intro.php - 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();	$Menu 	= new Menu();		include($App->getProjectCommon());    # All on the same line to unclutter the user's desktop'

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

 #
 # Begin: page-specific settings.  Change these.
 $pageTitle 		= "STEM Introduction";
 $pageKeywords	= "STEM";
 $pageAuthor		= "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
 #
 	function getRssFeed()
 	{
 		$rssFilePath = "http://dev.eclipse.org/newslists/news.eclipse.stem/maillist.rss";
 		//$rssFilePath = $_SERVER['DOCUMENT_ROOT'] . "/stem/feeds/news.xml";

 		$xmlData = file_get_contents($rssFilePath);

 		$xmlResult = new SimpleXMLElement($xmlData);

 		$rssResults = $xmlResult->channel->item;

 		$rssMaxResults = 5;


 		if (sizeof($rssResults) > 0) {
 			$rssCount = 0;
 			foreach ($rssResults as $rssResult) {
 				if ($rssCount >= $rssMaxResults) {
 					break;
 				}

 				$title = $rssResult->title;
 				$title = substr($title, 20); // Skip [news.eclipse.stem]
 				$url = $rssResult->link;

 				$date = strtotime($rssResult->pubDate);
 				if (!$date || $date === -1) {
 					$date = time();
 				}
 				$formattedDate = date('d-M y', $date);
 				echo "<img src=\"images/arrow.jpg\" width=\"11\" height=\"10\" alt=\"\" border=\"0\">&nbsp;" .$formattedDate . ": &nbsp;<a href=\"". $url ."\" target=\"_blank\">". $title ."</a><br />";

 				$rssCount++;
 			}
 		}
 	}

 	function getData($file, $maxresults)
 	{
 		$filePath = $_SERVER['DOCUMENT_ROOT'] . $file;

 		$xmlData = file_get_contents($filePath);

 		$xmlResult = new SimpleXMLElement($xmlData);

 		$results = $xmlResult->item;

 		echo $results;
 		if (sizeof($results) > 0) {
 			$count = 0;
 			foreach ($results as $result) {
 				if ($count >= $maxresults) {
 					break;
 				}

 				$title = $result->title;
 				$url = $result->link;
 				$authors = $result->authors;
 				$source = $result->source;
 				$other = $result->other;

 				$markup = "";
 				if(!empty($authors))
 				   $markup = $markup. $authors;
 				if(!empty($url))
 					$markup = $markup. "<a href=\"". $url ."\" target=\"_blank\">";
 				if(!empty($title))
 					$markup = $markup. $title."</a>&nbsp;";
 				if(!empty($source))
 					$markup = $markup. "<div style=\"font-style: italic;\">".$source."</div>";
 				if(!empty($other))
 					$markup = $markup. "&nbsp;" . $other;
 				$markup = $markup . "<br/>";

 				echo $markup;
 				$count++;
 			}
 		}
 	}

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

     <div id="maincontent">
     	<div style="padding:3px;">
           	<img alt="STEM Banner" src="/stem/images/STEM_TOP_BAR.gif" width="750" height="63"/>
          </div>
 	<div id="midcolumn">


 		 <div class="homeitem3col">
 			<a name="about"></a>
 			<h3>More About STEM ... </h3>

