diff --git a/.gitignore b/.gitignore
index 86336eb3..7849ca26 100644
--- a/.gitignore
+++ b/.gitignore
@@ -13,3 +13,12 @@ benchmark/experiments/*/*result.xml
 *.csv
 benchmark/results
 benchamer/results-processed
+
+# Gradle cache and build directories
+.gradle
+build
+*.ipr
+*.iws
+
+# Idea project files
+.idea
\ No newline at end of file
diff --git a/application/build.gradle b/application/build.gradle
new file mode 100644
index 00000000..3ef9ee92
--- /dev/null
+++ b/application/build.gradle
@@ -0,0 +1,18 @@
+group = 'org.sybila.parasim.application'
+
+dependencies {
+	compile 'org.mod4j.org.apache.commons:cli:1.0.0'
+	compile project(':model:ode')
+	compile project(':model:space')
+	compile project(':model:trajectory')
+	compile project(':model:verification')
+	compile project(':extensions:computation-simulation-impl')
+	compile project(':extensions:computation-density-impl')
+	compile project(':extensions:computation-verification-impl')
+	compile project(':extensions:computation-lifecycle-impl')
+	compile project(':extensions:computation-cycledetection-impl')
+	compile project(':extensions:visualisation-plot-impl')
+	compile project(':extensions:result-export-impl')
+	compile project(':extensions:project-manager-simple')
+	compile project(':extensions:progress-logger')
+}
\ No newline at end of file
diff --git a/build.gradle b/build.gradle
new file mode 100644
index 00000000..1eb102fc
--- /dev/null
+++ b/build.gradle
@@ -0,0 +1,44 @@
+buildscript {
+    repositories {
+        jcenter()
+    }
+    dependencies {
+        //place for global plugins
+    }
+}
+
+allprojects {
+    apply plugin: 'java'
+
+    version = '2.1.0-SNAPSHOT'
+    group = 'org.sybila.parasim'
+
+    repositories {
+        jcenter()
+        mavenCentral()        
+        // jsbml
+        maven { url "http://jsbml.sourceforge.net/m2repo" }
+        // mangosdk
+        maven { url 'http://www.ebi.ac.uk/~maven/m2repo' }
+        // javaoctave
+        maven { url 'https://kenai.com/svn/javaoctave~maven-repository/maven2/' }
+    }
+
+    //global configuration
+    ext {
+        javaoctave = '0.6.4'
+        commonsLogging = '1.1.1'
+        jsbml = '1.2-beta1'
+    }
+
+    //common dependencies for everyone
+    dependencies {
+        testCompile group: 'junit', name: 'junit', version: '4.11'  
+        testCompile 'org.testng:testng:6.9.12'
+        compile 'net.jcip:jcip-annotations:1.0'
+        compile 'javassist:javassist:3.12.1.GA'
+        compile 'org.slf4j:slf4j-log4j12:1.7.21'
+        compile 'org.apache.commons:commons-lang3:3.5'
+    }
+
+}
diff --git a/core/build.gradle b/core/build.gradle
new file mode 100644
index 00000000..363be12e
--- /dev/null
+++ b/core/build.gradle
@@ -0,0 +1,5 @@
+group = 'org.sybila.parasim.model.core'
+
+dependencies {
+	compile 'org.testng:testng:6.9.12'
+}
\ No newline at end of file
diff --git a/extensions/computation-cycledetection-api/build.gradle b/extensions/computation-cycledetection-api/build.gradle
new file mode 100644
index 00000000..e2880382
--- /dev/null
+++ b/extensions/computation-cycledetection-api/build.gradle
@@ -0,0 +1,5 @@
+group = 'org.sybila.parasim.computation.cycledetection.api'
+
+dependencies {
+	compile project(':model:trajectory')
+}
\ No newline at end of file
diff --git a/extensions/computation-cycledetection-impl/build.gradle b/extensions/computation-cycledetection-impl/build.gradle
new file mode 100644
