Merge branch 'master' of ssh://git.eclipse.org/gitroot/www.eclipse.org/stem

9 files changed, 55 insertions, 46 deletions

diff --git a/STEM-ProjectPlan.xml b/STEM-ProjectPlan.xml
index e81b0a4..336d518 100644
--- a/STEM-ProjectPlan.xml
+++ b/STEM-ProjectPlan.xml
@@ -4,7 +4,7 @@
 	plan-format="1.0" xmlns="http://www.eclipse.org/project/plan"
 	xmlns:html="http://www.w3.org/1999/xhtml" 
 	name="Spatiotemporal Epidemiological Modeler">
-	<release projectid="technology.stem" version="2.0.3" />
+	<release projectid="technology.stem" version="3.0.0M2" />
 	<introduction>
 		<html:div>
 			The Spatiotemporal Epidemiological Modeler (STEM) tool is designed to
@@ -18,8 +18,10 @@
 		<html:div>
 			<html:p />
 			STEM is delivered as an Eclipse Rich Client Platform (RCP)
-			application runnable on Windows, Linux, and Mac OS X platforms. It
-			requires a Java 6 or later JVM. The STEM application includes tools
+			application runnable on Windows, Linux, and Mac OS X platforms.  
+			STEM 3.0 is based on and compatible with Eclipse 4.x
+			Starting with STEM V3.0.0M1, STEM supports and required (J2SE) 8.0 JVM. 
+			The STEM application includes tools
 			for designing, simulating, and analyzing epidemiological models.
 			STEM contains a wealth of prepackaged data in the form of existing
 			disease models and simulations as well as geographic/demographic data
@@ -28,10 +30,9 @@
 
