A bit of comfort:

Implemented basic configuration system
Saves previously stored yoshiko library location

src/main/java/de/hhu/ba/yoshikoWrapper/CyActivator.java

@@ -9,7 +9,9 @@ import org.cytoscape.application.swing.CytoPanelComponent;
 import org.cytoscape.service.util.AbstractCyActivator;
 import org.osgi.framework.BundleContext;
 
+import de.hhu.ba.yoshikoWrapper.core.ConfigurationManager;
 import de.hhu.ba.yoshikoWrapper.core.Core;
+import de.hhu.ba.yoshikoWrapper.core.YoshikoLoader;
 import de.hhu.ba.yoshikoWrapper.gui.MainPanel;
 import de.hhu.ba.yoshikoWrapper.gui.MainPanelAction;
 
@@ -22,7 +24,19 @@ public class CyActivator extends AbstractCyActivator {
 		
 	@Override
 	public void start(BundleContext context) throws Exception {
-		//TODO: Load shared library if installed on startup
+		//Initialize cytoscape configuration system
+		ConfigurationManager cm = new ConfigurationManager("yoshikoWrapper", "yoshiko.props");
+		Properties propsReaderServiceProps = new Properties();
+		propsReaderServiceProps.setProperty("cyPropertyName", "yoshiko.props");
+		registerAllServices(context,cm,propsReaderServiceProps);
+
+
+		//Attempt to find the yoshiko lib in r a previously stored location
+		YoshikoLoader.provideConfiguration(cm);
+		if (!YoshikoLoader.isLibraryLoaded()){
+			YoshikoLoader.loadLibrary(cm.getProperties().getProperty("pathToYoshiko"));
+		}
+		
 		CyApplicationManager cyApplicationManager = getService(context, CyApplicationManager.class);
 		Core.registerApplicationManager(cyApplicationManager);
 		

src/main/java/de/hhu/ba/yoshikoWrapper/core/ConfigurationManager.java

+package de.hhu.ba.yoshikoWrapper.core;
+
+import org.cytoscape.property.AbstractConfigDirPropsReader;
+import org.cytoscape.property.CyProperty;
+
+public class ConfigurationManager extends AbstractConfigDirPropsReader{
+		
+	public ConfigurationManager(String appName, String fileName){
+		super(appName, fileName, CyProperty.SavePolicy.CONFIG_DIR);
+		this.getProperties().list(System.out);
+	}   
+}

src/main/java/de/hhu/ba/yoshikoWrapper/core/NetworkParser.java

 package de.hhu.ba.yoshikoWrapper.core;
 
-import java.util.HashMap;
 import java.util.List;
 
-import org.cytoscape.application.CyApplicationManager;
-import org.cytoscape.model.CyColumn;
 import org.cytoscape.model.CyEdge;
 import org.cytoscape.model.CyNetwork;
-import org.cytoscape.model.CyNode;
 import org.cytoscape.model.CyRow;
 
 import de.hhu.ba.yoshikoWrapper.swig.LibraryInterface;

src/main/java/de/hhu/ba/yoshikoWrapper/core/YoshikoLoader.java

 package de.hhu.ba.yoshikoWrapper.core;
 
-public class YoshikoLoader {
+import java.io.File;
 
-	//SINGLETON TEMPLATE
+public class YoshikoLoader {
 	
-	private static YoshikoLoader instance;
 	private static boolean libraryLoaded;
+	private static ConfigurationManager cm;
 	
-	public static YoshikoLoader getInstance() {
-		if (instance == null){
-			instance = new YoshikoLoader();
-		}
-		return instance;
-	}
-	
-	private YoshikoLoader() {
-		libraryLoaded = false;
-	}
-	
+	public static void loadLibrary(String libPath) {
 		
-	public void loadLibrary() {
 		if (libraryLoaded) {
 			return;
 		}
-		try {
-			System.loadLibrary("libyoshikoLibrary");
-		}
-		catch (Exception e) {
-			e.printStackTrace();
-		}
-	}
-	
 		
-	public void loadLibrary(String libPath) {
-		if (libraryLoaded) {
+		File f = new File (libPath);
+		if (!f.exists()) {
+			System.out.println("Could not find a previously saved yoshiko library path, needs to be set manually!");
 			return;
 		}
+		
 		try {
+			System.out.println("Attempting to load library @: "+libPath);
 			System.load(libPath);
+			//update cfg
+			cm.getProperties().setProperty("pathToYoshiko", libPath);
 			libraryLoaded = true;
 		}
-		catch(UnsatisfiedLinkError e) {
+		catch(Exception e) {
 			e.printStackTrace();
-			libraryLoaded = false;
 		}
-		finally {
-			
-		}
-
 	}
 	
