diff --git a/.idea/.name b/.idea/.name
deleted file mode 100644
index 25dd2a9fd672ddcee1a0dbe914393f0e0c939e7c..0000000000000000000000000000000000000000
--- a/.idea/.name
+++ /dev/null
@@ -1 +0,0 @@
-parent
\ No newline at end of file
diff --git a/.idea/artifacts/web_war.xml b/.idea/artifacts/web_war.xml
deleted file mode 100644
index 1a8b7b5da0bdedb9cc76511d29327e9a6f7430ca..0000000000000000000000000000000000000000
--- a/.idea/artifacts/web_war.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<component name="ArtifactManager">
-  <artifact type="war" name="web:war">
-    <output-path>$PROJECT_DIR$/web/target</output-path>
-    <root id="archive" name="web-1.0.war">
-      <element id="artifact" artifact-name="web:war exploded" />
-    </root>
-  </artifact>
-</component>
\ No newline at end of file
diff --git a/.idea/artifacts/web_war_exploded.xml b/.idea/artifacts/web_war_exploded.xml
deleted file mode 100644
index 17bd68e9d9d95599c6d9a598a6ad4297626aa0d8..0000000000000000000000000000000000000000
--- a/.idea/artifacts/web_war_exploded.xml
+++ /dev/null
@@ -1,175 +0,0 @@
-<component name="ArtifactManager">
-  <artifact type="exploded-war" name="web:war exploded">
-    <output-path>$PROJECT_DIR$/web/target/web-1.0</output-path>
-    <root id="root">
-      <element id="directory" name="WEB-INF">
-        <element id="directory" name="classes">
-          <element id="module-output" name="web" />
-        </element>
-        <element id="directory" name="lib">
-          <element id="archive" name="service-1.0.jar">
-            <element id="module-output" name="service" />
-          </element>
-          <element id="archive" name="model-1.0.jar">
-            <element id="module-output" name="model" />
-          </element>
-          <element id="archive" name="commons-1.0.jar">
-            <element id="module-output" name="commons" />
-          </element>
-          <element id="library" level="project" name="Maven: commons-io:commons-io:2.4" />
-          <element id="library" level="project" name="Maven: org.hibernate:hibernate-core:4.1.0.Final" />
-          <element id="library" level="project" name="Maven: commons-collections:commons-collections:3.2.1" />
-          <element id="library" level="project" name="Maven: antlr:antlr:2.7.7" />
-          <element id="library" level="project" name="Maven: org.jboss.spec.javax.transaction:jboss-transaction-api_1.1_spec:1.0.0.Final" />
-          <element id="library" level="project" name="Maven: dom4j:dom4j:1.6.1" />
-          <element id="library" level="project" name="Maven: org.hibernate.javax.persistence:hibernate-jpa-2.0-api:1.0.1.Final" />
-          <element id="library" level="project" name="Maven: org.jboss.logging:jboss-logging:3.1.0.CR2" />
-          <element id="library" level="project" name="Maven: org.javassist:javassist:3.15.0-GA" />
-          <element id="library" level="project" name="Maven: org.hibernate.common:hibernate-commons-annotations:4.0.1.Final" />
-          <element id="library" level="project" name="Maven: xml-apis:xml-apis:1.4.01" />
-          <element id="library" level="project" name="Maven: org.reflections:reflections:0.9.9-RC1" />
-          <element id="library" level="project" name="Maven: com.google.guava:guava:11.0.2" />
-          <element id="library" level="project" name="Maven: com.google.code.findbugs:jsr305:1.3.9" />
-          <element id="archive" name="persist-1.0.jar">
-            <element id="module-output" name="persist" />
-          </element>
-          <element id="library" level="project" name="Maven: commons-net:commons-net:3.5" />
-          <element id="library" level="project" name="Maven: postgresql:postgresql:9.1-901.jdbc4" />
-          <element id="archive" name="model-command-1.0.jar">
-            <element id="module-output" name="model-command" />
-          </element>
-          <element id="archive" name="annotation-1.0.jar">
-            <element id="module-output" name="annotation" />
-          </element>
-          <element id="archive" name="converter-1.0.jar">
-            <element id="module-output" name="converter" />
-          </element>
-          <element id="library" level="project" name="Maven: xerces:xercesImpl:2.11.0" />
-          <element id="library" level="project" name="Maven: uk.ac.ebi.chebi.webapps.chebiWS.client:chebiWS-client:2.2.2" />
-          <element id="library" level="project" name="Maven: com.sun.xml.ws:jaxws-rt:2.1.7" />
-          <element id="library" level="project" name="Maven: com.sun.xml.stream.buffer:streambuffer:0.9" />
-          <element id="library" level="project" name="Maven: org.codehaus.woodstox:wstx-asl:3.2.3" />
-          <element id="library" level="project" name="Maven: org.jvnet.staxex:stax-ex:1.2" />
-          <element id="library" level="project" name="Maven: javax.xml.stream:stax-api:1.0" />
-          <element id="library" level="project" name="Maven: com.sun.org.apache.xml.internal:resolver:20050927" />
-          <element id="library" level="project" name="Maven: org.jvnet:mimepull:1.3" />
-          <element id="library" level="project" name="Maven: javax.xml.ws:jaxws-api:2.1" />
-          <element id="library" level="project" name="Maven: com.sun.xml.ws:jaxws-tools:2.1.3" />
-          <element id="library" level="project" name="Maven: com.sun.xml.bind:jaxb-xjc:2.1.6" />
-          <element id="library" level="project" name="Maven: com.sun.xml.messaging.saaj:saaj-impl:1.3.2" />
-          <element id="library" level="project" name="Maven: javax.xml.soap:saaj-api:1.3" />
-          <element id="library" level="project" name="Maven: uk.ac.ebi.miriam:miriam-lib:1.1.5" />
-          <element id="library" level="project" name="Maven: axis:axis:1.4" />
-          <element id="library" level="project" name="Maven: org.apache.axis:axis-jaxrpc:1.4" />
-          <element id="library" level="project" name="Maven: org.apache.axis:axis-saaj:1.4" />
-          <element id="library" level="project" name="Maven: axis:axis-wsdl4j:1.5.1" />
-          <element id="library" level="project" name="Maven: commons-discovery:commons-discovery:0.2" />
-          <element id="library" level="project" name="Maven: javax.activation:activation:1.1" />
-          <element id="library" level="project" name="Maven: javax.mail:mail:1.4" />
-          <element id="library" level="project" name="Maven: org.apache.httpcomponents:httpclient:4.4" />
-          <element id="library" level="project" name="Maven: org.apache.httpcomponents:httpmime:4.4" />
-          <element id="library" level="project" name="Maven: org.apache.httpcomponents:httpcore:4.4" />
-          <element id="library" level="project" name="Maven: javax.xml.bind:jaxb-api:2.2.7" />
-          <element id="library" level="project" name="Maven: com.sun.xml.bind:jaxb-impl:2.2.7" />
-          <element id="library" level="project" name="Maven: com.sun.xml.bind:jaxb-core:2.2.7" />
-          <element id="library" level="project" name="Maven: com.sun.istack:istack-commons-runtime:2.16" />
-          <element id="library" level="project" name="Maven: com.sun.xml.fastinfoset:FastInfoset:1.2.12" />
-          <element id="library" level="project" name="Maven: javax.xml.bind:jsr173_api:1.0" />
-          <element id="library" level="project" name="Maven: org.apache.poi:poi-ooxml-schemas:3.12" />
-          <element id="library" level="project" name="Maven: org.apache.xmlbeans:xmlbeans:2.6.0" />
-          <element id="library" level="project" name="Maven: stax:stax-api:1.0.1" />
-          <element id="archive" name="converter-CellDesigner-1.0.jar">
-            <element id="module-output" name="converter-CellDesigner" />
-          </element>
-          <element id="archive" name="converter-SBGNML-1.0.jar">
-            <element id="module-output" name="converter-SBGNML" />
-          </element>
-          <element id="library" level="project" name="Maven: org.sbgn:libsbgn:0.2" />
-          <element id="library" level="project" name="Maven: commons-cli:commons-cli:1.2" />
-          <element id="archive" name="converter-graphics-1.0.jar">
-            <element id="module-output" name="converter-graphics" />
-          </element>
-          <element id="library" level="project" name="Maven: org.apache.xmlgraphics:batik-rasterizer:1.8" />
-          <element id="library" level="project" name="Maven: org.apache.xmlgraphics:batik-parser:1.8" />
-          <element id="library" level="project" name="Maven: org.apache.xmlgraphics:batik-xml:1.8" />
-          <element id="library" level="project" name="Maven: org.apache.xmlgraphics:batik-transcoder:1.8" />
-          <element id="library" level="project" name="Maven: org.apache.xmlgraphics:batik-anim:1.8" />
-          <element id="library" level="project" name="Maven: org.apache.xmlgraphics:batik-css:1.8" />
-          <element id="library" level="project" name="Maven: org.apache.xmlgraphics:batik-ext:1.8" />
-          <element id="library" level="project" name="Maven: org.apache.xmlgraphics:batik-svg-dom:1.8" />
-          <element id="library" level="project" name="Maven: org.apache.xmlgraphics:batik-bridge:1.8" />
-          <element id="library" level="project" name="Maven: org.apache.xmlgraphics:batik-script:1.8" />
-          <element id="library" level="project" name="Maven: xalan:xalan:2.7.0" />
-          <element id="library" level="project" name="Maven: org.apache.xmlgraphics:batik-dom:1.8" />
-          <element id="library" level="project" name="Maven: org.apache.xmlgraphics:batik-gvt:1.8" />
-          <element id="library" level="project" name="Maven: xml-apis:xml-apis-ext:1.3.04" />
-          <element id="library" level="project" name="Maven: org.apache.xmlgraphics:batik-util:1.8" />
-          <element id="library" level="project" name="Maven: org.apache.xmlgraphics:batik-svggen:1.8" />
-          <element id="library" level="project" name="Maven: org.apache.xmlgraphics:batik-awt-util:1.8" />
-          <element id="library" level="project" name="Maven: com.itextpdf:itextpdf:5.5.6" />
-          <element id="library" level="project" name="Maven: com.google.code.gson:gson:2.2.2" />
-          <element id="library" level="project" name="Maven: org.apache.poi:poi:3.12" />
-          <element id="library" level="project" name="Maven: commons-codec:commons-codec:1.9" />
-          <element id="library" level="project" name="Maven: org.apache.poi:poi-ooxml:3.12" />
-          <element id="archive" name="rest-api-1.0.jar">
-            <element id="module-output" name="rest-api" />
-          </element>
-          <element id="library" level="project" name="Maven: com.sun.jersey:jersey-server:1.18.1" />
-          <element id="library" level="project" name="Maven: com.sun.jersey:jersey-core:1.18.1" />
-          <element id="library" level="project" name="Maven: com.sun.jersey:jersey-servlet:1.18.1" />
-          <element id="library" level="project" name="Maven: com.fasterxml.jackson.core:jackson-core:2.8.8" />
-          <element id="library" level="project" name="Maven: com.fasterxml.jackson.core:jackson-databind:2.8.8" />
-          <element id="library" level="project" name="Maven: com.fasterxml.jackson.core:jackson-annotations:2.8.0" />
-          <element id="archive" name="frontend-js-1.0.jar">
-            <element id="module-output" name="frontend-js" />
-          </element>
-          <element id="library" level="project" name="Maven: com.sun.faces:jsf-api:2.1.7" />
-          <element id="library" level="project" name="Maven: com.sun.faces:jsf-impl:2.1.7" />
-          <element id="library" level="project" name="Maven: javax.servlet:jstl:1.2" />
-          <element id="library" level="project" name="Maven: org.primefaces:primefaces:4.0" />
-          <element id="library" level="project" name="Maven: org.primefaces.themes:home:1.0.8" />
-          <element id="library" level="project" name="Maven: org.springframework.webflow:spring-faces:2.4.2.RELEASE" />
-          <element id="library" level="project" name="Maven: commons-logging:commons-logging:1.1.1" />
-          <element id="library" level="project" name="Maven: org.springframework.webflow:spring-binding:2.4.2.RELEASE" />
-          <element id="library" level="project" name="Maven: opensymphony:ognl:2.6.11" />
-          <element id="library" level="project" name="Maven: org.springframework.webflow:spring-webflow:2.4.2.RELEASE" />
-          <element id="library" level="project" name="Maven: org.springframework.webflow:spring-js:2.4.2.RELEASE" />
-          <element id="library" level="project" name="Maven: org.springframework.webflow:spring-js-resources:2.4.2.RELEASE" />
-          <element id="library" level="project" name="Maven: org.springframework:spring-beans:4.2.0.RELEASE" />
-          <element id="library" level="project" name="Maven: org.springframework:spring-expression:4.2.0.RELEASE" />
-          <element id="library" level="project" name="Maven: org.springframework:spring-context:4.2.0.RELEASE" />
-          <element id="library" level="project" name="Maven: org.springframework:spring-aop:4.2.0.RELEASE" />
-          <element id="library" level="project" name="Maven: org.springframework:spring-core:4.2.0.RELEASE" />
-          <element id="library" level="project" name="Maven: org.springframework:spring-web:4.2.0.RELEASE" />
-          <element id="library" level="project" name="Maven: log4j:log4j:1.2.17" />
-          <element id="library" level="project" name="Maven: org.springframework:spring-tx:4.2.0.RELEASE" />
-          <element id="library" level="project" name="Maven: org.springframework:spring-orm:4.2.0.RELEASE" />
-          <element id="library" level="project" name="Maven: org.springframework:spring-jdbc:4.2.0.RELEASE" />
-          <element id="library" level="project" name="Maven: org.springframework:spring-test:4.2.0.RELEASE" />
-          <element id="library" level="project" name="Maven: org.springframework:spring-webmvc:4.2.0.RELEASE" />
-          <element id="library" level="project" name="Maven: org.springframework.security:spring-security-taglibs:4.0.2.RELEASE" />
-          <element id="library" level="project" name="Maven: org.springframework.security:spring-security-acl:4.0.2.RELEASE" />
-          <element id="library" level="project" name="Maven: org.springframework.security:spring-security-config:4.0.2.RELEASE" />
-          <element id="library" level="project" name="Maven: aopalliance:aopalliance:1.0" />
-          <element id="library" level="project" name="Maven: org.springframework.security:spring-security-web:4.0.2.RELEASE" />
-          <element id="library" level="project" name="Maven: org.springframework.security:spring-security-core:4.0.2.RELEASE" />
-          <element id="library" level="project" name="Maven: c3p0:c3p0:0.9.1.2" />
-          <element id="library" level="project" name="Maven: cglib:cglib:2.2.2" />
-          <element id="library" level="project" name="Maven: asm:asm:3.3.1" />
-          <element id="library" level="project" name="Maven: commons-fileupload:commons-fileupload:1.2.2" />
-          <element id="library" level="project" name="Maven: org.primefaces.extensions:primefaces-extensions:0.7.1" />
-          <element id="library" level="project" name="Maven: org.apache.commons:commons-lang3:3.1" />
-          <element id="library" level="project" name="Maven: commons-validator:commons-validator:1.4.0" />
-          <element id="library" level="project" name="Maven: commons-beanutils:commons-beanutils:1.8.3" />
-          <element id="library" level="project" name="Maven: commons-digester:commons-digester:1.8" />
-          <element id="library" level="project" name="Maven: junit:junit:4.12" />
-          <element id="library" level="project" name="Maven: org.hamcrest:hamcrest-core:1.3" />
-        </element>
-      </element>
-      <element id="directory" name="META-INF">
-        <element id="file-copy" path="$PROJECT_DIR$/web/target/web-1.0/META-INF/MANIFEST.MF" />
-      </element>
-      <element id="javaee-facet-resources" facet="web/web/Web" />
-    </root>
-  </artifact>
-</component>
\ No newline at end of file
diff --git a/.idea/compiler.xml b/.idea/compiler.xml
deleted file mode 100644
index 89c969d46c57d246a74a06161a9f3675abe78a60..0000000000000000000000000000000000000000
--- a/.idea/compiler.xml
+++ /dev/null
@@ -1,55 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
-  <component name="CompilerConfiguration">
-    <annotationProcessing>
-      <profile name="Maven default annotation processors profile" enabled="true">
-        <sourceOutputDir name="target/generated-sources/annotations" />
-        <sourceTestOutputDir name="target/generated-test-sources/test-annotations" />
-        <outputRelativeToContentRoot value="true" />
-        <module name="annotation" />
-        <module name="CellDesigner-plugin" />
-        <module name="commons" />
-        <module name="comparison" />
-        <module name="console" />
-        <module name="converter" />
-        <module name="converter-CellDesigner" />
-        <module name="converter-graphics" />
-        <module name="converter-SBGNML" />
-        <module name="editor" />
-        <module name="frontend-js" />
-        <module name="model" />
-        <module name="model-command" />
-        <module name="pathvisio" />
-        <module name="persist" />
-        <module name="quadTrees" />
-        <module name="reactome" />
-        <module name="rest-api" />
-        <module name="service" />
-        <module name="web" />
-      </profile>
-    </annotationProcessing>
-    <bytecodeTargetLevel>
-      <module name="annotation" target="1.8" />
-      <module name="CellDesigner-plugin" target="1.8" />
-      <module name="commons" target="1.8" />
-      <module name="comparison" target="1.8" />
-      <module name="console" target="1.8" />
-      <module name="converter" target="1.8" />
-      <module name="converter-CellDesigner" target="1.8" />
-      <module name="converter-graphics" target="1.8" />
-      <module name="converter-SBGNML" target="1.8" />
-      <module name="editor" target="1.8" />
-      <module name="frontend-js" target="1.8" />
-      <module name="model" target="1.8" />
-      <module name="model-command" target="1.8" />
-      <module name="parent" target="1.5" />
-      <module name="pathvisio" target="1.8" />
-      <module name="persist" target="1.8" />
-      <module name="quadTrees" target="1.8" />
-      <module name="reactome" target="1.8" />
-      <module name="rest-api" target="1.8" />
-      <module name="service" target="1.8" />
-      <module name="web" target="1.8" />
-    </bytecodeTargetLevel>
-  </component>
-</project>
\ No newline at end of file
diff --git a/.idea/dictionaries/gawi.xml b/.idea/dictionaries/gawi.xml
deleted file mode 100644
index d586f913d6180c60c3f45339746df56adc6e0bd7..0000000000000000000000000000000000000000
--- a/.idea/dictionaries/gawi.xml
+++ /dev/null
@@ -1,7 +0,0 @@
-<component name="ProjectDictionaryState">
-  <dictionary name="gawi">
-    <words>
-      <w>mkdirp</w>
-    </words>
-  </dictionary>
-</component>
\ No newline at end of file
diff --git a/.idea/encodings.xml b/.idea/encodings.xml
deleted file mode 100644
index 5fc2649a0dc189c09831261aff29e4931c7993b3..0000000000000000000000000000000000000000
--- a/.idea/encodings.xml
+++ /dev/null
@@ -1,26 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
-  <component name="Encoding">
-    <file url="file://$PROJECT_DIR$" charset="UTF-8" />
-    <file url="file://$PROJECT_DIR$/CellDesigner-plugin" charset="UTF-8" />
-    <file url="file://$PROJECT_DIR$/annotation" charset="UTF-8" />
-    <file url="file://$PROJECT_DIR$/commons" charset="UTF-8" />
-    <file url="file://$PROJECT_DIR$/comparison" charset="UTF-8" />
-    <file url="file://$PROJECT_DIR$/console" charset="UTF-8" />
-    <file url="file://$PROJECT_DIR$/converter" charset="UTF-8" />
-    <file url="file://$PROJECT_DIR$/converter-CellDesigner" charset="UTF-8" />
-    <file url="file://$PROJECT_DIR$/converter-SBGNML" charset="UTF-8" />
-    <file url="file://$PROJECT_DIR$/converter-graphics" charset="UTF-8" />
-    <file url="file://$PROJECT_DIR$/editor" charset="UTF-8" />
-    <file url="file://$PROJECT_DIR$/frontend-js" charset="UTF-8" />
-    <file url="file://$PROJECT_DIR$/model" charset="UTF-8" />
-    <file url="file://$PROJECT_DIR$/model-command" charset="UTF-8" />
-    <file url="file://$PROJECT_DIR$/pathvisio" charset="UTF-8" />
-    <file url="file://$PROJECT_DIR$/persist" charset="UTF-8" />
-    <file url="file://$PROJECT_DIR$/quadTrees" charset="UTF-8" />
-    <file url="file://$PROJECT_DIR$/reactome" charset="UTF-8" />
-    <file url="file://$PROJECT_DIR$/rest-api" charset="UTF-8" />
-    <file url="file://$PROJECT_DIR$/service" charset="UTF-8" />
-    <file url="file://$PROJECT_DIR$/web" charset="UTF-8" />
-  </component>
-</project>
\ No newline at end of file
diff --git a/.idea/modules.xml b/.idea/modules.xml
index 0e732d0743d1e7fdf56d6f83b8e35eb12811f3a9..6e6dd9acbdd939bf1c110062e928a9ee7c27aa96 100644
--- a/.idea/modules.xml
+++ b/.idea/modules.xml
@@ -2,27 +2,7 @@
 <project version="4">
   <component name="ProjectModuleManager">
     <modules>
-      <module fileurl="file://$PROJECT_DIR$/CellDesigner-plugin/CellDesigner-plugin.iml" filepath="$PROJECT_DIR$/CellDesigner-plugin/CellDesigner-plugin.iml" />
-      <module fileurl="file://$PROJECT_DIR$/annotation/annotation.iml" filepath="$PROJECT_DIR$/annotation/annotation.iml" />
-      <module fileurl="file://$PROJECT_DIR$/commons/commons.iml" filepath="$PROJECT_DIR$/commons/commons.iml" />
-      <module fileurl="file://$PROJECT_DIR$/comparison/comparison.iml" filepath="$PROJECT_DIR$/comparison/comparison.iml" />
-      <module fileurl="file://$PROJECT_DIR$/console/console.iml" filepath="$PROJECT_DIR$/console/console.iml" />
-      <module fileurl="file://$PROJECT_DIR$/converter/converter.iml" filepath="$PROJECT_DIR$/converter/converter.iml" />
-      <module fileurl="file://$PROJECT_DIR$/converter-CellDesigner/converter-CellDesigner.iml" filepath="$PROJECT_DIR$/converter-CellDesigner/converter-CellDesigner.iml" />
-      <module fileurl="file://$PROJECT_DIR$/converter-SBGNML/converter-SBGNML.iml" filepath="$PROJECT_DIR$/converter-SBGNML/converter-SBGNML.iml" />
-      <module fileurl="file://$PROJECT_DIR$/converter-graphics/converter-graphics.iml" filepath="$PROJECT_DIR$/converter-graphics/converter-graphics.iml" />
-      <module fileurl="file://$PROJECT_DIR$/editor/editor.iml" filepath="$PROJECT_DIR$/editor/editor.iml" />
-      <module fileurl="file://$PROJECT_DIR$/frontend-js/frontend-js.iml" filepath="$PROJECT_DIR$/frontend-js/frontend-js.iml" />
-      <module fileurl="file://$PROJECT_DIR$/model/model.iml" filepath="$PROJECT_DIR$/model/model.iml" />
-      <module fileurl="file://$PROJECT_DIR$/model-command/model-command.iml" filepath="$PROJECT_DIR$/model-command/model-command.iml" />
-      <module fileurl="file://$PROJECT_DIR$/parent.iml" filepath="$PROJECT_DIR$/parent.iml" />
-      <module fileurl="file://$PROJECT_DIR$/pathvisio/pathvisio.iml" filepath="$PROJECT_DIR$/pathvisio/pathvisio.iml" />
-      <module fileurl="file://$PROJECT_DIR$/persist/persist.iml" filepath="$PROJECT_DIR$/persist/persist.iml" />
-      <module fileurl="file://$PROJECT_DIR$/quadTrees/quadTrees.iml" filepath="$PROJECT_DIR$/quadTrees/quadTrees.iml" />
-      <module fileurl="file://$PROJECT_DIR$/reactome/reactome.iml" filepath="$PROJECT_DIR$/reactome/reactome.iml" />
-      <module fileurl="file://$PROJECT_DIR$/rest-api/rest-api.iml" filepath="$PROJECT_DIR$/rest-api/rest-api.iml" />
-      <module fileurl="file://$PROJECT_DIR$/service/service.iml" filepath="$PROJECT_DIR$/service/service.iml" />
-      <module fileurl="file://$PROJECT_DIR$/web/web.iml" filepath="$PROJECT_DIR$/web/web.iml" />
+      <module fileurl="file://$PROJECT_DIR$/.idea/minerva.iml" filepath="$PROJECT_DIR$/.idea/minerva.iml" />
     </modules>
   </component>
 </project>
\ No newline at end of file
diff --git a/.idea/vcs.xml b/.idea/vcs.xml