index 00000000..035d9904
--- /dev/null
+++ b/extensions/computation-cycledetection-impl/build.gradle
@@ -0,0 +1,7 @@
+group = 'org.sybila.parasim.computation.cycledetection.impl'
+
+dependencies {
+	compile project(':core')
+	compile project(':util')
+	compile project(':extensions:computation-cycledetection-api')
+}
\ No newline at end of file
diff --git a/extensions/computation-density-api/build.gradle b/extensions/computation-density-api/build.gradle
new file mode 100644
index 00000000..efd18b70
--- /dev/null
+++ b/extensions/computation-density-api/build.gradle
@@ -0,0 +1,7 @@
+group = 'org.sybila.parasim.computation.density.api'
+
+dependencies {
+	compile project(':core')
+	compile project(':model:space')
+	compile project(':model:trajectory')
+}
\ No newline at end of file
diff --git a/extensions/computation-density-impl/build.gradle b/extensions/computation-density-impl/build.gradle
new file mode 100644
index 00000000..6b7b8615
--- /dev/null
+++ b/extensions/computation-density-impl/build.gradle
@@ -0,0 +1,8 @@
+group = 'org.sybila.parasim.computation.density.impl'
+
+dependencies {
+	testCompile project(':extensions:computation-lifecycle-impl')
+	compile project(':core')
+	compile project(':extensions:computation-density-api')
+	compile project(':extensions:computation-lifecycle-api')
+}
\ No newline at end of file
diff --git a/extensions/computation-lifecycle-api/build.gradle b/extensions/computation-lifecycle-api/build.gradle
new file mode 100644
index 00000000..2eb4f01f
--- /dev/null
+++ b/extensions/computation-lifecycle-api/build.gradle
@@ -0,0 +1,6 @@
+group = 'org.sybila.parasim.computation.lifecycle.api'
+
+dependencies {
+	compile project(':core')
+	compile project(':model:model-core')	
+}
\ No newline at end of file
diff --git a/extensions/computation-lifecycle-impl/build.gradle b/extensions/computation-lifecycle-impl/build.gradle
new file mode 100644
index 00000000..c66c8354
--- /dev/null
+++ b/extensions/computation-lifecycle-impl/build.gradle
@@ -0,0 +1,5 @@
+group = 'org.sybila.parasim.computation.lifecycle.impl'
+
+dependencies {
+	compile project(':extensions:computation-lifecycle-api')
+}
\ No newline at end of file
diff --git a/extensions/computation-simulation-api/build.gradle b/extensions/computation-simulation-api/build.gradle
new file mode 100644
index 00000000..8fdf452a
--- /dev/null
+++ b/extensions/computation-simulation-api/build.gradle
@@ -0,0 +1,10 @@
+group = 'org.sybila.parasim.computation.simulation.api'
+
+dependencies {
+	compile project(':model:ode')
+	compile project(':model:trajectory')
+	compile project(':model:space')
+	compile project(':core')
+	compile "dk.ange:javaoctave:$javaoctave"
+	compile "commons-logging:commons-logging:$commonsLogging"
+}
\ No newline at end of file
diff --git a/extensions/computation-simulation-impl/build.gradle b/extensions/computation-simulation-impl/build.gradle
new file mode 100644
index 00000000..49541d60
--- /dev/null
+++ b/extensions/computation-simulation-impl/build.gradle
@@ -0,0 +1,7 @@
+group = 'org.sybila.parasim.computation.simulation.impl'
+
+dependencies {
+	compile project(':core')
+	compile project(':extensions:computation-simulation-api')
+	compile project(':extensions:computation-lifecycle-api')
+}
\ No newline at end of file
diff --git a/extensions/computation-verification-api/build.gradle b/extensions/computation-verification-api/build.gradle
new file mode 100644
index 00000000..51db83fb