 	//SETTER / GETTER
 	
-	public boolean isLibraryLoaded() {
+	public static boolean isLibraryLoaded() {
 		return libraryLoaded;
 	}
 
+
+	public static void provideConfiguration(ConfigurationManager _cm) {
+		cm = _cm;
+	}
+
 }

src/main/java/de/hhu/ba/yoshikoWrapper/gui/MainPanel.java

@@ -14,7 +14,6 @@ import org.cytoscape.application.swing.CytoPanelComponent;
 import org.cytoscape.application.swing.CytoPanelName;
 import de.hhu.ba.yoshikoWrapper.core.Core;
 import de.hhu.ba.yoshikoWrapper.core.YoshikoLoader;
-import de.hhu.ba.yoshikoWrapper.gui.*;
 import de.hhu.ba.yoshikoWrapper.swig.LibraryInterface;
 
 /**This class describes the Swing Panel that the user interacts with in cytoscape
@@ -29,7 +28,6 @@ public class MainPanel extends JPanel implements CytoPanelComponent {
 	private static final long serialVersionUID = 6214827920591046457L;
 	
 	//SYMBOLIC LINKS
-	private YoshikoLoader yoshikoLoader = YoshikoLoader.getInstance();
 	private MainPanel self = this; //for lambda function references
 	//SWING COMPONENTS
 	
@@ -48,7 +46,7 @@ public class MainPanel extends JPanel implements CytoPanelComponent {
 		//SWING COMPONENT INITIALIZATION
 		
 		libStatusPanel = new LibStatusPanel();
-		libStatusPanel.setStyle(yoshikoLoader.isLibraryLoaded());
+		libStatusPanel.setStyle(YoshikoLoader.isLibraryLoaded());
 		this.add(libStatusPanel);
 		
 		searchLibButton = new JButton("SHOW YOSHIKO LIB");
@@ -59,35 +57,31 @@ public class MainPanel extends JPanel implements CytoPanelComponent {
 				final YLibChooser c = new YLibChooser();
 				int returnVal = c.showOpenDialog(self);
 				if (returnVal == JFileChooser.APPROVE_OPTION) {
-					yoshikoLoader.loadLibrary(c.getSelectedFile().getAbsolutePath());
+					YoshikoLoader.loadLibrary(c.getSelectedFile().getAbsolutePath());
 				}
-				libStatusPanel.setStyle(yoshikoLoader.isLibraryLoaded());
+				libStatusPanel.setStyle(YoshikoLoader.isLibraryLoaded());
 				yoshikoVersionLabel.setText(LibraryInterface.getVersionString());
 			}
 			
 		});
 		this.add(searchLibButton);
 
-		//
-		//
-		//TODO: REMOVE IN FINAL RELEASE
-		JButton debugGraphActionButton = new JButton("DO MYSTERIOUS DEBUG STUFF");
-		debugGraphActionButton.addActionListener(new ActionListener() {
+		JButton runButton = new JButton("RUN");
+		runButton.addActionListener(new ActionListener() {
 
 
 			@Override
 			public void actionPerformed(ActionEvent e) {
-				if (yoshikoLoader.isLibraryLoaded()){
+				if (YoshikoLoader.isLibraryLoaded()){
 					Core.performYoshiko(timeLimitSetter.getTimeLimit());
 
 				}
 			}
 			
 		});
-		this.add(debugGraphActionButton);
-		//
-		//
-		//
+		this.add(runButton);
+
+		
 		timeLimitSetter = new TimeLimitSetter();
 		this.add(timeLimitSetter);
 		

src/main/java/de/hhu/ba/yoshikoWrapper/gui/NumberInputField.java

 package de.hhu.ba.yoshikoWrapper.gui;
 
-import java.text.NumberFormat;
-
 import javax.swing.JFormattedTextField;
-import javax.swing.text.NumberFormatter;
 
 /**
  * Provides a more strict input field that only accepts integers

src/main/java/de/hhu/ba/yoshikoWrapper/gui/TimeLimitSetter.java

 package de.hhu.ba.yoshikoWrapper.gui;
 
-import java.awt.Dimension;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 

src/main/resources/yoshiko

+yoshiko.pathToYoshiko = "NO PATH SET"
\ No newline at end of file