index 94a25f7f4cb416c083d265558da75d457237d671..35eb1ddfbbc029bcab630581847471d7f238ec53 100644
--- a/.idea/vcs.xml
+++ b/.idea/vcs.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <project version="4">
   <component name="VcsDirectoryMappings">
-    <mapping directory="$PROJECT_DIR$" vcs="Git" />
+    <mapping directory="" vcs="Git" />
   </component>
 </project>
\ No newline at end of file
diff --git a/CellDesigner-plugin/CellDesigner-plugin.iml b/CellDesigner-plugin/CellDesigner-plugin.iml
deleted file mode 100644
index 20aff5378cd416639d08c580d7f98d6a57d45fad..0000000000000000000000000000000000000000
--- a/CellDesigner-plugin/CellDesigner-plugin.iml
+++ /dev/null
@@ -1,41 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<module org.jetbrains.idea.maven.project.MavenProjectsManager.isMavenModule="true" type="JAVA_MODULE" version="4">
-  <component name="NewModuleRootManager" LANGUAGE_LEVEL="JDK_1_8">
-    <output url="file://$MODULE_DIR$/target/classes" />
-    <output-test url="file://$MODULE_DIR$/target/test-classes" />
-    <content url="file://$MODULE_DIR$">
-      <sourceFolder url="file://$MODULE_DIR$/src/main/java" isTestSource="false" />
-      <sourceFolder url="file://$MODULE_DIR$/src/main/resources" type="java-resource" />
-      <sourceFolder url="file://$MODULE_DIR$/src/test/java" isTestSource="true" />
-      <sourceFolder url="file://$MODULE_DIR$/src/test/resources" type="java-test-resource" />
-      <excludeFolder url="file://$MODULE_DIR$/target" />
-    </content>
-    <orderEntry type="inheritedJdk" />
-    <orderEntry type="sourceFolder" forTests="false" />
-    <orderEntry type="module" module-name="model" />
-    <orderEntry type="library" name="Maven: org.hibernate:hibernate-core:4.1.0.Final" level="project" />
-    <orderEntry type="library" name="Maven: commons-collections:commons-collections:3.2.1" level="project" />
-    <orderEntry type="library" name="Maven: antlr:antlr:2.7.7" level="project" />
-    <orderEntry type="library" name="Maven: org.jboss.spec.javax.transaction:jboss-transaction-api_1.1_spec:1.0.0.Final" level="project" />
-    <orderEntry type="library" name="Maven: dom4j:dom4j:1.6.1" level="project" />
-    <orderEntry type="library" name="Maven: org.hibernate.javax.persistence:hibernate-jpa-2.0-api:1.0.1.Final" level="project" />
-    <orderEntry type="library" name="Maven: org.jboss.logging:jboss-logging:3.1.0.CR2" level="project" />
-    <orderEntry type="library" name="Maven: org.javassist:javassist:3.15.0-GA" level="project" />
-    <orderEntry type="library" name="Maven: org.hibernate.common:hibernate-commons-annotations:4.0.1.Final" level="project" />
-    <orderEntry type="library" name="Maven: xml-apis:xml-apis:1.4.01" level="project" />
-    <orderEntry type="library" name="Maven: log4j:log4j:1.2.17" level="project" />
-    <orderEntry type="library" name="Maven: org.reflections:reflections:0.9.9-RC1" level="project" />
-    <orderEntry type="library" name="Maven: com.google.guava:guava:11.0.2" level="project" />
-    <orderEntry type="library" name="Maven: com.google.code.findbugs:jsr305:1.3.9" level="project" />
-    <orderEntry type="module" module-name="commons" />
-    <orderEntry type="library" name="Maven: commons-io:commons-io:2.4" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.commons:commons-lang3:3.1" level="project" />
-    <orderEntry type="module" module-name="converter-CellDesigner" />
-    <orderEntry type="module" module-name="converter" />
-    <orderEntry type="library" name="Maven: xerces:xercesImpl:2.11.0" level="project" />
-    <orderEntry type="library" name="Maven: jp.sbi:celldesigner:4.4" level="project" />
-    <orderEntry type="library" name="Maven: org.sbml:libsbml:1.0" level="project" />
-    <orderEntry type="library" name="Maven: junit:junit:4.12" level="project" />
-    <orderEntry type="library" name="Maven: org.hamcrest:hamcrest-core:1.3" level="project" />
-  </component>
-</module>
\ No newline at end of file
diff --git a/annotation/.classpath b/annotation/.classpath
index ea8d16b080f914d14fd2fb4936fd06c7a160e3d2..fae1a2b37d5e3386c9651caedb78b9bd107715bd 100644
--- a/annotation/.classpath
+++ b/annotation/.classpath
@@ -1,37 +1,36 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<classpath>
-	<classpathentry kind="src" output="target/classes" path="src/main/java">
-		<attributes>
-			<attribute name="optional" value="true"/>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources">
-		<attributes>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="src" output="target/test-classes" path="src/test/java">
-		<attributes>
-			<attribute name="optional" value="true"/>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry excluding="**" kind="src" output="target/test-classes" path="src/test/resources">
-		<attributes>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8">
-		<attributes>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
-		<attributes>
-			<attribute name="maven.pomderived" value="true"/>
-			<attribute name="org.eclipse.jst.component.nondependency" value=""/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="output" path="target/classes"/>
-</classpath>
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+	<classpathentry kind="src" output="target/classes" path="src/main/java">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="src" output="target/test-classes" path="src/test/java">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry excluding="**" kind="src" output="target/test-classes" path="src/test/resources">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="output" path="target/classes"/>
+</classpath>
diff --git a/annotation/annotation.iml b/annotation/annotation.iml
deleted file mode 100644
index 2c466bf93d664b135a4e39019816c9929fda81e8..0000000000000000000000000000000000000000
--- a/annotation/annotation.iml
+++ /dev/null
@@ -1,104 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<module org.jetbrains.idea.maven.project.MavenProjectsManager.isMavenModule="true" type="JAVA_MODULE" version="4">
-  <component name="FacetManager">
-    <facet type="Spring" name="Spring">
-      <configuration />
-    </facet>
-  </component>
-  <component name="NewModuleRootManager" LANGUAGE_LEVEL="JDK_1_8">
-    <output url="file://$MODULE_DIR$/target/classes" />
-    <output-test url="file://$MODULE_DIR$/target/test-classes" />
-    <content url="file://$MODULE_DIR$">
-      <sourceFolder url="file://$MODULE_DIR$/src/main/java" isTestSource="false" />
-      <sourceFolder url="file://$MODULE_DIR$/src/main/resources" type="java-resource" />
-      <sourceFolder url="file://$MODULE_DIR$/src/test/java" isTestSource="true" />
-      <sourceFolder url="file://$MODULE_DIR$/src/test/resources" type="java-test-resource" />
-      <excludeFolder url="file://$MODULE_DIR$/target" />
-    </content>
-    <orderEntry type="inheritedJdk" />
-    <orderEntry type="sourceFolder" forTests="false" />
-    <orderEntry type="module" module-name="model" />
-    <orderEntry type="module" module-name="commons" />
-    <orderEntry type="library" name="Maven: commons-io:commons-io:2.4" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.commons:commons-lang3:3.1" level="project" />
-    <orderEntry type="library" name="Maven: org.hibernate:hibernate-core:4.1.0.Final" level="project" />
-    <orderEntry type="library" name="Maven: commons-collections:commons-collections:3.2.1" level="project" />
-    <orderEntry type="library" name="Maven: antlr:antlr:2.7.7" level="project" />
-    <orderEntry type="library" name="Maven: org.jboss.spec.javax.transaction:jboss-transaction-api_1.1_spec:1.0.0.Final" level="project" />
-    <orderEntry type="library" name="Maven: dom4j:dom4j:1.6.1" level="project" />
-    <orderEntry type="library" name="Maven: org.hibernate.javax.persistence:hibernate-jpa-2.0-api:1.0.1.Final" level="project" />
-    <orderEntry type="library" name="Maven: org.jboss.logging:jboss-logging:3.1.0.CR2" level="project" />
-    <orderEntry type="library" name="Maven: org.javassist:javassist:3.15.0-GA" level="project" />
-    <orderEntry type="library" name="Maven: org.hibernate.common:hibernate-commons-annotations:4.0.1.Final" level="project" />
-    <orderEntry type="library" name="Maven: xml-apis:xml-apis:1.4.01" level="project" />
-    <orderEntry type="library" name="Maven: org.reflections:reflections:0.9.9-RC1" level="project" />
-    <orderEntry type="library" name="Maven: com.google.guava:guava:11.0.2" level="project" />
-    <orderEntry type="library" name="Maven: com.google.code.findbugs:jsr305:1.3.9" level="project" />
-    <orderEntry type="module" module-name="persist" />
-    <orderEntry type="library" name="Maven: commons-net:commons-net:3.5" level="project" />
-    <orderEntry type="library" name="Maven: org.springframework:spring-core:4.2.0.RELEASE" level="project" />
-    <orderEntry type="library" name="Maven: org.springframework:spring-web:4.2.0.RELEASE" level="project" />
-    <orderEntry type="library" name="Maven: org.springframework:spring-tx:4.2.0.RELEASE" level="project" />
-    <orderEntry type="library" name="Maven: org.springframework:spring-orm:4.2.0.RELEASE" level="project" />
-    <orderEntry type="library" name="Maven: org.springframework:spring-jdbc:4.2.0.RELEASE" level="project" />
-    <orderEntry type="library" name="Maven: org.springframework.security:spring-security-taglibs:4.0.2.RELEASE" level="project" />
-    <orderEntry type="library" name="Maven: org.springframework.security:spring-security-acl:4.0.2.RELEASE" level="project" />
-    <orderEntry type="library" name="Maven: org.springframework.security:spring-security-core:4.0.2.RELEASE" level="project" />
-    <orderEntry type="library" name="Maven: org.springframework.security:spring-security-web:4.0.2.RELEASE" level="project" />
-    <orderEntry type="library" name="Maven: org.springframework:spring-test:4.2.0.RELEASE" level="project" />
-    <orderEntry type="library" name="Maven: postgresql:postgresql:9.1-901.jdbc4" level="project" />
-    <orderEntry type="library" name="Maven: c3p0:c3p0:0.9.1.2" level="project" />
-    <orderEntry type="library" name="Maven: cglib:cglib:2.2.2" level="project" />
-    <orderEntry type="library" name="Maven: asm:asm:3.3.1" level="project" />
-    <orderEntry type="library" name="Maven: com.google.code.gson:gson:2.2.2" level="project" />
-    <orderEntry type="module" module-name="converter-CellDesigner" />
-    <orderEntry type="module" module-name="converter" />
-    <orderEntry type="library" name="Maven: log4j:log4j:1.2.17" level="project" />
-    <orderEntry type="library" name="Maven: xerces:xercesImpl:2.11.0" level="project" />
-    <orderEntry type="library" name="Maven: uk.ac.ebi.chebi.webapps.chebiWS.client:chebiWS-client:2.2.2" level="project" />
-    <orderEntry type="library" name="Maven: com.sun.xml.ws:jaxws-rt:2.1.7" level="project" />
-    <orderEntry type="library" name="Maven: com.sun.xml.stream.buffer:streambuffer:0.9" level="project" />
-    <orderEntry type="library" name="Maven: org.codehaus.woodstox:wstx-asl:3.2.3" level="project" />
-    <orderEntry type="library" name="Maven: org.jvnet.staxex:stax-ex:1.2" level="project" />
-    <orderEntry type="library" name="Maven: javax.xml.stream:stax-api:1.0" level="project" />
-    <orderEntry type="library" name="Maven: com.sun.org.apache.xml.internal:resolver:20050927" level="project" />
-    <orderEntry type="library" name="Maven: org.jvnet:mimepull:1.3" level="project" />
-    <orderEntry type="library" name="Maven: javax.xml.ws:jaxws-api:2.1" level="project" />
-    <orderEntry type="library" name="Maven: com.sun.xml.ws:jaxws-tools:2.1.3" level="project" />
-    <orderEntry type="library" name="Maven: com.sun.xml.bind:jaxb-xjc:2.1.6" level="project" />
-    <orderEntry type="library" name="Maven: com.sun.xml.messaging.saaj:saaj-impl:1.3.2" level="project" />
-    <orderEntry type="library" name="Maven: javax.xml.soap:saaj-api:1.3" level="project" />
-    <orderEntry type="library" name="Maven: org.springframework:spring-context:4.2.0.RELEASE" level="project" />
-    <orderEntry type="library" name="Maven: org.springframework:spring-aop:4.2.0.RELEASE" level="project" />
-    <orderEntry type="library" name="Maven: aopalliance:aopalliance:1.0" level="project" />
-    <orderEntry type="library" name="Maven: org.springframework:spring-beans:4.2.0.RELEASE" level="project" />
-    <orderEntry type="library" name="Maven: org.springframework:spring-expression:4.2.0.RELEASE" level="project" />
-    <orderEntry type="library" name="Maven: uk.ac.ebi.miriam:miriam-lib:1.1.5" level="project" />
-    <orderEntry type="library" name="Maven: axis:axis:1.4" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.axis:axis-jaxrpc:1.4" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.axis:axis-saaj:1.4" level="project" />
-    <orderEntry type="library" scope="RUNTIME" name="Maven: axis:axis-wsdl4j:1.5.1" level="project" />
-    <orderEntry type="library" scope="RUNTIME" name="Maven: commons-discovery:commons-discovery:0.2" level="project" />
-    <orderEntry type="library" name="Maven: javax.activation:activation:1.1" level="project" />
-    <orderEntry type="library" name="Maven: javax.mail:mail:1.4" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.httpcomponents:httpclient:4.4" level="project" />
-    <orderEntry type="library" name="Maven: commons-logging:commons-logging:1.2" level="project" />
-    <orderEntry type="library" name="Maven: commons-codec:commons-codec:1.9" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.httpcomponents:httpmime:4.4" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.httpcomponents:httpcore:4.4" level="project" />
-    <orderEntry type="library" name="Maven: javax.xml.bind:jaxb-api:2.2.7" level="project" />
-    <orderEntry type="library" name="Maven: com.sun.xml.bind:jaxb-impl:2.2.7" level="project" />
-    <orderEntry type="library" name="Maven: com.sun.xml.bind:jaxb-core:2.2.7" level="project" />
-    <orderEntry type="library" name="Maven: com.sun.istack:istack-commons-runtime:2.16" level="project" />
-    <orderEntry type="library" name="Maven: com.sun.xml.fastinfoset:FastInfoset:1.2.12" level="project" />
-    <orderEntry type="library" name="Maven: javax.xml.bind:jsr173_api:1.0" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.poi:poi:3.12" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.poi:poi-ooxml-schemas:3.12" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.xmlbeans:xmlbeans:2.6.0" level="project" />
-    <orderEntry type="library" name="Maven: stax:stax-api:1.0.1" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.poi:poi-ooxml:3.12" level="project" />
-    <orderEntry type="library" scope="TEST" name="Maven: org.mockito:mockito-all:1.10.19" level="project" />
-    <orderEntry type="library" name="Maven: junit:junit:4.12" level="project" />
-    <orderEntry type="library" name="Maven: org.hamcrest:hamcrest-core:1.3" level="project" />
-  </component>
-</module>
\ No newline at end of file
diff --git a/commons/.classpath b/commons/.classpath
index 62d4b8e4723486982a42cd5dd2b44363281a0bd8..ace82666f2f113cdb835230548bb1c0ddf6ca559 100644
--- a/commons/.classpath
+++ b/commons/.classpath
@@ -1,37 +1,36 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<classpath>
-	<classpathentry kind="src" output="target/classes" path="src/main/java">
-		<attributes>
-			<attribute name="optional" value="true"/>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources">
-		<attributes>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="src" output="target/test-classes" path="src/test/java">
-		<attributes>
-			<attribute name="optional" value="true"/>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry excluding="**" kind="src" output="target/test-classes" path="src/test/resources">
-		<attributes>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
-		<attributes>
-			<attribute name="maven.pomderived" value="true"/>
-			<attribute name="org.eclipse.jst.component.nondependency" value=""/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8">
-		<attributes>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="output" path="target/classes"/>
-</classpath>
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+	<classpathentry kind="src" output="target/classes" path="src/main/java">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="src" output="target/test-classes" path="src/test/java">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry excluding="**" kind="src" output="target/test-classes" path="src/test/resources">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="output" path="target/classes"/>
+</classpath>
diff --git a/commons/commons.iml b/commons/commons.iml
deleted file mode 100644
index 879234cda491dcaecb6e503e2e9f2558cc7b5f8c..0000000000000000000000000000000000000000
--- a/commons/commons.iml
+++ /dev/null
@@ -1,23 +0,0 @@
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diff --git a/comparison/.settings/org.eclipse.core.resources.prefs b/comparison/.settings/org.eclipse.core.resources.prefs
index 30b8b670b12fcdb8fe34d704d8244269b1746de3..365bbd6097a6b1bb6e06963e12b1bea10c30d0f4 100644
--- a/comparison/.settings/org.eclipse.core.resources.prefs
+++ b/comparison/.settings/org.eclipse.core.resources.prefs
@@ -1,4 +1,5 @@
 eclipse.preferences.version=1
+encoding//src/main/java=UTF-8
 encoding//src/main/resources=UTF-8
 encoding//src/test/java=UTF-8
 encoding/<project>=UTF-8
diff --git a/comparison/comparison.iml b/comparison/comparison.iml
deleted file mode 100644
index 1dad1245c2b2bbd7b4dc48e7834dd3d407cf726c..0000000000000000000000000000000000000000
--- a/comparison/comparison.iml
+++ /dev/null
@@ -1,123 +0,0 @@
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diff --git a/console/console.iml b/console/console.iml
deleted file mode 100644
index b66c7c73aa897ac2d995cded176e6f9884b22760..0000000000000000000000000000000000000000
--- a/console/console.iml
+++ /dev/null
@@ -1,143 +0,0 @@
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-    <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-rasterizer:1.8" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-parser:1.8" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-xml:1.8" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-transcoder:1.8" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-anim:1.8" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-css:1.8" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-ext:1.8" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-svg-dom:1.8" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-bridge:1.8" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-script:1.8" level="project" />
-    <orderEntry type="library" name="Maven: xalan:xalan:2.7.0" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-dom:1.8" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-gvt:1.8" level="project" />
-    <orderEntry type="library" name="Maven: xml-apis:xml-apis-ext:1.3.04" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-util:1.8" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-svggen:1.8" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-awt-util:1.8" level="project" />
-    <orderEntry type="library" name="Maven: com.itextpdf:itextpdf:5.5.6" level="project" />
-    <orderEntry type="library" name="Maven: log4j:log4j:1.2.17" level="project" />
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-    <orderEntry type="library" name="Maven: org.springframework:spring-aop:4.2.0.RELEASE" level="project" />
-    <orderEntry type="library" name="Maven: aopalliance:aopalliance:1.0" level="project" />
-    <orderEntry type="library" name="Maven: org.springframework:spring-beans:4.2.0.RELEASE" level="project" />
-    <orderEntry type="library" name="Maven: org.springframework:spring-expression:4.2.0.RELEASE" level="project" />
-    <orderEntry type="library" name="Maven: org.primefaces:primefaces:4.0" level="project" />
-    <orderEntry type="library" name="Maven: com.sun.faces:jsf-api:2.1.7" level="project" />
-    <orderEntry type="library" name="Maven: com.google.code.gson:gson:2.2.2" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.poi:poi:3.12" level="project" />
-    <orderEntry type="library" name="Maven: commons-codec:commons-codec:1.9" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.poi:poi-ooxml:3.12" level="project" />
-    <orderEntry type="module" module-name="reactome" />
-    <orderEntry type="library" name="Maven: org.springframework:spring-core:4.2.0.RELEASE" level="project" />
-    <orderEntry type="library" name="Maven: commons-logging:commons-logging:1.2" level="project" />
-    <orderEntry type="library" name="Maven: org.springframework:spring-web:4.2.0.RELEASE" level="project" />
-    <orderEntry type="library" name="Maven: org.springframework:spring-test:4.2.0.RELEASE" level="project" />
-    <orderEntry type="library" name="Maven: org.springframework.webflow:spring-faces:2.4.2.RELEASE" level="project" />
-    <orderEntry type="library" name="Maven: org.springframework.webflow:spring-binding:2.4.2.RELEASE" level="project" />
-    <orderEntry type="library" name="Maven: opensymphony:ognl:2.6.11" level="project" />
-    <orderEntry type="library" name="Maven: org.springframework.webflow:spring-webflow:2.4.2.RELEASE" level="project" />
-    <orderEntry type="library" name="Maven: org.springframework.webflow:spring-js:2.4.2.RELEASE" level="project" />
-    <orderEntry type="library" name="Maven: org.springframework.webflow:spring-js-resources:2.4.2.RELEASE" level="project" />
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-    <orderEntry type="module" module-name="pathvisio" />
-    <orderEntry type="library" name="Maven: org.pathvisio:core:3.2.0" level="project" />
-    <orderEntry type="library" name="Maven: org.pathvisio:desktop:3.2.0" level="project" />
-    <orderEntry type="library" name="Maven: org.pathvisio:gui:3.2.0" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.felix:org.osgi.core:1.0.0" level="project" />
-    <orderEntry type="library" name="Maven: commons-cli:commons-cli:1.2" level="project" />
-    <orderEntry type="library" name="Maven: junit:junit:4.12" level="project" />
-    <orderEntry type="library" name="Maven: org.hamcrest:hamcrest-core:1.3" level="project" />
-  </component>
-</module>
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diff --git a/converter-CellDesigner/.classpath b/converter-CellDesigner/.classpath
index ea8d16b080f914d14fd2fb4936fd06c7a160e3d2..fae1a2b37d5e3386c9651caedb78b9bd107715bd 100644
--- a/converter-CellDesigner/.classpath
+++ b/converter-CellDesigner/.classpath
@@ -1,37 +1,36 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<classpath>
-	<classpathentry kind="src" output="target/classes" path="src/main/java">
-		<attributes>
-			<attribute name="optional" value="true"/>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources">
-		<attributes>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="src" output="target/test-classes" path="src/test/java">
-		<attributes>
-			<attribute name="optional" value="true"/>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry excluding="**" kind="src" output="target/test-classes" path="src/test/resources">
-		<attributes>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8">
-		<attributes>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
-		<attributes>
-			<attribute name="maven.pomderived" value="true"/>
-			<attribute name="org.eclipse.jst.component.nondependency" value=""/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="output" path="target/classes"/>
-</classpath>
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+	<classpathentry kind="src" output="target/classes" path="src/main/java">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="src" output="target/test-classes" path="src/test/java">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry excluding="**" kind="src" output="target/test-classes" path="src/test/resources">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="output" path="target/classes"/>