--- /dev/null
+++ b/extensions/computation-verification-api/build.gradle
@@ -0,0 +1,8 @@
+group = 'org.sybila.parasim.computation.verification.api'
+
+dependencies {
+	compile project(':model:verification')
+	compile project(':model:trajectory')
+	compile project(':extensions:computation-density-api')
+	compile project(':extensions:computation-cycledetection-api')
+}
\ No newline at end of file
diff --git a/extensions/computation-verification-impl/build.gradle b/extensions/computation-verification-impl/build.gradle
new file mode 100644
index 00000000..0027e271
--- /dev/null
+++ b/extensions/computation-verification-impl/build.gradle
@@ -0,0 +1,7 @@
+group = 'org.sybila.parasim.computation.verification.impl'
+
+dependencies {
+	compile project(':core')
+	compile project(':util')
+	compile project(':extensions:computation-verification-api')
+}
\ No newline at end of file
diff --git a/extensions/progress-logger/build.gradle b/extensions/progress-logger/build.gradle
new file mode 100644
index 00000000..d59725f6
--- /dev/null
+++ b/extensions/progress-logger/build.gradle
@@ -0,0 +1,8 @@
+group = 'org.sybila.parasim.extension.progresslogger'
+
+dependencies {
+	compile project(':core')
+	compile project(':util')
+	compile project(':resources')
+	compile project(':model:verification')	
+}
\ No newline at end of file
diff --git a/extensions/project-manager-api/build.gradle b/extensions/project-manager-api/build.gradle
new file mode 100644
index 00000000..029c0bac
--- /dev/null
+++ b/extensions/project-manager-api/build.gradle
@@ -0,0 +1,11 @@
+group = 'org.sybila.parasim.extension.projectmanager.api'
+
+dependencies {
+	compile project(':core')
+	compile project(':resources')
+	compile project(':util')
+	compile project(':model:ode')
+	compile project(':model:space')
+	compile project(':model:verification')
+	compile project(':extensions:computation-simulation-api')
+}
\ No newline at end of file
diff --git a/extensions/project-manager-simple/build.gradle b/extensions/project-manager-simple/build.gradle
new file mode 100644
index 00000000..dc4a9e98
--- /dev/null
+++ b/extensions/project-manager-simple/build.gradle
@@ -0,0 +1,5 @@
+group = 'org.sybila.parasim.extension.projectmanager.impl'
+
+dependencies {
+	compile project(':extensions:project-manager-api')
+}
\ No newline at end of file
diff --git a/extensions/result-export-api/build.gradle b/extensions/result-export-api/build.gradle
new file mode 100644
index 00000000..6132f957
--- /dev/null
+++ b/extensions/result-export-api/build.gradle
@@ -0,0 +1,6 @@
+group = 'org.sybila.parasim.extension.exporter.api'
+
+dependencies {
+	compile project(':core')
+	compile project(':model:verification')
+}
\ No newline at end of file
diff --git a/extensions/result-export-impl/build.gradle b/extensions/result-export-impl/build.gradle
new file mode 100644
index 00000000..7cd4a9cd
--- /dev/null
+++ b/extensions/result-export-impl/build.gradle
@@ -0,0 +1,5 @@
+group = 'org.sybila.parasim.extension.exporter.impl'
+
+dependencies {
+	compile project(':extensions:result-export-api')
+}
\ No newline at end of file
diff --git a/extensions/visualisation-plot-api/build.gradle b/extensions/visualisation-plot-api/build.gradle
new file mode 100644
index 00000000..be49a690
--- /dev/null
+++ b/extensions/visualisation-plot-api/build.gradle
@@ -0,0 +1,6 @@
+group = 'org.sybila.parasim.visualisation.plot.api'
+
+dependencies {
+	compile project(':core')