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

 		<div class="homeitem3col">
 			<b>
 			<a name="introduction"></a>
 			</b>
 			<p>An open source tool, the
 			Spatiotemporal Epidemiological Modeler (STEM) allows users to create
 			spatial and temporal models of emerging infectious diseases.
 			Designed to be extensible, flexible and re-usable, STEM provides a
 			set of <a href="http://wiki.eclipse.org/Analysis">validation tools</a>
 			researchers and public health officials can
 			use to understand the spread of disease in space and time and to
 			assess the impact of
 			<a href="http://wiki.eclipse.org/Batch_Mode_%28Running_Experiments%29">preventive actions</a>
 			in an increasingly global world.
 			</p>
 			<p>
 			Platform independent, STEM is available in versions for Microsoft,
 			Apple, and Linux operating systems. Users can access all its main
 			components as separate <a href="http://wiki.eclipse.org/index.php/STEM#STEM_Plugins">plug-ins</a>
 			to build on existing models and create new ones.
 			</p>
 			<p>
 			Users can independently deploy the plug-ins - the core
 			representational framework, graphical user interface, simulation
 			engine, disease model computations, and various data sets - and use
 			them with declarative software extension points to develop, run, and
 			analyze sophisticated simulations.
 			 </p>
 			 <p>
 			STEM's
 			<a href="http://wiki.eclipse.org/index.php/STEM#Data">data sets</a> describe
 			the geography, transportation systems (including airports and roads),
 			and population for the world's 244 countries and dependent areas down to administrative level 2 for
 			most countries (the county level in the United States).
 			</p>
 			<p>
 			Its disease model computations are based on
 			<a href="http://wiki.eclipse.org/Introduction_to_Compartment_Models">compartment models</a>
 			Parameters within the models can be modified
 			by the researcher who, for example, may wish to adjust the
 			infectious period or the initial number of infectious individuals.
 			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>
 			Tools provided by STEM support researchers in a range of functions,
 			as they perform analysis, fitting, and model comparisons across
 			multiple simulations and data sets.
 			</p>
 			<p>
 			Using the <a href="http://wiki.eclipse.org/Analysis">Analysis Perspective</a>,
 			researchers can visualize the results of STEM scenarios from log files and compare two scenarios
 			side-by-side across different dimensions. Utilities in this
 			perspective can estimate disease parameters from imported time
 			series data and integrate historic incidence data to arrive at
 			counts for disease models over time.
 			</p>
 			<p>
 			Using the <a href="http://wiki.eclipse.org/Creating_a_STEM_Scenario">Designer Perspective</a>,
 			users can create custom <a href="http://wiki.eclipse.org/Batch_Mode_%28Running_Experiments%29">experiments</a>,
 			which express public health policies as a collection of
 			predicates, modifiers, and triggers. Researchers can run a collection of simulations,
 			based on a single scenario, modifying each
 			simulation slightly by varying one or more parameters, and examine
 			how the model is affected.
 			</p>
 			<p>
 			With the <a href="http://wiki.eclipse.org/STEM_Design_Document">components</a>
 			STEM provides, users can create their own model
 			for a country, a region, or even the entire world. If there is a
 			sub-model for the area under study, it can simply be plugged into
 			simulations by referencing it. For example, a country model can
 			contain a sub-model for its transportation infrastructure and that
 			sub-model itself can contain sub-models for air, rail, and/or roads.
 			</p>
 			<p>
 			The ability of one STEM model to contain another allows researchers
 			to plug detailed and highly complex subcomponents into a single
 			encompassing model. Because the underlying components are the same,
 			models can be easily shared and their components validated. One
 			researcher can import another researcher's specialized disease
 			model, combine it with an existing country model that includes
 			population demographics, and re-export the new combination for
 			others to use.
 			</p>
 			<p>
 			By making data (with descriptive metadata) available as plug-ins,
 			STEM makes new avenues of collaboration possible. For example,
 			biologists studying bird migrations can contribute data of use to
 			epidemiologists studying avian influenza. Economists studying
 			workforce productivity contribute data of use to public health
 			officials studying the economic impact of pandemic influenza.
 			</p>
 			<p>
 			By providing a common collaborative platform and components that are
 			extensible, flexible and re-usable, STEM makes possible greater
 			understanding of the phenomena that affect public health and
 			potentially have social, economic, and environmental impacts as
 			well. <br>
 			</p>
 			<p>
             <a href="./index.php">... home</a>
             </p>
             </p>
 		</div>
 	</div>

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

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

	#
	# Begin: page-specific settings. Change these.
	$pageTitle = "STEM Introduction";
	$pageKeywords = "STEM";
	$pageAuthor = "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
	#
	function getRssFeed()
	{
	$rssFilePath = "http://dev.eclipse.org/newslists/news.eclipse.stem/maillist.rss";
	//$rssFilePath = $_SERVER['DOCUMENT_ROOT'] . "/stem/feeds/news.xml";

	$xmlData = file_get_contents($rssFilePath);

	$xmlResult = new SimpleXMLElement($xmlData);

	$rssResults = $xmlResult->channel->item;

	$rssMaxResults = 5;


	if (sizeof($rssResults) > 0) {
	$rssCount = 0;
	foreach ($rssResults as $rssResult) {
	if ($rssCount >= $rssMaxResults) {
	break;
	}

	$title = $rssResult->title;
	$title = substr($title, 20); // Skip [news.eclipse.stem]
	$url = $rssResult->link;

	$date = strtotime($rssResult->pubDate);
	if (!$date \|\| $date === -1) {
	$date = time();
	}
	$formattedDate = date('d-M y', $date);
	echo "<img src=\"images/arrow.jpg\" width=\"11\" height=\"10\" alt=\"\" border=\"0\"> " .$formattedDate . ":  <a href=\"". $url ."\" target=\"_blank\">". $title ."</a><br />";

	$rssCount++;
	}
	}
	}

	function getData($file, $maxresults)
	{
	$filePath = $_SERVER['DOCUMENT_ROOT'] . $file;

	$xmlData = file_get_contents($filePath);

	$xmlResult = new SimpleXMLElement($xmlData);

	$results = $xmlResult->item;

	echo $results;
	if (sizeof($results) > 0) {
	$count = 0;
	foreach ($results as $result) {
	if ($count >= $maxresults) {
	break;
	}

	$title = $result->title;
	$url = $result->link;
	$authors = $result->authors;
	$source = $result->source;
	$other = $result->other;