+</classpath>
diff --git a/converter-CellDesigner/converter-CellDesigner.iml b/converter-CellDesigner/converter-CellDesigner.iml
deleted file mode 100644
index 4175676f92fdda11264b5f26ca1d4b6951622042..0000000000000000000000000000000000000000
--- a/converter-CellDesigner/converter-CellDesigner.iml
+++ /dev/null
@@ -1,39 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<module org.jetbrains.idea.maven.project.MavenProjectsManager.isMavenModule="true" type="JAVA_MODULE" version="4">
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-    <output-test url="file://$MODULE_DIR$/target/test-classes" />
-    <content url="file://$MODULE_DIR$">
-      <sourceFolder url="file://$MODULE_DIR$/src/main/java" isTestSource="false" />
-      <sourceFolder url="file://$MODULE_DIR$/src/main/resources" type="java-resource" />
-      <sourceFolder url="file://$MODULE_DIR$/src/test/java" isTestSource="true" />
-      <sourceFolder url="file://$MODULE_DIR$/src/test/resources" type="java-test-resource" />
-      <excludeFolder url="file://$MODULE_DIR$/target" />
-    </content>
-    <orderEntry type="inheritedJdk" />
-    <orderEntry type="sourceFolder" forTests="false" />
-    <orderEntry type="module" module-name="model" />
-    <orderEntry type="module" module-name="commons" />
-    <orderEntry type="library" name="Maven: commons-io:commons-io:2.4" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.commons:commons-lang3:3.1" level="project" />
-    <orderEntry type="library" name="Maven: org.hibernate:hibernate-core:4.1.0.Final" level="project" />
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-    <orderEntry type="library" name="Maven: org.hamcrest:hamcrest-core:1.3" level="project" />
-  </component>
-</module>
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diff --git a/converter-SBGNML/.classpath b/converter-SBGNML/.classpath
index d70cb6ff1e53a879f928b394e99606692975d383..dfd0043c35667ac6def2c25153c043b5476272e0 100644
--- a/converter-SBGNML/.classpath
+++ b/converter-SBGNML/.classpath
@@ -1,37 +1,36 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<classpath>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8">
-		<attributes>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="src" output="target/classes" path="src/main/java">
-		<attributes>
-			<attribute name="optional" value="true"/>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources">
-		<attributes>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="src" output="target/test-classes" path="src/test/java">
-		<attributes>
-			<attribute name="optional" value="true"/>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry excluding="**" kind="src" output="target/test-classes" path="src/test/resources">
-		<attributes>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
-		<attributes>
-			<attribute name="maven.pomderived" value="true"/>
-			<attribute name="org.eclipse.jst.component.nondependency" value=""/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="output" path="target/classes"/>
-</classpath>
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="src" output="target/classes" path="src/main/java">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="src" output="target/test-classes" path="src/test/java">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry excluding="**" kind="src" output="target/test-classes" path="src/test/resources">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="output" path="target/classes"/>
+</classpath>
diff --git a/converter-SBGNML/converter-SBGNML.iml b/converter-SBGNML/converter-SBGNML.iml
deleted file mode 100644
index 5338a83e1a4099ce88d7d976467d602056097536..0000000000000000000000000000000000000000
--- a/converter-SBGNML/converter-SBGNML.iml
+++ /dev/null
@@ -1,89 +0,0 @@
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-    <facet type="Spring" name="Spring">
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-  <component name="NewModuleRootManager" LANGUAGE_LEVEL="JDK_1_8">
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-    <content url="file://$MODULE_DIR$">
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-      <sourceFolder url="file://$MODULE_DIR$/src/main/resources" type="java-resource" />
-      <sourceFolder url="file://$MODULE_DIR$/src/test/java" isTestSource="true" />
-      <sourceFolder url="file://$MODULE_DIR$/src/test/resources" type="java-test-resource" />
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-    <orderEntry type="inheritedJdk" />
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-    <orderEntry type="library" name="Maven: org.hibernate:hibernate-core:4.1.0.Final" level="project" />
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-    <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-css:1.8" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-ext:1.8" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-svg-dom:1.8" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-bridge:1.8" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-script:1.8" level="project" />
-    <orderEntry type="library" name="Maven: xalan:xalan:2.7.0" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-dom:1.8" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-gvt:1.8" level="project" />
-    <orderEntry type="library" name="Maven: xml-apis:xml-apis-ext:1.3.04" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-util:1.8" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-svggen:1.8" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-awt-util:1.8" level="project" />
-    <orderEntry type="library" name="Maven: com.itextpdf:itextpdf:5.5.6" level="project" />
-    <orderEntry type="library" name="Maven: xerces:xercesImpl:2.11.0" level="project" />
-    <orderEntry type="library" name="Maven: org.sbgn:libsbgn:0.2" level="project" />
-    <orderEntry type="library" name="Maven: commons-cli:commons-cli:1.2" level="project" />
-    <orderEntry type="library" name="Maven: junit:junit:4.12" level="project" />
-    <orderEntry type="library" name="Maven: org.hamcrest:hamcrest-core:1.3" level="project" />
-  </component>
-</module>
\ No newline at end of file
diff --git a/converter-graphics/.classpath b/converter-graphics/.classpath
index 62d4b8e4723486982a42cd5dd2b44363281a0bd8..ace82666f2f113cdb835230548bb1c0ddf6ca559 100644
--- a/converter-graphics/.classpath
+++ b/converter-graphics/.classpath
@@ -1,37 +1,36 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<classpath>
-	<classpathentry kind="src" output="target/classes" path="src/main/java">
-		<attributes>
-			<attribute name="optional" value="true"/>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources">
-		<attributes>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="src" output="target/test-classes" path="src/test/java">
-		<attributes>
-			<attribute name="optional" value="true"/>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry excluding="**" kind="src" output="target/test-classes" path="src/test/resources">
-		<attributes>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
-		<attributes>
-			<attribute name="maven.pomderived" value="true"/>
-			<attribute name="org.eclipse.jst.component.nondependency" value=""/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8">
-		<attributes>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="output" path="target/classes"/>
-</classpath>
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+	<classpathentry kind="src" output="target/classes" path="src/main/java">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="src" output="target/test-classes" path="src/test/java">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry excluding="**" kind="src" output="target/test-classes" path="src/test/resources">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="output" path="target/classes"/>
+</classpath>
diff --git a/converter-graphics/converter-graphics.iml b/converter-graphics/converter-graphics.iml
deleted file mode 100644
index d17adbc39b6add3f49104c7cd50581cf823b4ab6..0000000000000000000000000000000000000000
--- a/converter-graphics/converter-graphics.iml
+++ /dev/null
@@ -1,56 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<module org.jetbrains.idea.maven.project.MavenProjectsManager.isMavenModule="true" type="JAVA_MODULE" version="4">
-  <component name="NewModuleRootManager" LANGUAGE_LEVEL="JDK_1_8">
-    <output url="file://$MODULE_DIR$/target/classes" />
-    <output-test url="file://$MODULE_DIR$/target/test-classes" />
-    <content url="file://$MODULE_DIR$">
-      <sourceFolder url="file://$MODULE_DIR$/src/main/java" isTestSource="false" />
-      <sourceFolder url="file://$MODULE_DIR$/src/main/resources" type="java-resource" />
-      <sourceFolder url="file://$MODULE_DIR$/src/test/java" isTestSource="true" />
-      <sourceFolder url="file://$MODULE_DIR$/src/test/resources" type="java-test-resource" />
-      <excludeFolder url="file://$MODULE_DIR$/target" />
-    </content>
-    <orderEntry type="inheritedJdk" />
-    <orderEntry type="sourceFolder" forTests="false" />
-    <orderEntry type="module" module-name="model" />
-    <orderEntry type="module" module-name="commons" />
-    <orderEntry type="library" name="Maven: commons-io:commons-io:2.4" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.commons:commons-lang3:3.1" level="project" />
-    <orderEntry type="library" name="Maven: org.hibernate:hibernate-core:4.1.0.Final" level="project" />
-    <orderEntry type="library" name="Maven: commons-collections:commons-collections:3.2.1" level="project" />
-    <orderEntry type="library" name="Maven: antlr:antlr:2.7.7" level="project" />
-    <orderEntry type="library" name="Maven: org.jboss.spec.javax.transaction:jboss-transaction-api_1.1_spec:1.0.0.Final" level="project" />
-    <orderEntry type="library" name="Maven: dom4j:dom4j:1.6.1" level="project" />
-    <orderEntry type="library" name="Maven: org.hibernate.javax.persistence:hibernate-jpa-2.0-api:1.0.1.Final" level="project" />
-    <orderEntry type="library" name="Maven: org.jboss.logging:jboss-logging:3.1.0.CR2" level="project" />
-    <orderEntry type="library" name="Maven: org.javassist:javassist:3.15.0-GA" level="project" />
-    <orderEntry type="library" name="Maven: org.hibernate.common:hibernate-commons-annotations:4.0.1.Final" level="project" />
-    <orderEntry type="library" name="Maven: xml-apis:xml-apis:1.4.01" level="project" />
-    <orderEntry type="library" name="Maven: org.reflections:reflections:0.9.9-RC1" level="project" />
-    <orderEntry type="library" name="Maven: com.google.guava:guava:11.0.2" level="project" />
-    <orderEntry type="library" name="Maven: com.google.code.findbugs:jsr305:1.3.9" level="project" />
-    <orderEntry type="module" module-name="model-command" />
-    <orderEntry type="library" name="Maven: log4j:log4j:1.2.17" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-rasterizer:1.8" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-parser:1.8" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-xml:1.8" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-transcoder:1.8" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-anim:1.8" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-css:1.8" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-ext:1.8" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-svg-dom:1.8" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-bridge:1.8" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-script:1.8" level="project" />
-    <orderEntry type="library" name="Maven: xalan:xalan:2.7.0" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-dom:1.8" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-gvt:1.8" level="project" />
-    <orderEntry type="library" name="Maven: xml-apis:xml-apis-ext:1.3.04" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-util:1.8" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-svggen:1.8" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-awt-util:1.8" level="project" />
-    <orderEntry type="library" scope="TEST" name="Maven: org.mockito:mockito-all:1.10.19" level="project" />
-    <orderEntry type="library" name="Maven: com.itextpdf:itextpdf:5.5.6" level="project" />
-    <orderEntry type="library" name="Maven: junit:junit:4.12" level="project" />
-    <orderEntry type="library" name="Maven: org.hamcrest:hamcrest-core:1.3" level="project" />
-  </component>
-</module>
\ No newline at end of file
diff --git a/converter/.classpath b/converter/.classpath
index c30f41516ee3b2849002081a2c15cf83d457cd92..22c865221bbb05b20a9c038d748db0cbf2129ff6 100644
--- a/converter/.classpath
+++ b/converter/.classpath
@@ -1,32 +1,31 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<classpath>
-	<classpathentry kind="src" output="target/classes" path="src/main/java">
-		<attributes>
-			<attribute name="optional" value="true"/>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="src" output="target/test-classes" path="src/test/java">
-		<attributes>
-			<attribute name="optional" value="true"/>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry excluding="**" kind="src" output="target/test-classes" path="src/test/resources">
-		<attributes>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
-		<attributes>
-			<attribute name="maven.pomderived" value="true"/>
-			<attribute name="org.eclipse.jst.component.nondependency" value=""/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8">
-		<attributes>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="output" path="target/classes"/>
-</classpath>
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+	<classpathentry kind="src" output="target/classes" path="src/main/java">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="src" output="target/test-classes" path="src/test/java">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry excluding="**" kind="src" output="target/test-classes" path="src/test/resources">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="output" path="target/classes"/>
+</classpath>
diff --git a/converter/converter.iml b/converter/converter.iml
deleted file mode 100644
index e8e77af09df2199aaad07364558052acf7416aaf..0000000000000000000000000000000000000000
--- a/converter/converter.iml
+++ /dev/null
@@ -1,36 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<module org.jetbrains.idea.maven.project.MavenProjectsManager.isMavenModule="true" type="JAVA_MODULE" version="4">
-  <component name="NewModuleRootManager" LANGUAGE_LEVEL="JDK_1_8">
-    <output url="file://$MODULE_DIR$/target/classes" />
-    <output-test url="file://$MODULE_DIR$/target/test-classes" />
-    <content url="file://$MODULE_DIR$">
-      <sourceFolder url="file://$MODULE_DIR$/src/main/java" isTestSource="false" />
-      <sourceFolder url="file://$MODULE_DIR$/src/test/java" isTestSource="true" />
-      <sourceFolder url="file://$MODULE_DIR$/src/test/resources" type="java-test-resource" />
-      <excludeFolder url="file://$MODULE_DIR$/target" />
-    </content>
-    <orderEntry type="inheritedJdk" />
-    <orderEntry type="sourceFolder" forTests="false" />
-    <orderEntry type="module" module-name="model" />
-    <orderEntry type="module" module-name="commons" />
-    <orderEntry type="library" name="Maven: commons-io:commons-io:2.4" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.commons:commons-lang3:3.1" level="project" />
-    <orderEntry type="library" name="Maven: org.hibernate:hibernate-core:4.1.0.Final" level="project" />
-    <orderEntry type="library" name="Maven: commons-collections:commons-collections:3.2.1" level="project" />
-    <orderEntry type="library" name="Maven: antlr:antlr:2.7.7" level="project" />
-    <orderEntry type="library" name="Maven: org.jboss.spec.javax.transaction:jboss-transaction-api_1.1_spec:1.0.0.Final" level="project" />
-    <orderEntry type="library" name="Maven: dom4j:dom4j:1.6.1" level="project" />
-    <orderEntry type="library" name="Maven: org.hibernate.javax.persistence:hibernate-jpa-2.0-api:1.0.1.Final" level="project" />
-    <orderEntry type="library" name="Maven: org.jboss.logging:jboss-logging:3.1.0.CR2" level="project" />
-    <orderEntry type="library" name="Maven: org.javassist:javassist:3.15.0-GA" level="project" />
-    <orderEntry type="library" name="Maven: org.hibernate.common:hibernate-commons-annotations:4.0.1.Final" level="project" />
-    <orderEntry type="library" name="Maven: xml-apis:xml-apis:1.4.01" level="project" />
-    <orderEntry type="library" name="Maven: log4j:log4j:1.2.17" level="project" />
-    <orderEntry type="library" name="Maven: org.reflections:reflections:0.9.9-RC1" level="project" />
-    <orderEntry type="library" name="Maven: com.google.guava:guava:11.0.2" level="project" />
-    <orderEntry type="library" name="Maven: com.google.code.findbugs:jsr305:1.3.9" level="project" />
-    <orderEntry type="library" name="Maven: xerces:xercesImpl:2.11.0" level="project" />
-    <orderEntry type="library" name="Maven: junit:junit:4.12" level="project" />
-    <orderEntry type="library" name="Maven: org.hamcrest:hamcrest-core:1.3" level="project" />
-  </component>
-</module>
\ No newline at end of file
diff --git a/editor/editor.iml b/editor/editor.iml
deleted file mode 100644
index 012f288c841e4be85e7f35300d9468d08b903838..0000000000000000000000000000000000000000
--- a/editor/editor.iml
+++ /dev/null
@@ -1,58 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<module org.jetbrains.idea.maven.project.MavenProjectsManager.isMavenModule="true" type="JAVA_MODULE" version="4">
-  <component name="NewModuleRootManager" LANGUAGE_LEVEL="JDK_1_8">
-    <output url="file://$MODULE_DIR$/target/classes" />
-    <output-test url="file://$MODULE_DIR$/target/test-classes" />
-    <content url="file://$MODULE_DIR$">
-      <sourceFolder url="file://$MODULE_DIR$/src/main/java" isTestSource="false" />
-      <sourceFolder url="file://$MODULE_DIR$/src/main/resources" type="java-resource" />
-      <sourceFolder url="file://$MODULE_DIR$/src/test/resources" type="java-test-resource" />
-      <excludeFolder url="file://$MODULE_DIR$/target" />
-    </content>
-    <orderEntry type="inheritedJdk" />
-    <orderEntry type="sourceFolder" forTests="false" />
-    <orderEntry type="module" module-name="model" />
-    <orderEntry type="module" module-name="commons" />
-    <orderEntry type="library" name="Maven: commons-io:commons-io:2.4" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.commons:commons-lang3:3.1" level="project" />
-    <orderEntry type="library" name="Maven: org.hibernate:hibernate-core:4.1.0.Final" level="project" />
-    <orderEntry type="library" name="Maven: commons-collections:commons-collections:3.2.1" level="project" />
-    <orderEntry type="library" name="Maven: antlr:antlr:2.7.7" level="project" />
-    <orderEntry type="library" name="Maven: org.jboss.spec.javax.transaction:jboss-transaction-api_1.1_spec:1.0.0.Final" level="project" />
-    <orderEntry type="library" name="Maven: dom4j:dom4j:1.6.1" level="project" />
-    <orderEntry type="library" name="Maven: org.hibernate.javax.persistence:hibernate-jpa-2.0-api:1.0.1.Final" level="project" />
-    <orderEntry type="library" name="Maven: org.jboss.logging:jboss-logging:3.1.0.CR2" level="project" />
-    <orderEntry type="library" name="Maven: org.javassist:javassist:3.15.0-GA" level="project" />
-    <orderEntry type="library" name="Maven: org.hibernate.common:hibernate-commons-annotations:4.0.1.Final" level="project" />
-    <orderEntry type="library" name="Maven: xml-apis:xml-apis:1.4.01" level="project" />
-    <orderEntry type="library" name="Maven: org.reflections:reflections:0.9.9-RC1" level="project" />
-    <orderEntry type="library" name="Maven: com.google.guava:guava:11.0.2" level="project" />
-    <orderEntry type="library" name="Maven: com.google.code.findbugs:jsr305:1.3.9" level="project" />
-    <orderEntry type="module" module-name="converter-graphics" />
-    <orderEntry type="module" module-name="model-command" />
-    <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-rasterizer:1.8" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-parser:1.8" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-xml:1.8" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-transcoder:1.8" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-anim:1.8" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-css:1.8" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-ext:1.8" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-svg-dom:1.8" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-bridge:1.8" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-script:1.8" level="project" />
-    <orderEntry type="library" name="Maven: xalan:xalan:2.7.0" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-dom:1.8" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-gvt:1.8" level="project" />
-    <orderEntry type="library" name="Maven: xml-apis:xml-apis-ext:1.3.04" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-util:1.8" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-svggen:1.8" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.xmlgraphics:batik-awt-util:1.8" level="project" />
-    <orderEntry type="library" name="Maven: com.itextpdf:itextpdf:5.5.6" level="project" />
-    <orderEntry type="module" module-name="converter-CellDesigner" />
-    <orderEntry type="module" module-name="converter" />
-    <orderEntry type="library" name="Maven: xerces:xercesImpl:2.11.0" level="project" />
-    <orderEntry type="library" name="Maven: log4j:log4j:1.2.17" level="project" />
-    <orderEntry type="library" name="Maven: junit:junit:4.12" level="project" />
-    <orderEntry type="library" name="Maven: org.hamcrest:hamcrest-core:1.3" level="project" />
-  </component>
-</module>
\ No newline at end of file
diff --git a/frontend-js/.classpath b/frontend-js/.classpath
index b10870e6cf001a6629a2e0743fd65e1956d3f1e1..af1430be15836d78425a795565a49fcd23d562b4 100644
--- a/frontend-js/.classpath
+++ b/frontend-js/.classpath
@@ -20,7 +20,6 @@
 	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
 		<attributes>
 			<attribute name="maven.pomderived" value="true"/>
-			<attribute name="org.eclipse.jst.component.nondependency" value=""/>
 		</attributes>
 	</classpathentry>
 	<classpathentry kind="output" path="target/classes"/>
diff --git a/frontend-js/frontend-js.iml b/frontend-js/frontend-js.iml
deleted file mode 100644
index a5cc752c7a0ba92b2dae51325422a7f9f2e107f1..0000000000000000000000000000000000000000
--- a/frontend-js/frontend-js.iml
+++ /dev/null
@@ -1,14 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<module org.jetbrains.idea.maven.project.MavenProjectsManager.isMavenModule="true" type="JAVA_MODULE" version="4">
-  <component name="NewModuleRootManager" LANGUAGE_LEVEL="JDK_1_8">
-    <output url="file://$MODULE_DIR$/target/classes" />
-    <output-test url="file://$MODULE_DIR$/target/test-classes" />
-    <content url="file://$MODULE_DIR$">
-      <excludeFolder url="file://$MODULE_DIR$/target" />
-    </content>
-    <orderEntry type="inheritedJdk" />
-    <orderEntry type="sourceFolder" forTests="false" />
-    <orderEntry type="library" name="Maven: junit:junit:4.12" level="project" />
-    <orderEntry type="library" name="Maven: org.hamcrest:hamcrest-core:1.3" level="project" />
-  </component>
-</module>
\ No newline at end of file
diff --git a/frontend-js/src/main/js/gui/admin/ChooseValidatorsDialog.js b/frontend-js/src/main/js/gui/admin/ChooseValidatorsDialog.js
index eb2a04404efb32ed11bb64c3f1ee43c26d8a30ac..10b43ed57f4e88514e9d738120badaad008eeb51 100644
--- a/frontend-js/src/main/js/gui/admin/ChooseValidatorsDialog.js
+++ b/frontend-js/src/main/js/gui/admin/ChooseValidatorsDialog.js
@@ -58,74 +58,184 @@ ChooseValidatorsDialog.prototype.setElementType = function (elementType) {
       type: "select",
       className: "minerva-multi-select"
     });
+    element.appendChild(validAnnotationSelect);
+    self.createValidAnnotationsDualListBox(user, configuration, elementType, validAnnotationSelect);
 