 			<html:p style="font-weight:bold;">The 2.0.3 release planning:</html:p>
 			<html:ul style="line-height: 50%;">
-				<html:li>Bug fixes from 2.0.2</html:li>
-				<html:li>Admin 0 borders added</html:li>
+				<html:li>Bug fixes from 2.0.3</html:li>
+				<html:li>New Downloadable Scenarios</html:li>
 				<html:li>New models</html:li>
-				<html:li>Updated Google Earth(tm) Interface</html:li>
 			</html:ul>
 		</html:div>
 	</release_deliverables>
@@ -72,7 +73,7 @@
 		</milestone>
 		<milestone date="09/20/2013" milestone="2.0.0 M5">
 			<html:div>2.0.0 M5 (milestone complete)</html:div>
-		</milestone>
+		</milestone> 
 		<milestone date="10/15/2013" milestone="2.0.0">
 			<html:div>Release 2.0.0 (release complete)</html:div>
 		</milestone>
@@ -83,13 +84,22 @@
 			<html:div>Release 2.0.2 (release complete)</html:div>
 		</milestone>
 		<milestone date="01/09/2015" milestone="2.0.3">
-			<html:div>Release 2.0.3 (planned release)</html:div>
+			<html:div>Release 2.0.3 (release complete)</html:div>
+		</milestone>
+		<milestone date="10/09/2015" milestone="3.0.0M1">
+			<html:div>Release 3.0.0M1 (release complete)</html:div>
+		</milestone>
+		<milestone date="02/04/2016" milestone="3.0.0M2">
+			<html:div>Release 3.0.0M2 (release complete)</html:div>
+		</milestone>
+		<milestone date="04/02/2016" milestone="3.0.0M3">
+			<html:div>Release 3.0.0M3 (planned release)</html:div>
 		</milestone>
 	</release_milestones>
 	<target_environments>
 			<html:div>
 			STEM runs on 32-bit and 64-bit Windows, Linux, and Mac OS X
-			platforms. It is built using Eclipse 3.6 and requires Java 6 or
+			platforms. It is built using Eclipse 4.x and requires Java 8 or
 			later.
 			</html:div>
 		<internationalization>
@@ -102,7 +112,7 @@
 	</target_environments>
 	<compatibility_with_previous_releases>
 			<html:div>
-			STEM 2.0.0 has a new migration tool to upgrade STEM projects created using 1.4.1 (or earlier)
+			STEM 2.0.0 and later has a new migration tool to upgrade STEM projects created using 1.4.1 (or earlier)
 			</html:div>
 	</compatibility_with_previous_releases>
 	<themes_and_priorities>
@@ -116,9 +126,9 @@
 		<theme name="Hiding Complexity">
 			<description>
 				<html:p>
-					In 2014 we will continue improving STEM and support its community. 
-					We are also supporting the research community
-					response to the Ebola epidemic.
+					In 2016 we will continue improving STEM and support its community. 
+					We are extending STEM to explicitly add evolution and genomes to epidemiological models
+					and to add the capability to model evolution of multistrain diseases in real time.
 				</html:p>
 			</description>
 		</theme>
diff --git a/data/pubs.xml b/data/pubs.xml
index 6be9476..f8de541 100644
--- a/data/pubs.xml
+++ b/data/pubs.xml
@@ -3,22 +3,22 @@
 	xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
 	xsi:noNamespaceSchemaLocation="items.xsd">
 	<item>
-		<title>A Generic Open-Source Software Framework Supporting Scenario Simulations in Bioterrorist Crises.</title>
-		<authors>Alexander Falenski, Matthias Filter, Christian Thöns, Armin A. Weiser, Jan-Frederik Wigger, Matthew Davis, Judith V. Douglas, Stefan Edlund, Kun Hu, James H. Kaufman, Bernd Appel, and Annemarie Käsbohrer.</authors>
-		<source>Biosecurity and Bioterrorism: Biodefense Strategy, Practice, and Science</source>
-		<link>http://online.liebertpub.com/doi/abs/10.1089/bsp.2012.0071 </link>
+		<title>The impact of human behavioral changes in 2014 west Africa Ebola outbreak.</title>
+		<authors>Hu K, Bianco S, Edlund S, Kaufman J. </authors>
+		<source>SBP 15, 2015, Washington, DC. </source>
+		<link> </link>
+	</item>
+	<item>
+		<title>A likelihood-based approach to identifying contaminated food products using sales data: performance and challenges.</title>
+		<authors>Kaufman J, Lessler J, Harry A, Edlund S, Hu K, Douglas J, Thoens C, Appel B, Kasbohrer A, Filter M. </authors>
+		<source>PLoS Comput Biol 10(11): 2014</source>
+		<link>http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003999</link>
 	</item>
 	<item>
 		<title> The effect of antibody-dependent enhancement, cross immunity, and vector population on the dynamics of dengue fever.</title>
-		<authors>Hu K, Thoens C, Bianco S, Edlund S, Davis M, Douglas J, and Kaufman JH., 21 Feb 2013</authors>
+		<authors>Hu K, et al., 21 Feb 2013</authors>
 		<source>Journal of Theoretical Biology, 319:62–74, , doi:10.1016/j.jtbi.2012.11.021</source>
 		<link>http://www.sciencedirect.com/science/article/pii/S0022519312005966
 		</link>
 	</item>
-	<item>
-		<title>A global model of malaria climate sensitivity: comparing malaria response to historic climate data based on simulation and officially reported malaria incidence.</title>
-		<authors>Edlund S, Davis M, Douglas JV, Kershenbaum A, Waraporn N, Lessler J, Kaufman JH.</authors>
-		<source>Malaria Journal 2012, 11:331 doi:10.1186/1475-2875-11-331.</source>
-		<link>http://www.malariajournal.com/content/11/1/331</link>
-	</item>
 </items>
diff --git a/data/scenarios.xml b/data/scenarios.xml
index 6c8c8c7..b63a54c 100644
--- a/data/scenarios.xml
+++ b/data/scenarios.xml
@@ -13,11 +13,21 @@
 		<link>http://wiki.eclipse.org/Sample_Projects_available_for_Download</link>
 	</item>
 	<item>
-		<title>(new)Ebola Models</title>
+		<title>(new) Importing Shape Files</title>
+		<other>This single archive contains an example of how to import and create a STEM graph from a shape file (.shp) in your workspace. If uses STEM's pajek graph generator.</other>
+		<link>http://www.eclipse.org/stem/download_sample.php?file=ShapefilePajekImport.zip</link>
+	</item>
+	<item>
+		<title>Ebola Models</title>
 		<other>This single archive contains three different projects with several Ebola scenarios. Requires the latest STEM Integration build on or after Sept 26, 2014.</other>
 		<link>http://www.eclipse.org/stem/download_sample.php?file=EbolaModelsSIngleArchive.zip</link>
 	</item>
 	<item>
+		<title>Ebola Zoonotic (Re)Introduction</title>
+		<other>This archive contains a new model generator example extending the Ebola Model to support re-introduction from Zoonotic Reservoir, and a simple project demonstrating that model. See the readme.txt within the Archive !</other>
+		<link>http://www.eclipse.org/stem/download_sample.php?file=EbolaZoonoticReIntroduction.zip</link>
+	</item>
+	<item>
 		<title>Dengue Examples</title>
 		<other>This archive contains three different projects with several dengue fever models and scenarios. Requires any STEM build on or after April 2, 2014.</other>
 		<link>http://www.eclipse.org/stem/download_sample.php?file=DengueScenarios.zip</link>
diff --git a/data/talks.xml b/data/talks.xml
index fe3cc4c..773d97e 100644
--- a/data/talks.xml
+++ b/data/talks.xml
@@ -3,6 +3,12 @@
 	xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
 	xsi:noNamespaceSchemaLocation="items.xsd">
 	<item>
+		<title>Modeling the Dynamics of Dengue Fever</title>
+		<authors>Hu, K., et al.</authors>
+		<source>The International Society for Neglected Tropical Diseases (ISNTD Bites), March 19, 2015. London, England</source>
+		<link>http://www.isntdbites.com/#/speakers-programme-2015/4587437347</link>
+	</item>
+	<item>
 		<title>Estimating the impact of measles immunization uptake in GP clinics in a North West London Borough</title>
 		<authors>Edlund, S.,  Hu, K.,  Kaufman, J.H.,  Lovett, D., Van Wijgerden, J., Yagci Sokat, K., Poots, A.J</authors>
 		<source>Epidemics 4, Amsterdam, Holland, 11/21</source>
@@ -32,23 +38,4 @@
 		<source>The 2013 International Conference on Social Computing, Behavioral-Cultural Modeling, &amp; Prediction (SBP 2013): Washington D.C.</source>
 		<link>http://rd.springer.com/chapter/10.1007/978-3-642-37210-0_53</link>
 	</item>
-	<item>
-		<title>Extending Geospatial Data to Support Epidemiological Modeling</title>
-		<authors>Edlund S., Davis, M., Kaufman, J.</authors>
-		<source>ACM SIGSPATIAL GIS'12</source>
-		<link>http://acmgis2012.cs.umd.edu/</link>
-	</item>
-	<item>
-		<title>The SpatioTemporal Epidemiological Modeler: an open source framework for modeling food-borne disease.</title>
-		<authors>Kaufman JH (presenter), Davis M, Douglas JV, Edlund S, Hu K, Filter M, Wigger J-F, Thoens C, Weiser AA, Kaesbohrer A, Appel B.</authors>
-		<source>ISVEE 13, Maastricht</source>
-		<link>http://www.isvee13.org/</link>
-	</item>
-
-    <item>
-		<title>A community resource for spatial, temporal and food chain epidemiological modelling to assess risks in bio-terroristic or agro-terroristic crisis situations.</title>
-		<authors>Falenski A (presenter), Thoens C, Filter M, Kaesbohrer A, Appel B, Kaufman JH, Edlund S, Davis M, Douglas JV, Hu K.</authors>
-		<source>ISVEE 13, Maastricht</source>
-		<link>http://www.isvee13.org/</link>
-	</item>
 </items>
diff --git a/download_sample.php b/download_sample.php
index 2ea57cf..3cd49de 100644
--- a/download_sample.php
+++ b/download_sample.php
@@ -15,8 +15,8 @@ $cancelUrl = "/stem/downloads.php";
 