	$markup = "";
	if(!empty($authors))
	$markup = $markup. $authors;
	if(!empty($url))
	$markup = $markup. "<a href=\"". $url ."\" target=\"_blank\">";
	if(!empty($title))
	$markup = $markup. $title."</a> ";
	if(!empty($source))
	$markup = $markup. "<div style=\"font-style: italic;\">".$source."</div>";
	if(!empty($other))
	$markup = $markup. " " . $other;
	$markup = $markup . "<br/>";

	echo $markup;
	$count++;
	}
	}
	}

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

	<div id="maincontent">
	<div style="padding:3px;">
	<img alt="STEM Banner" src="/stem/images/STEM_TOP_BAR.gif" width="750" height="63"/>
	</div>
	<div id="midcolumn">


	<div class="homeitem3col">
	<a name="about"></a>
	<h3>More About STEM ... </h3>

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

	<div class="homeitem3col">
	<b>
	<a name="introduction"></a>
	</b>
	<p>An open source tool, the
	Spatiotemporal Epidemiological Modeler (STEM) allows users to create
	spatial and temporal models of emerging infectious diseases.
	Designed to be extensible, flexible and re-usable, STEM provides a
	set of <a href="http://wiki.eclipse.org/Analysis">validation tools</a>
	researchers and public health officials can
	use to understand the spread of disease in space and time and to
	assess the impact of
	<a href="http://wiki.eclipse.org/Batch_Mode_%28Running_Experiments%29">preventive actions</a>
	in an increasingly global world.
	</p>
	<p>
	Platform independent, STEM is available in versions for Microsoft,
	Apple, and Linux operating systems. Users can access all its main
	components as separate <a href="http://wiki.eclipse.org/index.php/STEM#STEM_Plugins">plug-ins</a>
	to build on existing models and create new ones.
	</p>
	<p>
	Users can independently deploy the plug-ins - the core
	representational framework, graphical user interface, simulation
	engine, disease model computations, and various data sets - and use
	them with declarative software extension points to develop, run, and
	analyze sophisticated simulations.
	</p>
	<p>
	STEM's
	<a href="http://wiki.eclipse.org/index.php/STEM#Data">data sets</a> describe
	the geography, transportation systems (including airports and roads),
	and population for the world's 244 countries and dependent areas down to administrative level 2 for
	most countries (the county level in the United States).
	</p>
	<p>
	Its disease model computations are based on
	<a href="http://wiki.eclipse.org/Introduction_to_Compartment_Models">compartment models</a>
	Parameters within the models can be modified
	by the researcher who, for example, may wish to adjust the
	infectious period or the initial number of infectious individuals.
	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>
	Tools provided by STEM support researchers in a range of functions,
	as they perform analysis, fitting, and model comparisons across
	multiple simulations and data sets.
	</p>
	<p>
	Using the <a href="http://wiki.eclipse.org/Analysis">Analysis Perspective</a>,
	researchers can visualize the results of STEM scenarios from log files and compare two scenarios
	side-by-side across different dimensions. Utilities in this
	perspective can estimate disease parameters from imported time
	series data and integrate historic incidence data to arrive at
	counts for disease models over time.
	</p>
	<p>
	Using the <a href="http://wiki.eclipse.org/Creating_a_STEM_Scenario">Designer Perspective</a>,
	users can create custom <a href="http://wiki.eclipse.org/Batch_Mode_%28Running_Experiments%29">experiments</a>,
	which express public health policies as a collection of
	predicates, modifiers, and triggers. Researchers can run a collection of simulations,
	based on a single scenario, modifying each
	simulation slightly by varying one or more parameters, and examine
	how the model is affected.
	</p>
	<p>
	With the <a href="http://wiki.eclipse.org/STEM_Design_Document">components</a>
	STEM provides, users can create their own model
	for a country, a region, or even the entire world. If there is a
	sub-model for the area under study, it can simply be plugged into
	simulations by referencing it. For example, a country model can
	contain a sub-model for its transportation infrastructure and that
	sub-model itself can contain sub-models for air, rail, and/or roads.
	</p>
	<p>
	The ability of one STEM model to contain another allows researchers
	to plug detailed and highly complex subcomponents into a single
	encompassing model. Because the underlying components are the same,
	models can be easily shared and their components validated. One
	researcher can import another researcher's specialized disease
	model, combine it with an existing country model that includes
	population demographics, and re-export the new combination for
	others to use.
	</p>
	<p>
	By making data (with descriptive metadata) available as plug-ins,
	STEM makes new avenues of collaboration possible. For example,
	biologists studying bird migrations can contribute data of use to
	epidemiologists studying avian influenza. Economists studying
	workforce productivity contribute data of use to public health
	officials studying the economic impact of pandemic influenza.
	</p>
	<p>
	By providing a common collaborative platform and components that are
	extensible, flexible and re-usable, STEM makes possible greater
	understanding of the phenomena that affect public health and
	potentially have social, economic, and environmental impacts as
	well. <br>
	</p>
	<p>
	<a href="./index.php">... home</a>
	</p>
	</p>
	</div>
	</div>

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

	</div>

	<?php

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

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

	?>