+	compile project(':model:verification')
+}
\ No newline at end of file
diff --git a/extensions/visualisation-plot-impl/build.gradle b/extensions/visualisation-plot-impl/build.gradle
new file mode 100644
index 00000000..de9bbeba
--- /dev/null
+++ b/extensions/visualisation-plot-impl/build.gradle
@@ -0,0 +1,7 @@
+group = 'org.sybila.parasim.visualisation.plot.impl'
+
+dependencies {
+	compile project(':extensions:visualisation-plot-api')
+	compile project(':core')
+	compile project(':util')
+}
\ No newline at end of file
diff --git a/gradle/wrapper/gradle-wrapper.jar b/gradle/wrapper/gradle-wrapper.jar
new file mode 100644
index 00000000..d3b83982
Binary files /dev/null and b/gradle/wrapper/gradle-wrapper.jar differ
diff --git a/gradle/wrapper/gradle-wrapper.properties b/gradle/wrapper/gradle-wrapper.properties
new file mode 100644
index 00000000..a12c6415
--- /dev/null
+++ b/gradle/wrapper/gradle-wrapper.properties
@@ -0,0 +1,6 @@
+#Thu Nov 24 14:07:31 CET 2016
+distributionBase=GRADLE_USER_HOME
+distributionPath=wrapper/dists
+zipStoreBase=GRADLE_USER_HOME
+zipStorePath=wrapper/dists
+distributionUrl=https\://services.gradle.org/distributions/gradle-3.1-all.zip
diff --git a/gradlew b/gradlew
new file mode 100755
index 00000000..27309d92
--- /dev/null
+++ b/gradlew
@@ -0,0 +1,164 @@
+#!/usr/bin/env bash
+
+##############################################################################
+##
+##  Gradle start up script for UN*X
+##
+##############################################################################
+
+# Attempt to set APP_HOME
+# Resolve links: $0 may be a link
+PRG="$0"
+# Need this for relative symlinks.
+while [ -h "$PRG" ] ; do
+    ls=`ls -ld "$PRG"`
+    link=`expr "$ls" : '.*-> \(.*\)$'`
+    if expr "$link" : '/.*' > /dev/null; then
+        PRG="$link"
+    else
+        PRG=`dirname "$PRG"`"/$link"
+    fi
+done
+SAVED="`pwd`"
+cd "`dirname \"$PRG\"`/" >/dev/null
+APP_HOME="`pwd -P`"
+cd "$SAVED" >/dev/null
+
+APP_NAME="Gradle"
+APP_BASE_NAME=`basename "$0"`
+
+# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
+DEFAULT_JVM_OPTS=""
+
+# Use the maximum available, or set MAX_FD != -1 to use that value.
+MAX_FD="maximum"
+
+warn ( ) {
+    echo "$*"
+}
+
+die ( ) {
+    echo
+    echo "$*"
+    echo
+    exit 1
+}
+
+# OS specific support (must be 'true' or 'false').
+cygwin=false
+msys=false
+darwin=false
+nonstop=false
+case "`uname`" in
+  CYGWIN* )
+    cygwin=true
+    ;;
+  Darwin* )
+    darwin=true
+    ;;
+  MINGW* )
+    msys=true
+    ;;
+  NONSTOP* )
+    nonstop=true
+    ;;
+esac
+
+CLASSPATH=$APP_HOME/gradle/wrapper/gradle-wrapper.jar
+
+# Determine the Java command to use to start the JVM.
+if [ -n "$JAVA_HOME" ] ; then
+    if [ -x "$JAVA_HOME/jre/sh/java" ] ; then
+        # IBM's JDK on AIX uses strange locations for the executables
+        JAVACMD="$JAVA_HOME/jre/sh/java"
+    else
+        JAVACMD="$JAVA_HOME/bin/java"
+    fi
+    if [ ! -x "$JAVACMD" ] ; then
+        die "ERROR: JAVA_HOME is set to an invalid directory: $JAVA_HOME
+
+Please set the JAVA_HOME variable in your environment to match the
+location of your Java installation."
+    fi
+else
+    JAVACMD="java"
+    which java >/dev/null 2>&1 || die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
+
+Please set the JAVA_HOME variable in your environment to match the
+location of your Java installation."
+fi
+
+# Increase the maximum file descriptors if we can.
