| <?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); |
| |
| ?> |