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

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 	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);


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

     <div id="maincontent">
 	<div id="midcolumn">

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

 		 <div class="homeitem3col">
 			<a name="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 name="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 name="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 name="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="http://wiki.eclipse.org/index.php/STEM_Source_Code">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">
 	 	<!--<div class="sideitem">
    			<h6>Incubation</h6>
    			<div align="center"><a href="/projects/what-is-incubation.php"><img
         	align="center" src="/images/egg-incubation.png"
         	border="0" alt="Incubation" /></a></div>
  		</div>-->
  		<!--<div class="sideitem">
 			<h6 style="color:red">Ebola News</h6>
 			<?php getRssFeed('https://dev.eclipse.org/mhonarc/lists/stem-ebola/maillist.rss', $_SERVER['DOCUMENT_ROOT'] . '/stem/data/rss_ebola_cache.xml'); ?>
 			<br.>
 			<i><a href="https://dev.eclipse.org/mhonarc/lists/stem-ebola/">more...</a></i>
 		</div>
 		-->
 		<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(); $Menu = new Menu(); include($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();
	?>

	<div id="maincontent">
	<div id="midcolumn">

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

	<div class="homeitem3col">
	<a name="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 name="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 name="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 name="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="http://wiki.eclipse.org/index.php/STEM_Source_Code">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">
	<!--<div class="sideitem">
	<h6>Incubation</h6>
	<div align="center"><a href="/projects/what-is-incubation.php"><img
	align="center" src="/images/egg-incubation.png"
	border="0" alt="Incubation" /></a></div>
	</div>-->
	<!--<div class="sideitem">
	<h6 style="color:red">Ebola News</h6>
	<?php getRssFeed('https://dev.eclipse.org/mhonarc/lists/stem-ebola/maillist.rss', $_SERVER['DOCUMENT_ROOT'] . '/stem/data/rss_ebola_cache.xml'); ?>
	<br.>
	<i><a href="https://dev.eclipse.org/mhonarc/lists/stem-ebola/">more...</a></i>
	</div>
	-->
	<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);

	?>