+if [ "$cygwin" = "false" -a "$darwin" = "false" -a "$nonstop" = "false" ] ; then
+    MAX_FD_LIMIT=`ulimit -H -n`
+    if [ $? -eq 0 ] ; then
+        if [ "$MAX_FD" = "maximum" -o "$MAX_FD" = "max" ] ; then
+            MAX_FD="$MAX_FD_LIMIT"
+        fi
+        ulimit -n $MAX_FD
+        if [ $? -ne 0 ] ; then
+            warn "Could not set maximum file descriptor limit: $MAX_FD"
+        fi
+    else
+        warn "Could not query maximum file descriptor limit: $MAX_FD_LIMIT"
+    fi
+fi
+
+# For Darwin, add options to specify how the application appears in the dock
+if $darwin; then
+    GRADLE_OPTS="$GRADLE_OPTS \"-Xdock:name=$APP_NAME\" \"-Xdock:icon=$APP_HOME/media/gradle.icns\""
+fi
+
+# For Cygwin, switch paths to Windows format before running java
+if $cygwin ; then
+    APP_HOME=`cygpath --path --mixed "$APP_HOME"`
+    CLASSPATH=`cygpath --path --mixed "$CLASSPATH"`
+    JAVACMD=`cygpath --unix "$JAVACMD"`
+
+    # We build the pattern for arguments to be converted via cygpath
+    ROOTDIRSRAW=`find -L / -maxdepth 1 -mindepth 1 -type d 2>/dev/null`
+    SEP=""
+    for dir in $ROOTDIRSRAW ; do
+        ROOTDIRS="$ROOTDIRS$SEP$dir"
+        SEP="|"
+    done
+    OURCYGPATTERN="(^($ROOTDIRS))"
+    # Add a user-defined pattern to the cygpath arguments
+    if [ "$GRADLE_CYGPATTERN" != "" ] ; then
+        OURCYGPATTERN="$OURCYGPATTERN|($GRADLE_CYGPATTERN)"
+    fi
+    # Now convert the arguments - kludge to limit ourselves to /bin/sh
+    i=0
+    for arg in "$@" ; do
+        CHECK=`echo "$arg"|egrep -c "$OURCYGPATTERN" -`
+        CHECK2=`echo "$arg"|egrep -c "^-"`                                 ### Determine if an option
+
+        if [ $CHECK -ne 0 ] && [ $CHECK2 -eq 0 ] ; then                    ### Added a condition
+            eval `echo args$i`=`cygpath --path --ignore --mixed "$arg"`
+        else
+            eval `echo args$i`="\"$arg\""
+        fi
+        i=$((i+1))
+    done
+    case $i in
+        (0) set -- ;;
+        (1) set -- "$args0" ;;
+        (2) set -- "$args0" "$args1" ;;
+        (3) set -- "$args0" "$args1" "$args2" ;;
+        (4) set -- "$args0" "$args1" "$args2" "$args3" ;;
+        (5) set -- "$args0" "$args1" "$args2" "$args3" "$args4" ;;
+        (6) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" ;;
+        (7) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" ;;
+        (8) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" ;;
+        (9) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" "$args8" ;;
+    esac
+fi
+
+# Split up the JVM_OPTS And GRADLE_OPTS values into an array, following the shell quoting and substitution rules
+function splitJvmOpts() {
+    JVM_OPTS=("$@")
+}
+eval splitJvmOpts $DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS
+JVM_OPTS[${#JVM_OPTS[*]}]="-Dorg.gradle.appname=$APP_BASE_NAME"
+
+exec "$JAVACMD" "${JVM_OPTS[@]}" -classpath "$CLASSPATH" org.gradle.wrapper.GradleWrapperMain "$@"
diff --git a/gradlew.bat b/gradlew.bat
new file mode 100644
index 00000000..832fdb60
--- /dev/null
+++ b/gradlew.bat
@@ -0,0 +1,90 @@
+@if "%DEBUG%" == "" @echo off
+@rem ##########################################################################
+@rem
+@rem  Gradle startup script for Windows
+@rem
+@rem ##########################################################################
+
+@rem Set local scope for the variables with windows NT shell
+if "%OS%"=="Windows_NT" setlocal
+
+set DIRNAME=%~dp0
+if "%DIRNAME%" == "" set DIRNAME=.