-    var miriamTypes = configuration.getMiriamTypes();
+    var verifyAnnotationSelect = Functions.createElement({
+      type: "select",
+      className: "minerva-multi-select"
+    });
+    element.appendChild(verifyAnnotationSelect);
+    self.createVerifyAnnotationsDualListBox(user, configuration, elementType, verifyAnnotationSelect);
+  });
 
-    var validAnnotations = user.getPreferences().getElementValidAnnotations(elementType.className);
+};
 
-    for (var i = 0; i < miriamTypes.length; i++) {
-      var miriamType = miriamTypes[i];
-      var selected = false;
-      for (var j = 0; j < validAnnotations.length; j++) {
-        if (miriamType.getName() === validAnnotations[j]) {
-          selected = true;
-        }
+ChooseValidatorsDialog.prototype.createValidAnnotationsDualListBox = function (user, configuration, elementType, validAnnotationSelect) {
+
+  var miriamTypes = configuration.getMiriamTypes();
+
+  var validAnnotations = user.getPreferences().getElementValidAnnotations(elementType.className);
+
+  for (var i = 0; i < miriamTypes.length; i++) {
+    var miriamType = miriamTypes[i];
+    var selected = false;
+    for (var j = 0; j < validAnnotations.length; j++) {
+      if (miriamType.getName() === validAnnotations[j]) {
+        selected = true;
       }
-      var option = new Option();
-      option.value = miriamType.getName();
-      option.attributes.selected = selected;
-      option.innerHTML = "<div>" + miriamType.getCommonName() + "</div>";
-      validAnnotationSelect.appendChild(option);
     }
+    var option = new Option();
+    option.value = miriamType.getName();
+    option.attributes.selected = selected;
+    option.innerHTML = "<div>" + miriamType.getCommonName() + "</div>";
+    validAnnotationSelect.appendChild(option);
+  }
 
