diff --git a/plugins/net.bioclipse.scripting.ui.tests/src/net/bioclipse/scripting/ui/tests/JsConsoleManagerTest.java b/plugins/net.bioclipse.scripting.ui.tests/src/net/bioclipse/scripting/ui/tests/JsConsoleManagerTest.java
index f25f107b2..295244d89 100644
--- a/plugins/net.bioclipse.scripting.ui.tests/src/net/bioclipse/scripting/ui/tests/JsConsoleManagerTest.java
+++ b/plugins/net.bioclipse.scripting.ui.tests/src/net/bioclipse/scripting/ui/tests/JsConsoleManagerTest.java
@@ -12,9 +12,23 @@
  ******************************************************************************/
 package net.bioclipse.scripting.ui.tests;
 
+import static org.junit.Assert.*;
+
 import java.io.ByteArrayInputStream;
+import java.util.ArrayList;
 
 import org.eclipse.core.resources.IFile;
+import org.eclipse.core.resources.IProject;
+import org.eclipse.core.resources.IWorkspaceRoot;
+import org.eclipse.core.resources.ResourcesPlugin;
+import org.eclipse.core.runtime.CoreException;
+import org.eclipse.core.runtime.IProgressMonitor;
+import org.eclipse.core.runtime.IStatus;
+import org.eclipse.core.runtime.NullProgressMonitor;
+import org.eclipse.core.runtime.Path;
+import org.eclipse.core.runtime.Status;
+import org.eclipse.core.runtime.jobs.Job;
+import org.junit.Assert;
 import org.junit.Test;
 
 import net.bioclipse.core.MockIFile;
@@ -74,4 +88,51 @@ public void testExecuteFile() {
         ).extension( "js" );
     	console.executeFile(file);
     }
+    
+    @Test
+    public void testExecute() throws Exception {
+        final IFile file1 = new MockIFile(
+            new ByteArrayInputStream("i = 5;".getBytes())
+        ).extension( "js" );
+        final IFile file2 = new MockIFile(
+            new ByteArrayInputStream("i = 5;".getBytes())
+        ).extension( "js" );
+        console.executeFile(file1);
+        console.execute( file1 );
+        console.execute( new ArrayList<IFile>() {{add(file1); add(file2);}} );
+
+        IWorkspaceRoot root = ResourcesPlugin.getWorkspace().getRoot();
+        IProject project = root.getProject("TEST");
+        project.create(new NullProgressMonitor());
+        project.open(new NullProgressMonitor());
+        String filePath = "/TEST/testFile99883423427.js";
+        final IFile file = ResourcesPlugin.getWorkspace().getRoot().getFile(
+                              new Path(filePath)
+                     );
+        Job job = new Job("test") {
+            @Override
+            protected IStatus run( IProgressMonitor monitor ) {
+                try {
+                    file.create( new ByteArrayInputStream(
+                                         "i = 5;".getBytes()), true, monitor );
+                } catch ( CoreException e ) {
+                    fail( e.getMessage() );
+                    return Status.CANCEL_STATUS;
+                }
+                return Status.OK_STATUS;
+            }
+        };
+        job.setRule( file );
+        job.schedule();
+        job.join();
+
+        final IFile savedFile = ResourcesPlugin.getWorkspace()
+                                               .getRoot()
+                                               .getFile( new Path(filePath) );
+        
+        console.execute( new ArrayList<String>() {{ 
+                                 add(file.getFullPath().toString()); 
+                                 add(file.getFullPath().toString());
+                              }} );
+    }
 }
diff --git a/plugins/net.bioclipse.scripting.ui/src/net/bioclipse/scripting/ui/business/IJsConsoleManager.java b/plugins/net.bioclipse.scripting.ui/src/net/bioclipse/scripting/ui/business/IJsConsoleManager.java
index 37c7ea0e4..1b703244a 100644
--- a/plugins/net.bioclipse.scripting.ui/src/net/bioclipse/scripting/ui/business/IJsConsoleManager.java
+++ b/plugins/net.bioclipse.scripting.ui/src/net/bioclipse/scripting/ui/business/IJsConsoleManager.java
@@ -12,6 +12,8 @@
  ******************************************************************************/
 package net.bioclipse.scripting.ui.business;
 