+set APP_BASE_NAME=%~n0
+set APP_HOME=%DIRNAME%
+
+@rem Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
+set DEFAULT_JVM_OPTS=
+
+@rem Find java.exe
+if defined JAVA_HOME goto findJavaFromJavaHome
+
+set JAVA_EXE=java.exe
+%JAVA_EXE% -version >NUL 2>&1
+if "%ERRORLEVEL%" == "0" goto init
+
+echo.
+echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
+echo.
+echo Please set the JAVA_HOME variable in your environment to match the
+echo location of your Java installation.
+
+goto fail
+
+:findJavaFromJavaHome
+set JAVA_HOME=%JAVA_HOME:"=%
+set JAVA_EXE=%JAVA_HOME%/bin/java.exe
+
+if exist "%JAVA_EXE%" goto init
+
+echo.
+echo ERROR: JAVA_HOME is set to an invalid directory: %JAVA_HOME%
+echo.
+echo Please set the JAVA_HOME variable in your environment to match the
+echo location of your Java installation.
+
+goto fail
+
+:init
+@rem Get command-line arguments, handling Windows variants
+
+if not "%OS%" == "Windows_NT" goto win9xME_args
+if "%@eval[2+2]" == "4" goto 4NT_args
+
+:win9xME_args
+@rem Slurp the command line arguments.
+set CMD_LINE_ARGS=
+set _SKIP=2
+
+:win9xME_args_slurp
+if "x%~1" == "x" goto execute
+
+set CMD_LINE_ARGS=%*
+goto execute
+
+:4NT_args
+@rem Get arguments from the 4NT Shell from JP Software
+set CMD_LINE_ARGS=%$
+
+:execute
+@rem Setup the command line
+
+set CLASSPATH=%APP_HOME%\gradle\wrapper\gradle-wrapper.jar
+
+@rem Execute Gradle
+"%JAVA_EXE%" %DEFAULT_JVM_OPTS% %JAVA_OPTS% %GRADLE_OPTS% "-Dorg.gradle.appname=%APP_BASE_NAME%" -classpath "%CLASSPATH%" org.gradle.wrapper.GradleWrapperMain %CMD_LINE_ARGS%
+
+:end
+@rem End local scope for the variables with windows NT shell
+if "%ERRORLEVEL%"=="0" goto mainEnd
+
+:fail
+rem Set variable GRADLE_EXIT_CONSOLE if you need the _script_ return code instead of
+rem the _cmd.exe /c_ return code!
+if  not "" == "%GRADLE_EXIT_CONSOLE%" exit 1
+exit /b 1
+
+:mainEnd
+if "%OS%"=="Windows_NT" endlocal
+
+:omega
diff --git a/model/model-core/build.gradle b/model/model-core/build.gradle
new file mode 100644
index 00000000..03638153
--- /dev/null
+++ b/model/model-core/build.gradle
@@ -0,0 +1 @@
+group = 'org.sybila.parasim.model.core'
\ No newline at end of file
diff --git a/model/core/pom.xml b/model/model-core/pom.xml
similarity index 100%
rename from model/core/pom.xml
rename to model/model-core/pom.xml
diff --git a/model/core/src/main/java/org/sybila/parasim/model/Mergeable.java b/model/model-core/src/main/java/org/sybila/parasim/model/Mergeable.java
similarity index 100%
rename from model/core/src/main/java/org/sybila/parasim/model/Mergeable.java
rename to model/model-core/src/main/java/org/sybila/parasim/model/Mergeable.java
diff --git a/model/core/src/main/java/org/sybila/parasim/model/MergeableBox.java b/model/model-core/src/main/java/org/sybila/parasim/model/MergeableBox.java
similarity index 100%
rename from model/core/src/main/java/org/sybila/parasim/model/MergeableBox.java
rename to model/model-core/src/main/java/org/sybila/parasim/model/MergeableBox.java
diff --git a/model/core/src/main/java/org/sybila/parasim/model/xml/FileXMLResource.java b/model/model-core/src/main/java/org/sybila/parasim/model/xml/FileXMLResource.java
similarity index 100%
rename from model/core/src/main/java/org/sybila/parasim/model/xml/FileXMLResource.java
rename to model/model-core/src/main/java/org/sybila/parasim/model/xml/FileXMLResource.java