-    element.appendChild(validAnnotationSelect);
-    new DualListbox(validAnnotationSelect, {
-      addEvent: function (value) {
-        var miriamTypes = configuration.getMiriamTypes();
-        var miriamType;
-        for (var i = 0; i < miriamTypes.length; i++) {
-          if (value === miriamTypes[i].getName()) {
-            miriamType = miriamTypes[i];
-          }
+  new DualListbox(validAnnotationSelect, {
+    addEvent: function (value) {
+      var miriamTypes = configuration.getMiriamTypes();
+      var miriamType;
+      for (var i = 0; i < miriamTypes.length; i++) {
+        if (value === miriamTypes[i].getName()) {
+          miriamType = miriamTypes[i];
         }
-        validAnnotations.push(miriamType.getName());
-
-        var data = new UserPreferences();
-
-        var elementAnnotators = {};
-        elementAnnotators[elementType.className] = validAnnotations;
-        data.setElementValidAnnotations(elementAnnotators);
-        return ServerConnector.updateUserPreferences({user: user, preferences: data}).then(null, GuiConnector.alert);
-      },
-      removeEvent: function (value) {
-        var miriamTypes = configuration.getMiriamTypes();
-        var miriamType;
-        for (var i = 0; i < miriamTypes.length; i++) {
-          if (value === miriamTypes[i].getName()) {
-            miriamType = miriamTypes[i];
-          }
-        }
-        var index = validAnnotations.indexOf(miriamType.getName());
-        if (index > -1) {
-          validAnnotations.splice(index, 1);
+      }
+      validAnnotations.push(miriamType.getName());
+
+      var data = new UserPreferences();
+
+      var elementAnnotators = {};
+      elementAnnotators[elementType.className] = validAnnotations;
+      data.setElementValidAnnotations(elementAnnotators);
+      return ServerConnector.updateUserPreferences({user: user, preferences: data}).then(null, GuiConnector.alert);
+    },
+    removeEvent: function (value) {
+      var miriamTypes = configuration.getMiriamTypes();
+      var miriamType;
+      for (var i = 0; i < miriamTypes.length; i++) {
+        if (value === miriamTypes[i].getName()) {
+          miriamType = miriamTypes[i];
         }
+      }
+      var index = validAnnotations.indexOf(miriamType.getName());
+      if (index > -1) {
+        validAnnotations.splice(index, 1);
+      }
 
-        var data = new UserPreferences();
-
-        var elementAnnotators = {};
-        elementAnnotators[elementType.className] = validAnnotations;
-        data.setElementValidAnnotations(elementAnnotators);
-        return ServerConnector.updateUserPreferences({user: user, preferences: data}).then(null, GuiConnector.alert);
-      },
-      availableTitle: 'Available',
-      selectedTitle: 'Used',
-      addButtonText: '>',
-      removeButtonText: '<',
-      addAllButtonText: '>>',
-      removeAllButtonText: '<<'
-    });
+      var data = new UserPreferences();
+
+      var elementAnnotators = {};
+      elementAnnotators[elementType.className] = validAnnotations;
+      data.setElementValidAnnotations(elementAnnotators);
+      return ServerConnector.updateUserPreferences({user: user, preferences: data}).then(null, GuiConnector.alert);
+    },
+    availableTitle: 'Available',
+    selectedTitle: 'Used',
+    addButtonText: '>',
+    removeButtonText: '<',
+    addAllButtonText: '>>',
+    removeAllButtonText: '<<'
   });
+};
 
+ChooseValidatorsDialog.prototype.createVerifyAnnotationsDualListBox = function (user, configuration, elementType, verifyAnnotationSelect) {
+  var requiredAnnotationsData = user.getPreferences().getElementRequiredAnnotations(elementType.className);
+
+  var verifyCheckboxDiv = Functions.createElement({type: "div"});
+  var checkbox = Functions.createElement({
+    id: "test",
+    type: "input",
+    inputType: "checkbox",
+    onclick: function () {
+      var data = new UserPreferences();
+
+      var elementRequiredAnnotations = {};
+      elementRequiredAnnotations[elementType.className] = {
+        "require-at-least-one": checkbox.checked,
+        "annotation-list": requiredAnnotationsData.list
+      };
+      data.setElementRequiredAnnotations(elementRequiredAnnotations);
+      return ServerConnector.updateUserPreferences({user: user, preferences: data}).then(null, GuiConnector.alert);
+    }
+  });
+  checkbox.checked = requiredAnnotationsData.requiredAtLeastOnce;
+  verifyCheckboxDiv.appendChild(checkbox);
+  verifyCheckboxDiv.appendChild(Functions.createElement({
+    type: "span",
+    content: "One of these miriam should be required"
+  }));
+  verifyAnnotationSelect.parentNode.insertBefore(verifyCheckboxDiv, verifyAnnotationSelect);
+
+  var miriamTypes = configuration.getMiriamTypes();
+
+
+  for (var i = 0; i < miriamTypes.length; i++) {
+    var miriamType = miriamTypes[i];
+    var selected = false;
+    for (var j = 0; j < requiredAnnotationsData.list.length; j++) {
+      if (miriamType.getName() === requiredAnnotationsData.list[j]) {
+        selected = true;
+      }
+    }
+    var option = new Option();
+    option.value = miriamType.getName();
+    option.attributes.selected = selected;
+    option.innerHTML = "<div>" + miriamType.getCommonName() + "</div>";
+    verifyAnnotationSelect.appendChild(option);
+  }
+
+  new DualListbox(verifyAnnotationSelect, {
+    addEvent: function (value) {
+      var miriamTypes = configuration.getMiriamTypes();
+      var miriamType;
+      for (var i = 0; i < miriamTypes.length; i++) {
+        if (value === miriamTypes[i].getName()) {
+          miriamType = miriamTypes[i];
+        }
+      }
+      requiredAnnotationsData.list.push(miriamType.getName());
+
+      var data = new UserPreferences();
+
+      var elementRequiredAnnotations = {};
+      elementRequiredAnnotations[elementType.className] = {
+        "require-at-least-one": requiredAnnotationsData.requiredAtLeastOnce,
+        "annotation-list": requiredAnnotationsData.list
+      };
+      data.setElementRequiredAnnotations(elementRequiredAnnotations);
+      return ServerConnector.updateUserPreferences({user: user, preferences: data}).then(null, GuiConnector.alert);
+    },
+    removeEvent: function (value) {
+      var miriamTypes = configuration.getMiriamTypes();
+      var miriamType;
+      for (var i = 0; i < miriamTypes.length; i++) {
+        if (value === miriamTypes[i].getName()) {
+          miriamType = miriamTypes[i];
+        }
+      }
+      var index = requiredAnnotationsData.list.indexOf(miriamType.getName());
+      if (index > -1) {
+        requiredAnnotationsData.list.splice(index, 1);
+      }
+
+      var data = new UserPreferences();
+
+      var elementRequiredAnnotations = {};
+      elementRequiredAnnotations[elementType.className] = {
+        "require-at-least-one": requiredAnnotationsData.requiredAtLeastOnce,
+        "annotation-list": requiredAnnotationsData.list
+      };
+      data.setElementRequiredAnnotations(elementRequiredAnnotations);
+      return ServerConnector.updateUserPreferences({user: user, preferences: data}).then(null, GuiConnector.alert);
+    },
+    availableTitle: 'Available',
+    selectedTitle: 'Used',
+    addButtonText: '>',
+    removeButtonText: '<',
+    addAllButtonText: '>>',
+    removeAllButtonText: '<<'
+  });
 };
 
 ChooseValidatorsDialog.prototype.init = function () {
diff --git a/frontend-js/src/main/js/map/data/UserPreferences.js b/frontend-js/src/main/js/map/data/UserPreferences.js
index e4591977b26143fb7cc54eea3b1b9e925ea68c56..c3807b066432534e4921bf05360509001d24913a 100644
--- a/frontend-js/src/main/js/map/data/UserPreferences.js
+++ b/frontend-js/src/main/js/map/data/UserPreferences.js
@@ -60,6 +60,17 @@ UserPreferences.prototype.getElementValidAnnotations = function (className) {
 };
 
 UserPreferences.prototype.toExport = function () {
+  var requiredAnnotations = {};
+  for (var key in this._elementRequiredAnnotations) {
+    if (this._elementRequiredAnnotations.hasOwnProperty(key)) {
+      var data = this._elementRequiredAnnotations[key];
+      requiredAnnotations[key] = {
+        "require-at-least-one": data.requiredAtLeastOnce,
+        "annotation-list": data.list,
+      };
+    }
+  }
+
   return {
     "project-upload": {
       "auto-resize": this._projectUpload.autoResize,
@@ -70,7 +81,8 @@ UserPreferences.prototype.toExport = function () {
       "semantic-zooming": this._projectUpload.semanticZooming
     },
     "element-annotators": this._elementAnnotators,
-    "element-valid-annotations": this._elementValidAnnotations
+    "element-valid-annotations": this._elementValidAnnotations,
+    "element-required-annotations": requiredAnnotations
   };
 };
 