+import java.util.List;
+
 import org.eclipse.core.resources.IFile;
 import org.eclipse.core.runtime.IProgressMonitor;
 
@@ -21,6 +23,7 @@
 import net.bioclipse.core.TestClasses;
 import net.bioclipse.core.TestMethods;
 import net.bioclipse.managers.business.IBioclipseManager;
+import net.bioclipse.core.business.BioclipseException;
 import net.bioclipse.core.util.IJavaScriptConsolePrinterChannel;
 
 /**
@@ -58,14 +61,34 @@ public interface IJsConsoleManager extends IBioclipseManager,
     @TestMethods("testEval")
     public String eval(String command);
 
+    @Recorded
+    @TestMethods("testExecute")
+    public void execute(IFile file);
+    
+    @Recorded
+    @TestMethods("testExecute")
+    @PublishedMethod( params="String file",
+                      methodSummary="Runs a js script file.")
+    public void execute(String file);
+    
+    @Recorded
+    @TestMethods("testExecute")
+    @PublishedMethod( params="List files",
+                      methodSummary="Runs a js script file.")
+    public void execute(List<?> files) throws BioclipseException;
+    
     @Recorded
     @TestMethods("testExecuteFile")
+    @Deprecated
     public void executeFile(IFile file);
 
     @Recorded
-    @PublishedMethod(params="String filePath",
-                     methodSummary="Runs a js script file.")
+    @PublishedMethod(
+        params="String filePath",
+        methodSummary="Runs a js script file. Marked for removal. " +
+                      "Use js.execute instead." )
     @TestMethods("testExecuteFile")
+    @Deprecated
     public void executeFile(String filePath);
 
     public void printError( Throwable t );
diff --git a/plugins/net.bioclipse.scripting.ui/src/net/bioclipse/scripting/ui/business/JsConsoleManager.java b/plugins/net.bioclipse.scripting.ui/src/net/bioclipse/scripting/ui/business/JsConsoleManager.java
index 41b166a5f..6c75cb6c8 100644
--- a/plugins/net.bioclipse.scripting.ui/src/net/bioclipse/scripting/ui/business/JsConsoleManager.java
+++ b/plugins/net.bioclipse.scripting.ui/src/net/bioclipse/scripting/ui/business/JsConsoleManager.java
@@ -12,6 +12,11 @@
  ******************************************************************************/
 package net.bioclipse.scripting.ui.business;
 
+import java.util.ArrayList;
+import java.util.List;
+
+import net.bioclipse.core.ResourcePathTransformer;
+import net.bioclipse.core.business.BioclipseException;
 import net.bioclipse.managers.business.IBioclipseManager;
 import net.bioclipse.scripting.Activator;
 import net.bioclipse.scripting.Hook;
@@ -92,8 +97,8 @@ public void run( Object result ) {
         );
         return evalResult[0];
     }
-
-    public void executeFile( final IFile file ) {
+    
+    public void execute( final IFile file ) {
         Job job = new Job("JavaScript execution") {
             @Override
             protected IStatus run(final IProgressMonitor monitor) {
@@ -152,9 +157,35 @@ public void run() {
             }
         };
         job.schedule();
+    
+    }
+
+    @Deprecated
+    public void executeFile( final IFile file ) {
+        execute(file);
     }
 
     public void printError( Throwable t ) {
         print( getJsConsoleView().getErrorMessage( t ) );
     }
+
+    public void execute( List<?> files ) throws BioclipseException {
+        int i = 0;
+        for ( Object o : files) {
+            if ( o instanceof IFile ) {
+                execute( (IFile)o );
+            }
+            else if ( o instanceof String ) {
+                execute( ResourcePathTransformer.getInstance()
+                                                .transform( (String)o ) );
+            }
+            else {
+                throw new BioclipseException(
+                    "List of files given to the js.execute method contained " +
+                    "an element at index " + i +  " which could not be " +
+                    "identified as a file. The element was: " + o.toString() );
+            }
+            i++;
+        }
+    }
 }