http://www.eclipse.org/stem/downloads.php#DownloadableScenarios">

            
                			...more Downloadable Scenarios</a>

            
                	</div>

            
                	<div class="sideitem">

            
                		<h6>Recent Publications</h6>

            
                			<?php getData('/stem/data/pubs.xml', 10); ?>

            
                			<br> <i><a href="http://wiki.eclipse.org/Publications_and_Presentations_on_STEM">

            
                				...more Publications</a></i>


                	</div>

            
                	<div class="sideitem">

            
                		<h6>Upcoming (and recent) talks</h6>

            
                			<?php getData('/stem/data/talks.xml', 10); ?>

            
                			<i><a href="http://wiki.eclipse.org/Publications_and_Presentations_on_STEM">

            
                				...more talks</a></i>

            
                	</div>

            
                	<div class="sideitem">

            
                		<h6>Acknowledgements</h6>

            
                		<!-- <img alt="Development of STEM was supported in part by USAF/SG" src="/stem/images/usaf.gif" style="float: left;width:150px;"/> -->

            
                			<?php getData('/stem/data/acknowledgements.xml', 15); ?>

            
                		</div>

            
                </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();
	$theme = "Nova";
	include ($App->getProjectCommon()); // All on the same line to unclutter the user's desktop'
	require_once ($_SERVER['DOCUMENT_ROOT'] . "/stem/functions.php");

	// *****************************************************************************
	//
	// template.php
	//
	// Author: Yossi Mesika
	// Date: 2009-07-19
	//
	// Description: Main web page for STEM
	//
	//
	// ****************************************************************************

	//
	// Begin: page-specific settings. Change these.
	$pageTitle = "STEM";
	$pageKeywords = "STEM";
	$pageAuthor = "James Kaufman, Stefan Edlund, Yossi Mesika";

	// Add page-specific Nav bars here
	// Format is Link text, link URL (can be http://www.someothersite.com/), target (_self, _blank), level (1, 2 or 3)
	// $Nav->addNavSeparator("My Page Links", "downloads.php");
	// $Nav->addCustomNav("My Link", "mypage.php", "_self", 3);
	// $Nav->addCustomNav("Google", "http://www.google.com/", "_blank", 3);

	// End: page-specific settings
	//

	// Paste your HTML content between the EOHTML markers!
	ob_start();
	?>

	<style>
	h1 {text-align:center;}
	.container {
	width: 90%;
	}
	</style>

	<div id="maincontent" style="width:95%" >
	<div id="midcolumn" style="width:70%">

	<h1>The Spatiotemporal Epidemiological Modeler (STEM) Project</h1>

	<div class="homeitem3col">
	<a id ="about"></a>
	<h3>About STEM</h3>
	<div style="padding: 3px;">
	<img alt="STEM Banner" src="/stem/images/STEM_SPLASH5_300.gif"
	style="float: right; width: 300px;; height: 172px" />
	<p>The Spatiotemporal Epidemiological Modeler (STEM) tool is
	designed to help scientists and public health officials create and
	use spatial and temporal models of emerging infectious diseases.
	These models can aid in understanding and potentially preventing
	the spread of such diseases.</p>
	<p>Policymakers responsible for strategies to contain disease and
	prevent epidemics need an accurate understanding of disease
	dynamics and the likely outcomes of preventive actions. In an
	increasingly connected world with extremely efficient global
	transportation links, the vectors of infection can be quite
	complex. STEM facilitates the development of advanced mathematical
	models, the creation of flexible models involving multiple
	populations (species) and interactions between diseases, and a
	better understanding of epidemiology.</p>
	<p>STEM is designed to make it easy for developers and researchers
	to plug in their choice of models. It comes with a large number of
	existing compartment models and a new model building framework that
	allows users to rapidly extend existing models or to create
	entirely new models. The model building framework provides a simple
	graphical users interface and automatically generates all of the
	model code and hot injects the code into STEM at runtime. In many
	cases, no knowledge of Eclipse or Java is required. The STEM code
	generator even allows users to build models affected by changes in
	climate data.</p>
	<p>
	Any STEM model can be run either stochastically or
	deterministically - simply by switching between solver plugins.
	Users can choose between many different numerical solvers of
	ordinary differential equations (including finite difference,
	Runge-Kutta, 4 solvers from The Apache Commons Mathematics Library,
	and Stochastic). The stochastic solver computes integer
	(individual) based transitions picking randomly from a binomial
	distribution (also from Apach Math). Simulation results can be
	output with a choice of pluggable loggers, including delimiting
	files, video loggers, and map loggers. STEM can be used to study
	quite complex models (for example a model of Dengue Fever with 51
	differential equations) and can run global scale simulations. <a
	href="http://wiki.eclipse.org/index.php/STEM">Click here</a> for
	the complete STEM documentation.
	</p>
	<p>
	<a href="./intro.php"> more.... </a>
	</p>
	</div>
	</div>