diff --git a/model-command/.classpath b/model-command/.classpath
index 62d4b8e4723486982a42cd5dd2b44363281a0bd8..ace82666f2f113cdb835230548bb1c0ddf6ca559 100644
--- a/model-command/.classpath
+++ b/model-command/.classpath
@@ -1,37 +1,36 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<classpath>
-	<classpathentry kind="src" output="target/classes" path="src/main/java">
-		<attributes>
-			<attribute name="optional" value="true"/>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources">
-		<attributes>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="src" output="target/test-classes" path="src/test/java">
-		<attributes>
-			<attribute name="optional" value="true"/>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry excluding="**" kind="src" output="target/test-classes" path="src/test/resources">
-		<attributes>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
-		<attributes>
-			<attribute name="maven.pomderived" value="true"/>
-			<attribute name="org.eclipse.jst.component.nondependency" value=""/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8">
-		<attributes>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="output" path="target/classes"/>
-</classpath>
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+	<classpathentry kind="src" output="target/classes" path="src/main/java">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="src" output="target/test-classes" path="src/test/java">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry excluding="**" kind="src" output="target/test-classes" path="src/test/resources">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="output" path="target/classes"/>
+</classpath>
diff --git a/model-command/model-command.iml b/model-command/model-command.iml
deleted file mode 100644
index b581f7dac6c8f5a4d3ad60214cb8e4481bc7c74e..0000000000000000000000000000000000000000
--- a/model-command/model-command.iml
+++ /dev/null
@@ -1,39 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<module org.jetbrains.idea.maven.project.MavenProjectsManager.isMavenModule="true" type="JAVA_MODULE" version="4">
-  <component name="NewModuleRootManager" LANGUAGE_LEVEL="JDK_1_8">
-    <output url="file://$MODULE_DIR$/target/classes" />
-    <output-test url="file://$MODULE_DIR$/target/test-classes" />
-    <content url="file://$MODULE_DIR$">
-      <sourceFolder url="file://$MODULE_DIR$/src/main/java" isTestSource="false" />
-      <sourceFolder url="file://$MODULE_DIR$/src/main/resources" type="java-resource" />
-      <sourceFolder url="file://$MODULE_DIR$/src/test/java" isTestSource="true" />
-      <sourceFolder url="file://$MODULE_DIR$/src/test/resources" type="java-test-resource" />
-      <excludeFolder url="file://$MODULE_DIR$/target" />
-    </content>
-    <orderEntry type="inheritedJdk" />
-    <orderEntry type="sourceFolder" forTests="false" />
-    <orderEntry type="module" module-name="model" />
-    <orderEntry type="module" module-name="commons" />
-    <orderEntry type="library" name="Maven: commons-io:commons-io:2.4" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.commons:commons-lang3:3.1" level="project" />
-    <orderEntry type="library" name="Maven: org.hibernate:hibernate-core:4.1.0.Final" level="project" />
-    <orderEntry type="library" name="Maven: commons-collections:commons-collections:3.2.1" level="project" />
-    <orderEntry type="library" name="Maven: antlr:antlr:2.7.7" level="project" />
-    <orderEntry type="library" name="Maven: org.jboss.spec.javax.transaction:jboss-transaction-api_1.1_spec:1.0.0.Final" level="project" />
-    <orderEntry type="library" name="Maven: dom4j:dom4j:1.6.1" level="project" />
-    <orderEntry type="library" name="Maven: org.hibernate.javax.persistence:hibernate-jpa-2.0-api:1.0.1.Final" level="project" />
-    <orderEntry type="library" name="Maven: org.jboss.logging:jboss-logging:3.1.0.CR2" level="project" />
-    <orderEntry type="library" name="Maven: org.javassist:javassist:3.15.0-GA" level="project" />
-    <orderEntry type="library" name="Maven: org.hibernate.common:hibernate-commons-annotations:4.0.1.Final" level="project" />
-    <orderEntry type="library" name="Maven: xml-apis:xml-apis:1.4.01" level="project" />
-    <orderEntry type="library" name="Maven: org.reflections:reflections:0.9.9-RC1" level="project" />
-    <orderEntry type="library" name="Maven: com.google.guava:guava:11.0.2" level="project" />
-    <orderEntry type="library" name="Maven: com.google.code.findbugs:jsr305:1.3.9" level="project" />
-    <orderEntry type="module" module-name="converter-CellDesigner" scope="TEST" />
-    <orderEntry type="module" module-name="converter" scope="TEST" />
-    <orderEntry type="library" scope="TEST" name="Maven: xerces:xercesImpl:2.11.0" level="project" />
-    <orderEntry type="library" name="Maven: log4j:log4j:1.2.17" level="project" />
-    <orderEntry type="library" name="Maven: junit:junit:4.12" level="project" />
-    <orderEntry type="library" name="Maven: org.hamcrest:hamcrest-core:1.3" level="project" />
-  </component>
-</module>
\ No newline at end of file
diff --git a/model/.classpath b/model/.classpath
index 62d4b8e4723486982a42cd5dd2b44363281a0bd8..ace82666f2f113cdb835230548bb1c0ddf6ca559 100644
--- a/model/.classpath
+++ b/model/.classpath
@@ -1,37 +1,36 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<classpath>
-	<classpathentry kind="src" output="target/classes" path="src/main/java">
-		<attributes>
-			<attribute name="optional" value="true"/>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources">
-		<attributes>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="src" output="target/test-classes" path="src/test/java">
-		<attributes>
-			<attribute name="optional" value="true"/>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry excluding="**" kind="src" output="target/test-classes" path="src/test/resources">
-		<attributes>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
-		<attributes>
-			<attribute name="maven.pomderived" value="true"/>
-			<attribute name="org.eclipse.jst.component.nondependency" value=""/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8">
-		<attributes>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="output" path="target/classes"/>
-</classpath>
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+	<classpathentry kind="src" output="target/classes" path="src/main/java">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="src" output="target/test-classes" path="src/test/java">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry excluding="**" kind="src" output="target/test-classes" path="src/test/resources">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="output" path="target/classes"/>
+</classpath>
diff --git a/model/model.iml b/model/model.iml
deleted file mode 100644
index 3887ea7ae0ddd5e62b7040edfe2bc966c44fe0e2..0000000000000000000000000000000000000000
--- a/model/model.iml
+++ /dev/null
@@ -1,36 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<module org.jetbrains.idea.maven.project.MavenProjectsManager.isMavenModule="true" type="JAVA_MODULE" version="4">
-  <component name="NewModuleRootManager" LANGUAGE_LEVEL="JDK_1_8">
-    <output url="file://$MODULE_DIR$/target/classes" />
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deleted file mode 100644
index fbe8d0356cb6f6a5a6a2872eb1e5f651afd0edb9..0000000000000000000000000000000000000000
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deleted file mode 100644
index 51f177eb5c0dc0826ea3f5ac591dbaf96889b194..0000000000000000000000000000000000000000
--- a/pathvisio/pathvisio.iml
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@@ -1,80 +0,0 @@
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\ No newline at end of file
diff --git a/persist/.classpath b/persist/.classpath
index 62d4b8e4723486982a42cd5dd2b44363281a0bd8..ace82666f2f113cdb835230548bb1c0ddf6ca559 100644
--- a/persist/.classpath
+++ b/persist/.classpath
@@ -1,37 +1,36 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<classpath>
-	<classpathentry kind="src" output="target/classes" path="src/main/java">
-		<attributes>
-			<attribute name="optional" value="true"/>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources">
-		<attributes>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="src" output="target/test-classes" path="src/test/java">
-		<attributes>
-			<attribute name="optional" value="true"/>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry excluding="**" kind="src" output="target/test-classes" path="src/test/resources">
-		<attributes>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
-		<attributes>
-			<attribute name="maven.pomderived" value="true"/>
-			<attribute name="org.eclipse.jst.component.nondependency" value=""/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8">
-		<attributes>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="output" path="target/classes"/>
-</classpath>
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+	<classpathentry kind="src" output="target/classes" path="src/main/java">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="src" output="target/test-classes" path="src/test/java">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry excluding="**" kind="src" output="target/test-classes" path="src/test/resources">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="output" path="target/classes"/>
+</classpath>
diff --git a/persist/persist.iml b/persist/persist.iml
deleted file mode 100644
index 1fee876a338b84c30dbc946192cd9c29d091f8b1..0000000000000000000000000000000000000000
--- a/persist/persist.iml
+++ /dev/null
@@ -1,63 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<module org.jetbrains.idea.maven.project.MavenProjectsManager.isMavenModule="true" type="JAVA_MODULE" version="4">
-  <component name="FacetManager">
-    <facet type="Spring" name="Spring">
-      <configuration />
-    </facet>
-  </component>
-  <component name="NewModuleRootManager" LANGUAGE_LEVEL="JDK_1_8">
-    <output url="file://$MODULE_DIR$/target/classes" />
-    <output-test url="file://$MODULE_DIR$/target/test-classes" />
-    <content url="file://$MODULE_DIR$">
-      <sourceFolder url="file://$MODULE_DIR$/src/main/java" isTestSource="false" />
-      <sourceFolder url="file://$MODULE_DIR$/src/main/resources" type="java-resource" />
-      <sourceFolder url="file://$MODULE_DIR$/src/test/java" isTestSource="true" />
-      <sourceFolder url="file://$MODULE_DIR$/src/test/resources" type="java-test-resource" />
-      <excludeFolder url="file://$MODULE_DIR$/target" />
-    </content>
-    <orderEntry type="inheritedJdk" />
-    <orderEntry type="sourceFolder" forTests="false" />
-    <orderEntry type="module" module-name="model" />
-    <orderEntry type="module" module-name="commons" />
-    <orderEntry type="library" name="Maven: commons-io:commons-io:2.4" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.commons:commons-lang3:3.1" level="project" />
-    <orderEntry type="library" name="Maven: org.reflections:reflections:0.9.9-RC1" level="project" />
-    <orderEntry type="library" name="Maven: com.google.guava:guava:11.0.2" level="project" />
-    <orderEntry type="library" name="Maven: com.google.code.findbugs:jsr305:1.3.9" level="project" />
-    <orderEntry type="library" name="Maven: commons-net:commons-net:3.5" level="project" />
-    <orderEntry type="library" name="Maven: org.hibernate:hibernate-core:4.1.0.Final" level="project" />
-    <orderEntry type="library" name="Maven: commons-collections:commons-collections:3.2.1" level="project" />
-    <orderEntry type="library" name="Maven: antlr:antlr:2.7.7" level="project" />
-    <orderEntry type="library" name="Maven: org.jboss.spec.javax.transaction:jboss-transaction-api_1.1_spec:1.0.0.Final" level="project" />
-    <orderEntry type="library" name="Maven: dom4j:dom4j:1.6.1" level="project" />
-    <orderEntry type="library" name="Maven: org.hibernate.javax.persistence:hibernate-jpa-2.0-api:1.0.1.Final" level="project" />
-    <orderEntry type="library" name="Maven: org.jboss.logging:jboss-logging:3.1.0.CR2" level="project" />
-    <orderEntry type="library" name="Maven: org.javassist:javassist:3.15.0-GA" level="project" />
-    <orderEntry type="library" name="Maven: org.hibernate.common:hibernate-commons-annotations:4.0.1.Final" level="project" />
-    <orderEntry type="library" name="Maven: xml-apis:xml-apis:1.4.01" level="project" />
-    <orderEntry type="library" name="Maven: log4j:log4j:1.2.17" level="project" />
-    <orderEntry type="library" name="Maven: org.springframework:spring-core:4.2.0.RELEASE" level="project" />
-    <orderEntry type="library" name="Maven: commons-logging:commons-logging:1.2" level="project" />
-    <orderEntry type="library" name="Maven: org.springframework:spring-context:4.2.0.RELEASE" level="project" />
-    <orderEntry type="library" name="Maven: org.springframework:spring-aop:4.2.0.RELEASE" level="project" />
-    <orderEntry type="library" name="Maven: aopalliance:aopalliance:1.0" level="project" />
-    <orderEntry type="library" name="Maven: org.springframework:spring-beans:4.2.0.RELEASE" level="project" />
-    <orderEntry type="library" name="Maven: org.springframework:spring-expression:4.2.0.RELEASE" level="project" />
-    <orderEntry type="library" name="Maven: org.springframework:spring-web:4.2.0.RELEASE" level="project" />
-    <orderEntry type="library" name="Maven: org.springframework:spring-tx:4.2.0.RELEASE" level="project" />
-    <orderEntry type="library" name="Maven: org.springframework:spring-orm:4.2.0.RELEASE" level="project" />
-    <orderEntry type="library" name="Maven: org.springframework:spring-jdbc:4.2.0.RELEASE" level="project" />
-    <orderEntry type="library" name="Maven: org.springframework.security:spring-security-taglibs:4.0.2.RELEASE" level="project" />
-    <orderEntry type="library" name="Maven: org.springframework.security:spring-security-acl:4.0.2.RELEASE" level="project" />
-    <orderEntry type="library" name="Maven: org.springframework.security:spring-security-core:4.0.2.RELEASE" level="project" />
-    <orderEntry type="library" name="Maven: org.springframework.security:spring-security-web:4.0.2.RELEASE" level="project" />
-    <orderEntry type="library" name="Maven: org.springframework:spring-test:4.2.0.RELEASE" level="project" />
-    <orderEntry type="library" name="Maven: postgresql:postgresql:9.1-901.jdbc4" level="project" />
-    <orderEntry type="library" name="Maven: c3p0:c3p0:0.9.1.2" level="project" />
-    <orderEntry type="library" name="Maven: cglib:cglib:2.2.2" level="project" />
-    <orderEntry type="library" name="Maven: asm:asm:3.3.1" level="project" />
-    <orderEntry type="library" name="Maven: com.google.code.gson:gson:2.2.2" level="project" />
-    <orderEntry type="library" name="Maven: junit:junit:4.12" level="project" />
-    <orderEntry type="library" name="Maven: org.hamcrest:hamcrest-core:1.3" level="project" />
-  </component>
-</module>
\ No newline at end of file
diff --git a/quadTrees/quadTrees.iml b/quadTrees/quadTrees.iml
deleted file mode 100644
index ae2a802e417e33733afa7a5e03c8d5d677093218..0000000000000000000000000000000000000000
--- a/quadTrees/quadTrees.iml
+++ /dev/null
@@ -1,19 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<module org.jetbrains.idea.maven.project.MavenProjectsManager.isMavenModule="true" type="JAVA_MODULE" version="4">
-  <component name="NewModuleRootManager" LANGUAGE_LEVEL="JDK_1_8">
-    <output url="file://$MODULE_DIR$/target/classes" />
-    <output-test url="file://$MODULE_DIR$/target/test-classes" />
-    <content url="file://$MODULE_DIR$">
-      <sourceFolder url="file://$MODULE_DIR$/src/main/java" isTestSource="false" />
-      <sourceFolder url="file://$MODULE_DIR$/src/main/resources" type="java-resource" />
-      <sourceFolder url="file://$MODULE_DIR$/src/test/java" isTestSource="true" />
-      <sourceFolder url="file://$MODULE_DIR$/src/test/resources" type="java-test-resource" />
-      <excludeFolder url="file://$MODULE_DIR$/target" />
-    </content>
-    <orderEntry type="inheritedJdk" />
-    <orderEntry type="sourceFolder" forTests="false" />
-    <orderEntry type="library" name="Maven: log4j:log4j:1.2.17" level="project" />
-    <orderEntry type="library" name="Maven: junit:junit:4.12" level="project" />
-    <orderEntry type="library" name="Maven: org.hamcrest:hamcrest-core:1.3" level="project" />
-  </component>
-</module>
\ No newline at end of file
diff --git a/reactome/reactome.iml b/reactome/reactome.iml
deleted file mode 100644
index 719ba8dc8171605a90ba1729fa1d77f790a72c8b..0000000000000000000000000000000000000000
--- a/reactome/reactome.iml
+++ /dev/null
@@ -1,111 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<module org.jetbrains.idea.maven.project.MavenProjectsManager.isMavenModule="true" type="JAVA_MODULE" version="4">
-  <component name="FacetManager">
-    <facet type="Spring" name="Spring">
-      <configuration />
-    </facet>
-  </component>
-  <component name="NewModuleRootManager" LANGUAGE_LEVEL="JDK_1_8">
-    <output url="file://$MODULE_DIR$/target/classes" />
-    <output-test url="file://$MODULE_DIR$/target/test-classes" />
-    <content url="file://$MODULE_DIR$">
-      <sourceFolder url="file://$MODULE_DIR$/src/main/java" isTestSource="false" />
-      <sourceFolder url="file://$MODULE_DIR$/src/main/resources" type="java-resource" />
-      <sourceFolder url="file://$MODULE_DIR$/src/test/java" isTestSource="true" />
-      <sourceFolder url="file://$MODULE_DIR$/src/test/resources" type="java-test-resource" />
-      <excludeFolder url="file://$MODULE_DIR$/target" />
-    </content>
-    <orderEntry type="inheritedJdk" />
-    <orderEntry type="sourceFolder" forTests="false" />
-    <orderEntry type="module" module-name="model" />
-    <orderEntry type="module" module-name="commons" />
-    <orderEntry type="library" name="Maven: commons-io:commons-io:2.4" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.commons:commons-lang3:3.1" level="project" />
-    <orderEntry type="library" name="Maven: org.hibernate:hibernate-core:4.1.0.Final" level="project" />
-    <orderEntry type="library" name="Maven: commons-collections:commons-collections:3.2.1" level="project" />
-    <orderEntry type="library" name="Maven: antlr:antlr:2.7.7" level="project" />
-    <orderEntry type="library" name="Maven: org.jboss.spec.javax.transaction:jboss-transaction-api_1.1_spec:1.0.0.Final" level="project" />
-    <orderEntry type="library" name="Maven: dom4j:dom4j:1.6.1" level="project" />
-    <orderEntry type="library" name="Maven: org.hibernate.javax.persistence:hibernate-jpa-2.0-api:1.0.1.Final" level="project" />
-    <orderEntry type="library" name="Maven: org.jboss.logging:jboss-logging:3.1.0.CR2" level="project" />
-    <orderEntry type="library" name="Maven: org.javassist:javassist:3.15.0-GA" level="project" />
-    <orderEntry type="library" name="Maven: org.hibernate.common:hibernate-commons-annotations:4.0.1.Final" level="project" />
-    <orderEntry type="library" name="Maven: xml-apis:xml-apis:1.4.01" level="project" />
-    <orderEntry type="library" name="Maven: org.reflections:reflections:0.9.9-RC1" level="project" />
-    <orderEntry type="library" name="Maven: com.google.guava:guava:11.0.2" level="project" />
-    <orderEntry type="library" name="Maven: com.google.code.findbugs:jsr305:1.3.9" level="project" />
-    <orderEntry type="module" module-name="converter-CellDesigner" />
-    <orderEntry type="module" module-name="converter" />
-    <orderEntry type="module" module-name="annotation" />
-    <orderEntry type="library" name="Maven: xerces:xercesImpl:2.11.0" level="project" />
-    <orderEntry type="library" name="Maven: uk.ac.ebi.chebi.webapps.chebiWS.client:chebiWS-client:2.2.2" level="project" />
-    <orderEntry type="library" name="Maven: com.sun.xml.ws:jaxws-rt:2.1.7" level="project" />
-    <orderEntry type="library" name="Maven: com.sun.xml.stream.buffer:streambuffer:0.9" level="project" />
-    <orderEntry type="library" name="Maven: org.codehaus.woodstox:wstx-asl:3.2.3" level="project" />
-    <orderEntry type="library" name="Maven: org.jvnet.staxex:stax-ex:1.2" level="project" />
-    <orderEntry type="library" name="Maven: javax.xml.stream:stax-api:1.0" level="project" />
-    <orderEntry type="library" name="Maven: com.sun.org.apache.xml.internal:resolver:20050927" level="project" />
-    <orderEntry type="library" name="Maven: org.jvnet:mimepull:1.3" level="project" />
-    <orderEntry type="library" name="Maven: javax.xml.ws:jaxws-api:2.1" level="project" />
-    <orderEntry type="library" name="Maven: com.sun.xml.ws:jaxws-tools:2.1.3" level="project" />
-    <orderEntry type="library" name="Maven: com.sun.xml.bind:jaxb-xjc:2.1.6" level="project" />
-    <orderEntry type="library" name="Maven: com.sun.xml.messaging.saaj:saaj-impl:1.3.2" level="project" />
-    <orderEntry type="library" name="Maven: javax.xml.soap:saaj-api:1.3" level="project" />
-    <orderEntry type="library" name="Maven: uk.ac.ebi.miriam:miriam-lib:1.1.5" level="project" />
-    <orderEntry type="library" name="Maven: axis:axis:1.4" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.axis:axis-jaxrpc:1.4" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.axis:axis-saaj:1.4" level="project" />
-    <orderEntry type="library" scope="RUNTIME" name="Maven: axis:axis-wsdl4j:1.5.1" level="project" />
-    <orderEntry type="library" scope="RUNTIME" name="Maven: commons-discovery:commons-discovery:0.2" level="project" />
-    <orderEntry type="library" name="Maven: javax.activation:activation:1.1" level="project" />
-    <orderEntry type="library" name="Maven: javax.mail:mail:1.4" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.httpcomponents:httpclient:4.4" level="project" />
-    <orderEntry type="library" name="Maven: commons-codec:commons-codec:1.9" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.httpcomponents:httpmime:4.4" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.httpcomponents:httpcore:4.4" level="project" />
-    <orderEntry type="library" name="Maven: javax.xml.bind:jaxb-api:2.2.7" level="project" />
-    <orderEntry type="library" name="Maven: com.sun.xml.bind:jaxb-impl:2.2.7" level="project" />
-    <orderEntry type="library" name="Maven: com.sun.xml.bind:jaxb-core:2.2.7" level="project" />
-    <orderEntry type="library" name="Maven: com.sun.istack:istack-commons-runtime:2.16" level="project" />
-    <orderEntry type="library" name="Maven: com.sun.xml.fastinfoset:FastInfoset:1.2.12" level="project" />
-    <orderEntry type="library" name="Maven: javax.xml.bind:jsr173_api:1.0" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.poi:poi:3.12" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.poi:poi-ooxml-schemas:3.12" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.xmlbeans:xmlbeans:2.6.0" level="project" />
-    <orderEntry type="library" name="Maven: stax:stax-api:1.0.1" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.poi:poi-ooxml:3.12" level="project" />
-    <orderEntry type="module" module-name="persist" />
-    <orderEntry type="library" name="Maven: commons-net:commons-net:3.5" level="project" />
-    <orderEntry type="library" name="Maven: org.springframework:spring-tx:4.2.0.RELEASE" level="project" />
-    <orderEntry type="library" name="Maven: org.springframework:spring-orm:4.2.0.RELEASE" level="project" />
-    <orderEntry type="library" name="Maven: org.springframework:spring-jdbc:4.2.0.RELEASE" level="project" />
-    <orderEntry type="library" name="Maven: org.springframework.security:spring-security-taglibs:4.0.2.RELEASE" level="project" />
-    <orderEntry type="library" name="Maven: org.springframework.security:spring-security-acl:4.0.2.RELEASE" level="project" />
-    <orderEntry type="library" name="Maven: org.springframework.security:spring-security-core:4.0.2.RELEASE" level="project" />
-    <orderEntry type="library" name="Maven: org.springframework.security:spring-security-web:4.0.2.RELEASE" level="project" />
-    <orderEntry type="library" name="Maven: postgresql:postgresql:9.1-901.jdbc4" level="project" />
-    <orderEntry type="library" name="Maven: c3p0:c3p0:0.9.1.2" level="project" />
-    <orderEntry type="library" name="Maven: cglib:cglib:2.2.2" level="project" />
-    <orderEntry type="library" name="Maven: asm:asm:3.3.1" level="project" />
-    <orderEntry type="library" name="Maven: com.google.code.gson:gson:2.2.2" level="project" />
-    <orderEntry type="library" name="Maven: log4j:log4j:1.2.17" level="project" />
-    <orderEntry type="library" name="Maven: org.springframework:spring-core:4.2.0.RELEASE" level="project" />
-    <orderEntry type="library" name="Maven: commons-logging:commons-logging:1.2" level="project" />
-    <orderEntry type="library" name="Maven: org.springframework:spring-context:4.2.0.RELEASE" level="project" />
-    <orderEntry type="library" name="Maven: org.springframework:spring-aop:4.2.0.RELEASE" level="project" />
-    <orderEntry type="library" name="Maven: aopalliance:aopalliance:1.0" level="project" />
-    <orderEntry type="library" name="Maven: org.springframework:spring-beans:4.2.0.RELEASE" level="project" />
-    <orderEntry type="library" name="Maven: org.springframework:spring-expression:4.2.0.RELEASE" level="project" />
-    <orderEntry type="library" name="Maven: org.springframework:spring-web:4.2.0.RELEASE" level="project" />
-    <orderEntry type="library" name="Maven: org.springframework:spring-test:4.2.0.RELEASE" level="project" />
-    <orderEntry type="library" name="Maven: org.springframework.webflow:spring-faces:2.4.2.RELEASE" level="project" />
-    <orderEntry type="library" name="Maven: org.springframework.webflow:spring-binding:2.4.2.RELEASE" level="project" />
-    <orderEntry type="library" name="Maven: opensymphony:ognl:2.6.11" level="project" />
-    <orderEntry type="library" name="Maven: org.springframework.webflow:spring-webflow:2.4.2.RELEASE" level="project" />
-    <orderEntry type="library" name="Maven: org.springframework.webflow:spring-js:2.4.2.RELEASE" level="project" />
-    <orderEntry type="library" name="Maven: org.springframework.webflow:spring-js-resources:2.4.2.RELEASE" level="project" />
-    <orderEntry type="library" name="Maven: org.springframework:spring-webmvc:4.2.0.RELEASE" level="project" />
-    <orderEntry type="library" name="Maven: junit:junit:4.12" level="project" />
-    <orderEntry type="library" name="Maven: org.hamcrest:hamcrest-core:1.3" level="project" />
-  </component>
-</module>
\ No newline at end of file
diff --git a/rest-api/.classpath b/rest-api/.classpath
index 3783d3d93c885fcd1b40df6fe49f64d056876503..ec5c30a80e0515905ae05019444910628e0743e6 100644
--- a/rest-api/.classpath
+++ b/rest-api/.classpath
@@ -30,7 +30,6 @@
 	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
 		<attributes>
 			<attribute name="maven.pomderived" value="true"/>
-			<attribute name="org.eclipse.jst.component.nondependency" value=""/>
 		</attributes>
 	</classpathentry>
 	<classpathentry kind="output" path="target/classes"/>
diff --git a/rest-api/rest-api.iml b/rest-api/rest-api.iml
deleted file mode 100644
index fa783be2e59f854b10836e188bf7cd63ecdd98c7..0000000000000000000000000000000000000000
--- a/rest-api/rest-api.iml
+++ /dev/null
@@ -1,146 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<module org.jetbrains.idea.maven.project.MavenProjectsManager.isMavenModule="true" type="JAVA_MODULE" version="4">
-  <component name="FacetManager">
-    <facet type="Spring" name="Spring">
-      <configuration />
-    </facet>
-  </component>
-  <component name="NewModuleRootManager" LANGUAGE_LEVEL="JDK_1_8">
-    <output url="file://$MODULE_DIR$/target/classes" />
-    <output-test url="file://$MODULE_DIR$/target/test-classes" />
-    <content url="file://$MODULE_DIR$">
-      <sourceFolder url="file://$MODULE_DIR$/src/main/java" isTestSource="false" />
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diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/users/UserController.java b/rest-api/src/main/java/lcsb/mapviewer/api/users/UserController.java
index c71a99ada9f66f16d1ae0308a8a24af4c51a9e00..cf2961dce83aa4896ddcc567ec453cce24ed0329 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/users/UserController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/users/UserController.java
@@ -27,141 +27,147 @@ import lcsb.mapviewer.services.view.AuthenticationToken;
 