diff --git a/model/core/src/main/java/org/sybila/parasim/model/xml/FloatFactory.java b/model/model-core/src/main/java/org/sybila/parasim/model/xml/FloatFactory.java
similarity index 100%
rename from model/core/src/main/java/org/sybila/parasim/model/xml/FloatFactory.java
rename to model/model-core/src/main/java/org/sybila/parasim/model/xml/FloatFactory.java
diff --git a/model/core/src/main/java/org/sybila/parasim/model/xml/StreamXMLResource.java b/model/model-core/src/main/java/org/sybila/parasim/model/xml/StreamXMLResource.java
similarity index 100%
rename from model/core/src/main/java/org/sybila/parasim/model/xml/StreamXMLResource.java
rename to model/model-core/src/main/java/org/sybila/parasim/model/xml/StreamXMLResource.java
diff --git a/model/core/src/main/java/org/sybila/parasim/model/xml/XMLException.java b/model/model-core/src/main/java/org/sybila/parasim/model/xml/XMLException.java
similarity index 100%
rename from model/core/src/main/java/org/sybila/parasim/model/xml/XMLException.java
rename to model/model-core/src/main/java/org/sybila/parasim/model/xml/XMLException.java
diff --git a/model/core/src/main/java/org/sybila/parasim/model/xml/XMLFormatException.java b/model/model-core/src/main/java/org/sybila/parasim/model/xml/XMLFormatException.java
similarity index 100%
rename from model/core/src/main/java/org/sybila/parasim/model/xml/XMLFormatException.java
rename to model/model-core/src/main/java/org/sybila/parasim/model/xml/XMLFormatException.java
diff --git a/model/core/src/main/java/org/sybila/parasim/model/xml/XMLRepresentable.java b/model/model-core/src/main/java/org/sybila/parasim/model/xml/XMLRepresentable.java
similarity index 100%
rename from model/core/src/main/java/org/sybila/parasim/model/xml/XMLRepresentable.java
rename to model/model-core/src/main/java/org/sybila/parasim/model/xml/XMLRepresentable.java
diff --git a/model/core/src/main/java/org/sybila/parasim/model/xml/XMLRepresentableFactory.java b/model/model-core/src/main/java/org/sybila/parasim/model/xml/XMLRepresentableFactory.java
similarity index 100%
rename from model/core/src/main/java/org/sybila/parasim/model/xml/XMLRepresentableFactory.java
rename to model/model-core/src/main/java/org/sybila/parasim/model/xml/XMLRepresentableFactory.java
diff --git a/model/core/src/main/java/org/sybila/parasim/model/xml/XMLResource.java b/model/model-core/src/main/java/org/sybila/parasim/model/xml/XMLResource.java
similarity index 100%
rename from model/core/src/main/java/org/sybila/parasim/model/xml/XMLResource.java
rename to model/model-core/src/main/java/org/sybila/parasim/model/xml/XMLResource.java
diff --git a/model/core/src/test/java/org/sybila/parasim/model/xml/TestStreamXMLResource.java b/model/model-core/src/test/java/org/sybila/parasim/model/xml/TestStreamXMLResource.java
similarity index 100%
rename from model/core/src/test/java/org/sybila/parasim/model/xml/TestStreamXMLResource.java
rename to model/model-core/src/test/java/org/sybila/parasim/model/xml/TestStreamXMLResource.java
diff --git a/model/core/src/test/resources/org/sybila/parasim/model/xml/testSchema.xsd b/model/model-core/src/test/resources/org/sybila/parasim/model/xml/testSchema.xsd
similarity index 100%
rename from model/core/src/test/resources/org/sybila/parasim/model/xml/testSchema.xsd