	<div class="homeitem3col">
	<a id="status"></a>
	<h3>Project Status</h3>
	<div style="padding: 3px;">
	<p>
	<b><a href="downloads.php">Download latest build today</a> </b>
	</p>
	</div>
	</div>

	<div class="homeitem3col">
	<a id="gettingstarted" /></a>
	<h3>Getting Started</h3>
	<div style="padding: 3px;">
	<p>


	<ul>
	<li><a href="downloads.php">Download STEM!</a> (available for
	Windows, Linux and Mac)</li>
	<li><a href="http://wiki.eclipse.org/Installation_Guide"
	title="Installation Guide">Installation Guide</a></li>
	<li><a href="http://wiki.eclipse.org/STEM_FAQ">FAQ</a></li>
	</ul>
	</div>
	</div>

	<div class="homeitem3col">
	<a id="resources" /></a>
	<h3>Resources</h3>
	<div style="padding: 3px;">
	<p>STEM Project Resources</p>
	<ul>
	<li><a
	href="https://bugs.eclipse.org/bugs/buglist.cgi?query_format=advanced&short_desc_type=allwordssubstr&short_desc=&classification=Technology&product=STEM&long_desc_type=allwordssubstr&long_desc=&bug_file_loc_type=allwordssubstr&bug_file_loc=&status_whiteboard_type=allwordssubstr&status_whiteboard=&keywords_type=allwords&keywords=&emailtype1=substring&email1=&emailtype2=substring&email2=&bugidtype=include&bug_id=&votes=&chfieldfrom=&chfieldto=Now&chfieldvalue=&cmdtype=doit&order=Reuse+same+sort+as+last+time&field0-0-0=noop&type0-0-0=noop&value0-0-0=">Existing
	STEM Bugs</a> on <a href="https://bugs.eclipse.org/bugs/">Bugzilla</a>.<br />
	<a href="https://bugs.eclipse.org/bugs/enter_bug.cgi?product=STEM">Submit
	a new bug</a></li>
	<li><a href="http://wiki.eclipse.org/Welcome_STEM_Developers">Developers
	Documentation</a> Guide</li>
	<li><a
	href="http://www.eclipse.org/newsportal/thread.php?group=eclipse.stem">Newsgroup</a>
	(See <a href="http://www.eclipse.org/newsgroups/">About the
	newsgroups</a> if you have access problems)</li>
	<li><a href="http://wiki.eclipse.org/index.php/STEM">Wiki</a></li>
	<li><a href="https://wiki.eclipse.org/STEM_Eclipse_Setup">Access
	the STEM source code</a></li>
	<li><a href="http://www.eclipse.org">Main Eclipse Foundation
	website</a></li>
	<li><a href="http://www.eclipse.org/legal/privacy.php">Privacy
	policy</a></li>
	<li><a href="http://www.eclipse.org/legal/termsofuse.php">Website
	terms of use</a></li>
	<li><a href="http://www.eclipse.org/legal/copyright.php">Copyright
	agent</a></li>
	<li><a href="http://www.eclipse.org/legal">Legal</a></li>

	</ul>
	</div>
	</div>
	</div>

	<div id="rightcolumn" style="width:30%">
	<div class="sideitem">
	<h6>News</h6>
	<?php getRssFeed('http://www.eclipse.org/forums/rdf.php?mode=m&l=1&basic=1&frm=72&n=5', $_SERVER['DOCUMENT_ROOT'] . '/stem/data/rss_cache.xml'); ?>
	<br> <i><a href="http://www.eclipse.org/forums/index.php?t=thread&frm_id=72">more...</a></i>

	</div>
	<div class="sideitem">
	<h6>Videos and presentations</h6>
	<?php getData('/stem/data/videos.xml', 10); ?>
	</div>
	<div class="sideitem">
	<h6>Downloadable Scenarios</h6>
	<?php getData('/stem/data/scenarios.xml', 4, 'images/icon-save.gif'); ?>
	<br /> <a href="http://www.eclipse.org/stem/downloads.php#DownloadableScenarios">
	...more Downloadable Scenarios</a>
	</div>
	<div class="sideitem">
	<h6>Recent Publications</h6>
	<?php getData('/stem/data/pubs.xml', 10); ?>
	<br> <i><a href="http://wiki.eclipse.org/Publications_and_Presentations_on_STEM">
	...more Publications</a></i>

	</div>
	<div class="sideitem">
	<h6>Upcoming (and recent) talks</h6>
	<?php getData('/stem/data/talks.xml', 10); ?>
	<i><a href="http://wiki.eclipse.org/Publications_and_Presentations_on_STEM">
	...more talks</a></i>
	</div>
	<div class="sideitem">
	<h6>Acknowledgements</h6>
	<!-- <img alt="Development of STEM was supported in part by USAF/SG" src="/stem/images/usaf.gif" style="float: left;width:150px;"/> -->
	<?php getData('/stem/data/acknowledgements.xml', 15); ?>
	</div>
	</div>

	</div>

	<?php

	$html .= ob_get_contents();
	ob_end_clean();

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

	?>