 @RestController
 public class UserController extends BaseController {
-	/**
-	 * Default class logger.
-	 */
-	@SuppressWarnings("unused")
-	private Logger			 logger	= Logger.getLogger(UserController.class);
-
-	@Autowired
-	private IUserService userService;
-
-	@Autowired
-	private UserRestImpl userRest;
-
-	@RequestMapping(value = "/doLogin", method = { RequestMethod.GET, RequestMethod.POST }, produces = { MediaType.APPLICATION_JSON_VALUE })
-	public Map<String, Object> login(//
-																	 @RequestParam(value = "login", defaultValue = Configuration.ANONYMOUS_LOGIN) String login, //
-																	 @RequestParam(value = "password", required = false) String password, //
-																	 HttpServletResponse response //
-	) throws SecurityException, IOException {
-		AuthenticationToken token = userService.login(login, password);
-		if (token == null) {
-			throw new SecurityException("Invalid credentials");
-		} else {
-			Map<String, Object> result = new HashMap<>();
-			final Boolean useSecureCookie = false;
-			final int expiryTime = (int) (token.getExpires().getTimeInMillis() - Calendar.getInstance().getTimeInMillis()) / 1000;
-			final String cookiePath = "/";
-
-			Cookie cookie = new Cookie("MINERVA_AUTH_TOKEN", token.getId());
-
-			cookie.setSecure(useSecureCookie);
-			cookie.setMaxAge(expiryTime);
-			cookie.setPath(cookiePath);
-
-			response.addCookie(cookie);
-			response.getWriter().write("{\"info\":\"Login successful. TOKEN returned as a cookie\"}");
-			response.getWriter().flush();
-			response.getWriter().close();
-			return result;
-		}
-	}
-
-	@RequestMapping(value = "/users/{login:.+}", method = { RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
-	public Map<String, Object> getUser(//
-			@CookieValue(value = Configuration.AUTH_TOKEN) String token, //
-			@PathVariable(value = "login") String login, //
-			@RequestParam(value = "columns", defaultValue = "") String columns//
-	) throws SecurityException, ObjectNotFoundException {
-		return userRest.getUser(token, login, columns);
-	}
-
-	@RequestMapping(value = "/users/{login}:updatePrivileges", method = { RequestMethod.PATCH }, produces = { MediaType.APPLICATION_JSON_VALUE })
-	public Map<String, Object> updatePrivileges(//
-			@RequestBody String body, //
-			@CookieValue(value = Configuration.AUTH_TOKEN) String token, //
-			@PathVariable(value = "login") String login //
-	) throws SecurityException, JsonParseException, JsonMappingException, IOException, QueryException {
-		Map<String, Object> node = parseBody(body);
-		Map<String, Object> data = getData(node, "privileges");
-		return userRest.updatePrivileges(token, login, data);
-	}
-
-	@RequestMapping(value = "/users/{login}:updatePreferences", method = { RequestMethod.PATCH }, produces = { MediaType.APPLICATION_JSON_VALUE })
-	public Map<String, Object> updatePreferences(//
-			@RequestBody String body, //
-			@CookieValue(value = Configuration.AUTH_TOKEN) String token, //
-			@PathVariable(value = "login") String login //
-	) throws SecurityException, JsonParseException, JsonMappingException, IOException, QueryException {
-		Map<String, Object> node = parseBody(body);
-		Map<String, Object> data = getData(node, "preferences");
-		return userRest.updatePreferences(token, login, data);
-	}
-
-	@RequestMapping(value = "/users/", method = { RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
-	public List<Map<String, Object>> getUsers(//
-			@CookieValue(value = Configuration.AUTH_TOKEN) String token, //
-			@RequestParam(value = "columns", defaultValue = "") String columns//
-	) throws SecurityException, ObjectNotFoundException {
-		return userRest.getUsers(token, columns);
-	}
-
-	@RequestMapping(value = "/doLogout", method = { RequestMethod.GET, RequestMethod.POST }, produces = { MediaType.APPLICATION_JSON_VALUE })
-	public Map<String, String> logout(@CookieValue(value = Configuration.AUTH_TOKEN) String token,
-			HttpServletResponse response //
-			) throws SecurityException, IOException {
-		userService.logout(token);
-		Map<String, String> result = new HashMap<>();
-		result.put("status", "OK");
-
-		final Boolean useSecureCookie = false;
-		final String cookiePath = "/";
-
-		Cookie cookie = new Cookie("MINERVA_AUTH_TOKEN", token);
-
-		cookie.setSecure(useSecureCookie);
-		cookie.setMaxAge(0);
-		cookie.setPath(cookiePath);
-
-		response.addCookie(cookie);
-		response.getWriter().write("{\"status\":\"OK\"}");
-		response.getWriter().flush();
-		response.getWriter().close();
-		return result;
-	}
-
-	/**
-	 * @return the userService
-	 * @see #userService
-	 */
-	public IUserService getUserService() {
-		return userService;
-	}
-
-	/**
-	 * @param userService
-	 *          the userService to set
-	 * @see #userService
-	 */
-	public void setUserService(IUserService userService) {
-		this.userService = userService;
-	}
-
-	/**
-	 * @return the userRest
-	 * @see #userRest
-	 */
-	public UserRestImpl getUserRest() {
-		return userRest;
-	}
-
-	/**
-	 * @param userRest
-	 *          the userRest to set
-	 * @see #userRest
-	 */
-	public void setUserRest(UserRestImpl userRest) {
-		this.userRest = userRest;
-	}
+  /**
+   * Default class logger.
+   */
+  @SuppressWarnings("unused")
+  private Logger logger = Logger.getLogger(UserController.class);
+
+  @Autowired
+  private IUserService userService;
+
+  @Autowired
+  private UserRestImpl userRest;
+
+  @RequestMapping(value = "/doLogin", method = { RequestMethod.GET, RequestMethod.POST }, produces = {
+      MediaType.APPLICATION_JSON_VALUE })
+  public Map<String, Object> login(//
+      @RequestParam(value = "login", defaultValue = Configuration.ANONYMOUS_LOGIN) String login, //
+      @RequestParam(value = "password", required = false) String password, //
+      HttpServletResponse response //
+  ) throws SecurityException, IOException {
+    AuthenticationToken token = userService.login(login, password);
+    if (token == null) {
+      throw new SecurityException("Invalid credentials");
+    } else {
+      Map<String, Object> result = new HashMap<>();
+      final Boolean useSecureCookie = false;
+      final int expiryTime = (int) (token.getExpires().getTimeInMillis() - Calendar.getInstance().getTimeInMillis())
+          / 1000;
+      final String cookiePath = "/";
+
+      Cookie cookie = new Cookie("MINERVA_AUTH_TOKEN", token.getId());
+
+      cookie.setSecure(useSecureCookie);
+      cookie.setMaxAge(expiryTime);
+      cookie.setPath(cookiePath);
+
+      response.addCookie(cookie);
+      response.getWriter().write("{\"info\":\"Login successful. TOKEN returned as a cookie\"}");
+      response.getWriter().flush();
+      response.getWriter().close();
+      return result;
+    }
+  }
+
+  @RequestMapping(value = "/users/{login:.+}", method = { RequestMethod.GET }, produces = {
+      MediaType.APPLICATION_JSON_VALUE })
+  public Map<String, Object> getUser(//
+      @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
+      @PathVariable(value = "login") String login, //
+      @RequestParam(value = "columns", defaultValue = "") String columns//
+  ) throws SecurityException, ObjectNotFoundException {
+    return userRest.getUser(token, login, columns);
+  }
+
+  @RequestMapping(value = "/users/{login}:updatePrivileges", method = { RequestMethod.PATCH }, produces = {
+      MediaType.APPLICATION_JSON_VALUE })
+  public Map<String, Object> updatePrivileges(//
+      @RequestBody String body, //
+      @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
+      @PathVariable(value = "login") String login //
+  ) throws SecurityException, JsonParseException, JsonMappingException, IOException, QueryException {
+    Map<String, Object> node = parseBody(body);
+    Map<String, Object> data = getData(node, "privileges");
+    return userRest.updatePrivileges(token, login, data);
+  }
+
+  @RequestMapping(value = "/users/{login}:updatePreferences", method = { RequestMethod.PATCH }, produces = {
+      MediaType.APPLICATION_JSON_VALUE })
+  public Map<String, Object> updatePreferences(//
+      @RequestBody String body, //
+      @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
+      @PathVariable(value = "login") String login //
+  ) throws SecurityException, JsonParseException, JsonMappingException, IOException, QueryException {
+    Map<String, Object> node = parseBody(body);
+    Map<String, Object> data = getData(node, "preferences");
+    return userRest.updatePreferences(token, login, data);
+  }
+
+  @RequestMapping(value = "/users/", method = { RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
+  public List<Map<String, Object>> getUsers(//
+      @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
+      @RequestParam(value = "columns", defaultValue = "") String columns//
+  ) throws SecurityException, ObjectNotFoundException {
+    return userRest.getUsers(token, columns);
+  }
+
+  @RequestMapping(value = "/doLogout", method = { RequestMethod.GET, RequestMethod.POST }, produces = {
+      MediaType.APPLICATION_JSON_VALUE })
+  public Map<String, String> logout(@CookieValue(value = Configuration.AUTH_TOKEN) String token,
+      HttpServletResponse response //
+  ) throws SecurityException, IOException {
+    userService.logout(token);
+    Map<String, String> result = new HashMap<>();
+    result.put("status", "OK");
+
+    final Boolean useSecureCookie = false;
+    final String cookiePath = "/";
+
+    Cookie cookie = new Cookie("MINERVA_AUTH_TOKEN", token);
+
+    cookie.setSecure(useSecureCookie);
+    cookie.setMaxAge(0);
+    cookie.setPath(cookiePath);
+
+    response.addCookie(cookie);
+    response.getWriter().write("{\"status\":\"OK\"}");
+    response.getWriter().flush();
+    response.getWriter().close();
+    return result;
+  }
+
+  /**
+   * @return the userService
+   * @see #userService
+   */
+  public IUserService getUserService() {
+    return userService;
+  }
+
+  /**
+   * @param userService
+   *          the userService to set
+   * @see #userService
+   */
+  public void setUserService(IUserService userService) {
+    this.userService = userService;
+  }
+
+  /**
+   * @return the userRest
+   * @see #userRest
+   */
+  public UserRestImpl getUserRest() {
+    return userRest;
+  }
+
+  /**
+   * @param userRest
+   *          the userRest to set
+   * @see #userRest
+   */
+  public void setUserRest(UserRestImpl userRest) {
+    this.userRest = userRest;
+  }
 }
\ No newline at end of file
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/users/UserRestImplTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/users/UserRestImplTest.java
index e5f026e7832ead26f5036e1f931b182c681b017f..07d064945bcb49597c5b02b0f4e7bb11546163e7 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/users/UserRestImplTest.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/users/UserRestImplTest.java
@@ -3,7 +3,6 @@ package lcsb.mapviewer.api.users;
 import static org.junit.Assert.assertFalse;
 import static org.junit.Assert.assertNotNull;
 import static org.junit.Assert.assertTrue;
-import static org.mockito.Mockito.CALLS_REAL_METHODS;
 