rename to model/model-core/src/test/resources/org/sybila/parasim/model/xml/testSchema.xsd
diff --git a/model/ode/build.gradle b/model/ode/build.gradle
new file mode 100644
index 00000000..dcf1369b
--- /dev/null
+++ b/model/ode/build.gradle
@@ -0,0 +1,8 @@
+group = 'org.sybila.parasim.model.ode'
+
+dependencies {
+	compile project(':model:trajectory')
+	compile "dk.ange:javaoctave:$javaoctave"
+	compile "commons-logging:commons-logging:$commonsLogging"
+	compile "org.sbml.jsbml:jsbml:$jsbml"	
+}
\ No newline at end of file
diff --git a/model/space/build.gradle b/model/space/build.gradle
new file mode 100644
index 00000000..d4581364
--- /dev/null
+++ b/model/space/build.gradle
@@ -0,0 +1,7 @@
+group = 'org.sybila.parasim.model.space'
+
+dependencies {
+	compile project(':model:model-core')
+	compile project(':model:trajectory')
+	compile project(':model:ode')
+}
\ No newline at end of file
diff --git a/model/trajectory/build.gradle b/model/trajectory/build.gradle
new file mode 100644
index 00000000..9fa34cff
--- /dev/null
+++ b/model/trajectory/build.gradle
@@ -0,0 +1,5 @@
+group = 'org.sybila.parasim.model.trajectory'
+
+dependencies {
+	compile project(':model:model-core')
+}
\ No newline at end of file
diff --git a/model/verification/build.gradle b/model/verification/build.gradle
new file mode 100644
index 00000000..e09763e0
--- /dev/null
+++ b/model/verification/build.gradle
@@ -0,0 +1,8 @@
+group = 'org.sybila.parasim.model.verification'
+
+dependencies {
+	compile project(':util')
+	compile project(':model:ode')
+	compile project(':model:model-core')
+	compile project(':model:space')
+}
\ No newline at end of file
diff --git a/resources/build.gradle b/resources/build.gradle
new file mode 100644
index 00000000..6255f8b5
--- /dev/null
+++ b/resources/build.gradle
@@ -0,0 +1 @@
+group = 'org.sybila.parasim.resources'
\ No newline at end of file
diff --git a/settings.gradle b/settings.gradle
new file mode 100644
index 00000000..4aa770e8
--- /dev/null
+++ b/settings.gradle
@@ -0,0 +1,35 @@
+rootProject.name = 'parasim'
+
+// main application module
+include ':application'
+
+// core parts
+include ':core'
+include ':resources'
+include ':util'
+
+// model modules
+include ':model:ode'
+include ':model:model-core'
+include ':model:space'
+include ':model:trajectory'
+include ':model:verification'
+
+// extensions
+include ':extensions:computation-cycledetection-api'
+include ':extensions:computation-cycledetection-impl'
+include ':extensions:computation-density-api'
+include ':extensions:computation-density-impl'
+include ':extensions:computation-lifecycle-api'
+include ':extensions:computation-lifecycle-impl'
+include ':extensions:computation-simulation-api'
+include ':extensions:computation-simulation-impl'
+include ':extensions:computation-verification-api'
+include ':extensions:computation-verification-impl'
+include ':extensions:progress-logger'
+include ':extensions:project-manager-api'
+include ':extensions:project-manager-simple'
+include ':extensions:result-export-api'
+include ':extensions:result-export-impl'
+include ':extensions:visualisation-plot-api'
+include ':extensions:visualisation-plot-impl'
diff --git a/util/build.gradle b/util/build.gradle
new file mode 100644
index 00000000..833200b0
--- /dev/null
+++ b/util/build.gradle
@@ -0,0 +1 @@
+group = 'org.sybila.parasim.util'
\ No newline at end of file