diff --git a/lib/galaxy/model/mapping.py b/lib/galaxy/model/mapping.py
index cafdb4e0bd3..b740377520f 100644
--- a/lib/galaxy/model/mapping.py
+++ b/lib/galaxy/model/mapping.py
@@ -48,12 +48,12 @@ User.table = Table( "galaxy_user", metadata,
 History.table = Table( "history", metadata,
     Column( "id", Integer, primary_key=True),
     Column( "create_time", DateTime, default=now ),
-    Column( "update_time", DateTime, default=now, onupdate=now ),
-    Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ) ),
+    Column( "update_time", DateTime, index=True, default=now, onupdate=now ),
+    Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ),
     Column( "name", TrimmedString( 255 ) ),
     Column( "hid_counter", Integer, default=1 ),
-    Column( "deleted", Boolean, default=False ),
-    Column( "purged", Boolean, default=False ),
+    Column( "deleted", Boolean, index=True, default=False ),
+    Column( "purged", Boolean, index=True, default=False ),
     Column( "genome_build", TrimmedString( 40 ) ) )
 
 # model.Query.table = Table( "query", engine,
@@ -66,9 +66,9 @@ History.table = Table( "history", metadata,
 Dataset.table = Table( "dataset", metadata, 
     Column( "id", Integer, primary_key=True ),
     Column( "create_time", DateTime, default=now ),
-    Column( "update_time", DateTime, default=now, onupdate=now ),
+    Column( "update_time", DateTime, index=True, default=now, onupdate=now ),
     Column( "hid", Integer ),
-    Column( "history_id", Integer, ForeignKey( "history.id" ) ),
+    Column( "history_id", Integer, ForeignKey( "history.id" ), index=True ),
     Column( "name", TrimmedString( 255 ) ),
     Column( "info", TrimmedString( 255 ) ),
     Column( "blurb", TrimmedString( 255 ) ),
@@ -79,10 +79,10 @@ Dataset.table = Table( "dataset", metadata,
     Column( "metadata", MetadataType(), key="_metadata" ),
     Column( "parent_id", Integer, nullable=True ),
     Column( "designation", TrimmedString( 255 ) ),
-    Column( "deleted", Boolean, default=False ),
-    Column( "purged", Boolean, default=False ),
+    Column( "deleted", Boolean, index=True, default=False ),
+    Column( "purged", Boolean, index=True, default=False ),
     Column( "visible", Boolean ),
-    Column( "filename_id", Integer, ForeignKey( "dataset_filename.id" ), nullable=True ),
+    Column( "filename_id", Integer, ForeignKey( "dataset_filename.id" ), index=True, nullable=True ),
     Column( 'file_size', Numeric( 15, 0 ) ),
     ForeignKeyConstraint(['parent_id'],['dataset.id'], ondelete="CASCADE") )
 
@@ -96,22 +96,22 @@ DatasetFileName.table = Table( "dataset_filename", metadata,
 
 ValidationError.table = Table( "validation_error", metadata,
     Column( "id", Integer, primary_key=True ),
-    Column( "dataset_id", Integer, ForeignKey( "dataset.id" ) ),
+    Column( "dataset_id", Integer, ForeignKey( "dataset.id" ), index=True ),
     Column( "message", TrimmedString( 255 ) ),
     Column( "err_type", TrimmedString( 64 ) ),
     Column( "attributes", TEXT ) )
 
 DatasetChildAssociation.table = Table( "dataset_child_association", metadata,
     Column( "id", Integer, primary_key=True ),
-    Column( "parent_dataset_id", Integer, ForeignKey( "dataset.id" ) ),
-    Column( "child_dataset_id", Integer, ForeignKey( "dataset.id" ) ),
+    Column( "parent_dataset_id", Integer, ForeignKey( "dataset.id" ), index=True ),
+    Column( "child_dataset_id", Integer, ForeignKey( "dataset.id" ), index=True ),
     Column( "designation", TrimmedString( 255 ) ) )
-    
+
 Job.table = Table( "job", metadata,
     Column( "id", Integer, primary_key=True ),
     Column( "create_time", DateTime, default=now ),
     Column( "update_time", DateTime, default=now, onupdate=now ),
-    Column( "history_id", Integer, ForeignKey( "history.id" ) ),
+    Column( "history_id", Integer, ForeignKey( "history.id" ), index=True ),
     Column( "tool_id", String( 255 ) ),
     Column( "tool_version", String, default="1.0.0" ),
     Column( "state", String( 64 ) ),
@@ -121,43 +121,43 @@ Job.table = Table( "job", metadata,
     Column( "stdout", String() ),
     Column( "stderr", String() ),
     Column( "traceback", String() ),
-    Column( "session_id", Integer, ForeignKey( "galaxy_session.id" ), nullable=True ),
+    Column( "session_id", Integer, ForeignKey( "galaxy_session.id" ), index=True, nullable=True ),
     Column( "job_runner_name", String( 255 ) ),
     Column( "job_runner_external_id", String( 255 ) ) )
     
 JobParameter.table = Table( "job_parameter", metadata,
     Column( "id", Integer, primary_key=True ),
-    Column( "job_id", Integer, ForeignKey( "job.id" ) ),
+    Column( "job_id", Integer, ForeignKey( "job.id" ), index=True ),
     Column( "name", String(255) ),
     Column( "value", TEXT ) )
     