 import java.io.IOException;
 import java.util.HashMap;
@@ -14,7 +13,6 @@ import org.junit.After;
 import org.junit.AfterClass;
 import org.junit.Before;
 import org.junit.Test;
-import org.mockito.Mockito;
 import org.springframework.beans.factory.annotation.Autowired;
 
 import com.fasterxml.jackson.core.JsonParseException;
@@ -23,86 +21,90 @@ import com.fasterxml.jackson.databind.ObjectMapper;
 import com.fasterxml.jackson.databind.node.ObjectNode;
 import com.google.gson.Gson;
 
-import lcsb.mapviewer.api.BaseController;
 import lcsb.mapviewer.api.RestTestFunctions;
 import lcsb.mapviewer.common.Configuration;
 import lcsb.mapviewer.model.user.PrivilegeType;
 
 public class UserRestImplTest extends RestTestFunctions {
-	Logger			 logger	= Logger.getLogger(UserRestImplTest.class);
-
-	@Autowired
-	UserRestImpl userRestImpl;
-
-	@AfterClass
-	public static void tearDownAfterClass() throws Exception {
-	}
-
-	@Before
-	public void setUp() throws Exception {
-	}
-
-	@After
-	public void tearDown() throws Exception {
-	}
-
-	@Test
-	public void testGetUser() throws Exception {
-		try {
-			Object response = userRestImpl.getUser(token.getId(), Configuration.ANONYMOUS_LOGIN, "");
-			assertNotNull(response);
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-
-	@Test
-	public void testUpdatePrivileges() throws Exception {
-		try {
-			Map<String, Object> data = new HashMap<>();
-			data.put(PrivilegeType.ADD_MAP.name(), 1);
-			userRestImpl.updatePrivileges(adminToken.getId(), Configuration.ANONYMOUS_LOGIN, data);
-			assertTrue(userService.userHasPrivilege(userService.getUserByLogin(Configuration.ANONYMOUS_LOGIN), PrivilegeType.ADD_MAP));
-
-			data.put(PrivilegeType.ADD_MAP.name(), 0);
-			userRestImpl.updatePrivileges(adminToken.getId(), Configuration.ANONYMOUS_LOGIN, data);
-			assertFalse(userService.userHasPrivilege(userService.getUserByLogin(Configuration.ANONYMOUS_LOGIN), PrivilegeType.ADD_MAP));
-
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-
-	@Test
-	public void testUpdatePreferences() throws Exception {
-		try {
-			Map<String, Object> data = deserialize(userRestImpl.getUser(adminToken.getId(), Configuration.ANONYMOUS_LOGIN, ""));
-			userRestImpl.updatePreferences(adminToken.getId(), Configuration.ANONYMOUS_LOGIN, (Map<String, Object>) data.get("preferences"));
-
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
-
-	private Map<String, Object> deserialize(Map<String, Object> data) throws JsonParseException, JsonMappingException, IOException {
-		String body = new Gson().toJson(data);
-		ObjectMapper mapper = new ObjectMapper();
-		ObjectNode result = mapper.readValue(body, ObjectNode.class);
-		return mapper.convertValue(result, Map.class);
-	}
-
-	@Test
-	public void testGetUsers() throws Exception {
-		try {
-			Object response = userRestImpl.getUsers(adminToken.getId(), "");
-			assertNotNull(response);
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
+  Logger logger = Logger.getLogger(UserRestImplTest.class);
+
+  @Autowired
+  UserRestImpl userRestImpl;
+
+  @AfterClass
+  public static void tearDownAfterClass() throws Exception {
+  }
+
+  @Before
+  public void setUp() throws Exception {
+  }
+
+  @After
+  public void tearDown() throws Exception {
+  }
+
+  @Test
+  public void testGetUser() throws Exception {
+    try {
+      Object response = userRestImpl.getUser(token.getId(), Configuration.ANONYMOUS_LOGIN, "");
+      assertNotNull(response);
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+  }
+
+  @Test
+  public void testUpdatePrivileges() throws Exception {
+    try {
+      Map<String, Object> data = new HashMap<>();
+      data.put(PrivilegeType.ADD_MAP.name(), 1);
+      userRestImpl.updatePrivileges(adminToken.getId(), Configuration.ANONYMOUS_LOGIN, data);
+      assertTrue(userService.userHasPrivilege(userService.getUserByLogin(Configuration.ANONYMOUS_LOGIN),
+          PrivilegeType.ADD_MAP));
+
+      data.put(PrivilegeType.ADD_MAP.name(), 0);
+      userRestImpl.updatePrivileges(adminToken.getId(), Configuration.ANONYMOUS_LOGIN, data);
+      assertFalse(userService.userHasPrivilege(userService.getUserByLogin(Configuration.ANONYMOUS_LOGIN),
+          PrivilegeType.ADD_MAP));
+
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+  }
+
+  @Test
+  public void testUpdatePreferences() throws Exception {
+    try {
+      Map<String, Object> data = deserialize(
+          userRestImpl.getUser(adminToken.getId(), Configuration.ANONYMOUS_LOGIN, ""));
+      userRestImpl.updatePreferences(adminToken.getId(), Configuration.ANONYMOUS_LOGIN,
+          (Map<String, Object>) data.get("preferences"));
+
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+  }
+
+  private Map<String, Object> deserialize(Map<String, Object> data)
+      throws JsonParseException, JsonMappingException, IOException {
+    String body = new Gson().toJson(data);
+    ObjectMapper mapper = new ObjectMapper();
+    ObjectNode result = mapper.readValue(body, ObjectNode.class);
+    return mapper.convertValue(result, Map.class);
+  }
+
+  @Test
+  public void testGetUsers() throws Exception {
+    try {
+      Object response = userRestImpl.getUsers(adminToken.getId(), "");
+      assertNotNull(response);
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+  }
 
 }
diff --git a/rest-api/src/test/resources/log4j.properties b/rest-api/src/test/resources/log4j.properties
index 5594c7999fbec1b09075e997f3710d6f0fdf888a..c36f0e8f0f2d1bc6becf9ac41a23e8ecd76ef358 100644
--- a/rest-api/src/test/resources/log4j.properties
+++ b/rest-api/src/test/resources/log4j.properties
@@ -1,5 +1,5 @@
 #Set root logger 's level and its appender to an appender called CONSOLE which is defined below.
-log4j.rootLogger=info, CONSOLE, R
+log4j.rootLogger=info, CONSOLE
 
 #Set the behavior of the CONSOLE appender 
 log4j.appender.CONSOLE=org.apache.log4j.ConsoleAppender
diff --git a/service/.classpath b/service/.classpath
index 62d4b8e4723486982a42cd5dd2b44363281a0bd8..ace82666f2f113cdb835230548bb1c0ddf6ca559 100644
--- a/service/.classpath
+++ b/service/.classpath
@@ -1,37 +1,36 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<classpath>
-	<classpathentry kind="src" output="target/classes" path="src/main/java">
-		<attributes>
-			<attribute name="optional" value="true"/>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources">
-		<attributes>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="src" output="target/test-classes" path="src/test/java">
-		<attributes>
-			<attribute name="optional" value="true"/>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry excluding="**" kind="src" output="target/test-classes" path="src/test/resources">
-		<attributes>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
-		<attributes>
-			<attribute name="maven.pomderived" value="true"/>
-			<attribute name="org.eclipse.jst.component.nondependency" value=""/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8">
-		<attributes>
-			<attribute name="maven.pomderived" value="true"/>
-		</attributes>
-	</classpathentry>
-	<classpathentry kind="output" path="target/classes"/>
-</classpath>
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+	<classpathentry kind="src" output="target/classes" path="src/main/java">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="src" output="target/test-classes" path="src/test/java">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry excluding="**" kind="src" output="target/test-classes" path="src/test/resources">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="output" path="target/classes"/>
+</classpath>
diff --git a/service/service.iml b/service/service.iml
deleted file mode 100644
index b4677809e8144a2d4b938dc6b27fdea3c60f350f..0000000000000000000000000000000000000000
--- a/service/service.iml
+++ /dev/null
@@ -1,130 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<module org.jetbrains.idea.maven.project.MavenProjectsManager.isMavenModule="true" type="JAVA_MODULE" version="4">
-  <component name="FacetManager">
-    <facet type="Spring" name="Spring">
-      <configuration />
-    </facet>
-  </component>
-  <component name="NewModuleRootManager" LANGUAGE_LEVEL="JDK_1_8">
-    <output url="file://$MODULE_DIR$/target/classes" />
-    <output-test url="file://$MODULE_DIR$/target/test-classes" />
-    <content url="file://$MODULE_DIR$">
-      <sourceFolder url="file://$MODULE_DIR$/src/main/java" isTestSource="false" />
-      <sourceFolder url="file://$MODULE_DIR$/src/main/resources" type="java-resource" />
-      <sourceFolder url="file://$MODULE_DIR$/src/test/java" isTestSource="true" />
-      <sourceFolder url="file://$MODULE_DIR$/src/test/resources" type="java-test-resource" />
-      <excludeFolder url="file://$MODULE_DIR$/target" />
-    </content>
-    <orderEntry type="inheritedJdk" />
-    <orderEntry type="sourceFolder" forTests="false" />
-    <orderEntry type="module" module-name="model" />
-    <orderEntry type="module" module-name="commons" />
-    <orderEntry type="library" name="Maven: commons-io:commons-io:2.4" level="project" />
-    <orderEntry type="library" name="Maven: org.apache.commons:commons-lang3:3.1" level="project" />
-    <orderEntry type="library" name="Maven: org.hibernate:hibernate-core:4.1.0.Final" level="project" />
-    <orderEntry type="library" name="Maven: commons-collections:commons-collections:3.2.1" level="project" />
-    <orderEntry type="library" name="Maven: antlr:antlr:2.7.7" level="project" />
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-    <orderEntry type="library" name="Maven: dom4j:dom4j:1.6.1" level="project" />
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\ No newline at end of file
diff --git a/web/.classpath b/web/.classpath
index 6acf3eeecaebe2d096ef46a44bf6988db916e316..ace82666f2f113cdb835230548bb1c0ddf6ca559 100644
--- a/web/.classpath
+++ b/web/.classpath
@@ -25,7 +25,6 @@
 	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
 		<attributes>
 			<attribute name="maven.pomderived" value="true"/>
-			<attribute name="org.eclipse.jst.component.dependency" value="/WEB-INF/lib"/>
 		</attributes>
 	</classpathentry>
 	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8">
diff --git a/web/web.iml b/web/web.iml
deleted file mode 100644
index 4f93374d1f69d16cade014ff7eee93de8b19a5c5..0000000000000000000000000000000000000000
--- a/web/web.iml
+++ /dev/null
@@ -1,170 +0,0 @@
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-    <facet type="Spring" name="Spring">
-      <configuration />
-    </facet>
-    <facet type="web" name="Web">
-      <configuration>
-        <descriptors>
-          <deploymentDescriptor name="web.xml" url="file://$MODULE_DIR$/src/main/webapp/WEB-INF/web.xml" />
-        </descriptors>
-        <webroots>
-          <root url="file://$MODULE_DIR$/src/main/webapp" relative="/" />
-        </webroots>
-        <sourceRoots>
-          <root url="file://$MODULE_DIR$/src/main/java" />
-          <root url="file://$MODULE_DIR$/src/main/resources" />
-        </sourceRoots>
-      </configuration>
-    </facet>
-  </component>
-  <component name="NewModuleRootManager" LANGUAGE_LEVEL="JDK_1_8">
-    <output url="file://$MODULE_DIR$/target/classes" />
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-    <content url="file://$MODULE_DIR$">
-      <sourceFolder url="file://$MODULE_DIR$/src/main/java" isTestSource="false" />
-      <sourceFolder url="file://$MODULE_DIR$/src/main/resources" type="java-resource" />
-      <sourceFolder url="file://$MODULE_DIR$/src/test/java" isTestSource="true" />
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\ No newline at end of file