 $disclaimerText = "The following sample archive files contain Content which can be downloaded and extracted into a STEM workspace and imported into STEM to help a Recipient set up A model of disease. For example, one sample archive file configures STEM to run a model with DATA FROM both Mexico and the United States, using a standard deterministic SEIR model with disease parameters which may characterize a new DISEASE. The disease parameters in the sample archive are provided only as examples and are NOT validated against any DISEASE data, including Swine Flu data. Recipients should not use these parameters as accurate predictions for the rate of spread of any specific disease. By following the instructions in STEM, a Recipient can change these parameters as desired and also adjust the parameters in the sample modifiers to create new models and to study the effects of social distancing or other public health policies.";
 
-
 $requestedFile = $_REQUEST['file'];
+$requestedFile = filter_var($requestedFile, FILTER_SANITIZE_STRING);
 
 if (!$requestedFile || $_REQUEST['cancel']) {
 	Header("Location: ". $cancelUrl);
diff --git a/downloads.php b/downloads.php
index e73b30e..56197de 100644
--- a/downloads.php
+++ b/downloads.php
@@ -208,10 +208,12 @@ ob_start();
         </div>    
         
 		<?php displayBuild("Release", "Release", $versions); ?>
+		
+		<?php displayBuild("Milestone", "Stable", $versions); ?>
 
         <?php displayBuild("Weekly Integration Build", "Integration", $versions); ?>
 
-		<?php //displayBuild("Release Candidate", "Stable", $versions); ?>
+		
 
 		<div class="homeiteM3u1col">
 			<a name="samples"></a>
diff --git a/samples/EbolaZoonoticReIntroduction.zip b/samples/EbolaZoonoticReIntroduction.zip
new file mode 100644
index 0000000..c2647c9
--- /dev/null
+++ b/samples/EbolaZoonoticReIntroduction.zip
diff --git a/samples/MultiPopulationExample_PajekGraphs.zip b/samples/MultiPopulationExample_PajekGraphs.zip
index d3c49db..f22198a 100644
--- a/samples/MultiPopulationExample_PajekGraphs.zip
+++ b/samples/MultiPopulationExample_PajekGraphs.zip
diff --git a/samples/ShapefilePajekImport.zip b/samples/ShapefilePajekImport.zip
new file mode 100644
index 0000000..b35c588
--- /dev/null
+++ b/samples/ShapefilePajekImport.zip