 JobToInputDatasetAssociation.table = Table( "job_to_input_dataset", metadata,
     Column( "id", Integer, primary_key=True ),
-    Column( "job_id", Integer, ForeignKey( "job.id" ) ),
-    Column( "dataset_id", Integer, ForeignKey( "dataset.id" ) ),
+    Column( "job_id", Integer, ForeignKey( "job.id" ), index=True ),
+    Column( "dataset_id", Integer, ForeignKey( "dataset.id" ), index=True ),
     Column( "name", String(255) ) )
     
 JobToOutputDatasetAssociation.table = Table( "job_to_output_dataset", metadata,
     Column( "id", Integer, primary_key=True ),
-    Column( "job_id", Integer, ForeignKey( "job.id" ) ),
-    Column( "dataset_id", Integer, ForeignKey( "dataset.id" ) ),
+    Column( "job_id", Integer, ForeignKey( "job.id" ), index=True ),
+    Column( "dataset_id", Integer, ForeignKey( "dataset.id" ), index=True ),
     Column( "name", String(255) ) )
     
 Event.table = Table( "event", metadata, 
     Column( "id", Integer, primary_key=True ),
     Column( "create_time", DateTime, default=now ),
     Column( "update_time", DateTime, default=now, onupdate=now ),
-    Column( "history_id", Integer, ForeignKey( "history.id" ), nullable=True ),
-    Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), nullable=True ),
+    Column( "history_id", Integer, ForeignKey( "history.id" ), index=True, nullable=True ),
+    Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True, nullable=True ),
     Column( "message", TrimmedString( 1024 ) ),
-    Column( "session_id", Integer, ForeignKey( "galaxy_session.id" ), nullable=True ),
+    Column( "session_id", Integer, ForeignKey( "galaxy_session.id" ), index=True, nullable=True ),
     Column( "tool_id", String( 255 ) ) )
 
 GalaxySession.table = Table( "galaxy_session", metadata,
     Column( "id", Integer, primary_key=True ),
     Column( "create_time", DateTime, default=now ),
     Column( "update_time", DateTime, default=now, onupdate=now ),
-    Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), nullable=True ),
+    Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True, nullable=True ),
     Column( "remote_host", String( 255 ) ),
     Column( "remote_addr", String( 255 ) ),
     Column( "referer", TEXT ) )
@@ -165,16 +165,16 @@ GalaxySession.table = Table( "galaxy_session", metadata,
 GalaxySessionToHistoryAssociation.table = Table( "galaxy_session_to_history", metadata,
     Column( "id", Integer, primary_key=True ),
     Column( "create_time", DateTime, default=now ),
-    Column( "session_id", Integer, ForeignKey( "galaxy_session.id" ) ),
-    Column( "history_id", Integer, ForeignKey( "history.id" ) ) )
+    Column( "session_id", Integer, ForeignKey( "galaxy_session.id" ), index=True ),
+    Column( "history_id", Integer, ForeignKey( "history.id" ), index=True ) )
 
 StoredWorkflow.table = Table( "stored_workflow", metadata,
     Column( "id", Integer, primary_key=True ),
     Column( "create_time", DateTime, default=now ),
     Column( "update_time", DateTime, default=now, onupdate=now ),
-    Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), nullable=False ),
+    Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True, nullable=False ),
     Column( "latest_workflow_id", Integer,
-            ForeignKey( "workflow.id", use_alter=True, name='stored_workflow_latest_workflow_id_fk' ) ),
+            ForeignKey( "workflow.id", use_alter=True, name='stored_workflow_latest_workflow_id_fk' ), index=True ),
     Column( "name", String ),
     Column( "deleted", Boolean, default=False ),
     )
@@ -183,7 +183,7 @@ Workflow.table = Table( "workflow", metadata,
     Column( "id", Integer, primary_key=True ),
     Column( "create_time", DateTime, default=now ),
     Column( "update_time", DateTime, default=now, onupdate=now ),
-    Column( "stored_workflow_id", Integer, ForeignKey( "stored_workflow.id" ), nullable=False ),
+    Column( "stored_workflow_id", Integer, ForeignKey( "stored_workflow.id" ), index=True, nullable=False ),
     Column( "name", String ),
     Column( "has_cycles", Boolean ),
     Column( "has_errors", Boolean )
@@ -193,7 +193,7 @@ WorkflowStep.table = Table( "workflow_step", metadata,
     Column( "id", Integer, primary_key=True ),
     Column( "create_time", DateTime, default=now ),
     Column( "update_time", DateTime, default=now, onupdate=now ),
-    Column( "workflow_id", Integer, ForeignKey( "workflow.id" ), nullable=False ),
+    Column( "workflow_id", Integer, ForeignKey( "workflow.id" ), index=True, nullable=False ),
     Column( "tool_id", String ),
     Column( "tool_version", String ), # Reserved for future
     Column( "tool_inputs", JSONType ),
@@ -205,8 +205,8 @@ WorkflowStep.table = Table( "workflow_step", metadata,
 
 WorkflowStepConnection.table = Table( "workflow_step_connection", metadata,
     Column( "id", Integer, primary_key=True ),
-    Column( "output_step_id", Integer, ForeignKey( "workflow_step.id" ) ),
-    Column( "input_step_id", Integer, ForeignKey( "workflow_step.id" ) ),
+    Column( "output_step_id", Integer, ForeignKey( "workflow_step.id" ), index=True ),
+    Column( "input_step_id", Integer, ForeignKey( "workflow_step.id" ), index=True ),
     Column( "output_name", String ),
     Column( "input_name", String)
     )