diff --git a/lib/galaxy/app.py b/lib/galaxy/app.py
index 49d718640f1..df79cc5969b 100644
--- a/lib/galaxy/app.py
+++ b/lib/galaxy/app.py
@@ -16,15 +16,16 @@ class UniverseApplication( object ):
         #Set up datatypes registry
         self.datatypes_registry = galaxy.datatypes.registry.Registry(datatypes=self.config.datatypes, sniff_order=self.config.sniff_order)
         galaxy.model.set_datatypes_registry(self.datatypes_registry)
-        # Connect up the object model
+        # Determine the database url
         if self.config.database_connection:
-            self.model = galaxy.model.mapping.init( self.config.file_path,
-                                                    self.config.database_connection,
-                                                    create_tables = True )
+            db_url = self.config.database_connection
         else:
-            self.model = galaxy.model.mapping.init( self.config.file_path,
-                                                    "sqlite://%s?isolation_level=IMMEDIATE" % self.config.database,
-                                                    create_tables = True )
+            db_url = "sqlite://%s?isolation_level=IMMEDIATE" % self.config.database
+        # Setup the database engine and ORM
+        self.model = galaxy.model.mapping.init( self.config.file_path,
+                                                db_url,
+                                                self.config.database_engine_options,
+                                                create_tables = True )
         # Initialize the tools
         self.toolbox = tools.ToolBox( self.config.tool_config, self.config.tool_path, self )
         #Load datatype converters
diff --git a/lib/galaxy/config.py b/lib/galaxy/config.py
index 6b49ba2aa6c..15b6ad4d6cc 100644
--- a/lib/galaxy/config.py
+++ b/lib/galaxy/config.py
@@ -6,6 +6,7 @@ import sys, os
 import logging, logging.config
 from optparse import OptionParser
 import ConfigParser
+from galaxy.util import string_as_bool
 
 log = logging.getLogger( __name__ )
 
@@ -23,8 +24,11 @@ class Configuration( object ):
         self.config_dict = kwargs
         self.root = kwargs.get( 'root_dir', '.' )
         self.enable_beta_features = kwargs.get( "enable_beta_features", False )
+        # Database related configuration
         self.database = resolve_path( kwargs.get( "database_file", "database/universe.d" ), self.root )
         self.database_connection =  kwargs.get( "database_connection", False )
+        self.database_engine_options = get_database_engine_options( kwargs )                        
+        # Where dataset files are stored
         self.file_path = resolve_path( kwargs.get( "file_path", "database/files" ), self.root )
         self.new_file_path = resolve_path( kwargs.get( "new_file_path", "database/tmp" ), self.root )
         self.tool_path = resolve_path( kwargs.get( "tool_path", "tools" ), self.root )
@@ -85,6 +89,32 @@ class Configuration( object ):
             if not os.path.isfile(path):
                 raise ConfigurationError("File not found: %s" % path )
 
+def get_database_engine_options( kwargs ):
+    """
+    Allow options for the SQLAlchemy database engine to be passed by using
+    the prefix "database_engine_option_".
+    """
+    conversions =  {
+        'convert_unicode': string_as_bool,
+        'pool_timeout': int,
+        'echo': string_as_bool,
+        'echo_pool': string_as_bool,
+        'pool_recycle': int,
+        'pool_size': int,
+        'max_overflow': int,
+        'pool_threadlocal': string_as_bool
+    }
+    prefix = "database_engine_option_"
+    prefix_len = len( prefix )
+    rval = {}
+    for key, value in kwargs.iteritems():
+        if key.startswith( prefix ):
+            key = key[prefix_len:]
+            if key in conversions:
+                value = conversions[key](value)
+            rval[ key  ] = value
+    return rval
+
 def configure_logging( config ):
     """
     Allow some basic logging configuration to be read from the cherrpy
diff --git a/lib/galaxy/model/mapping.py b/lib/galaxy/model/mapping.py
index ae4e84300ef..2c16fd13dd1 100644
--- a/lib/galaxy/model/mapping.py
+++ b/lib/galaxy/model/mapping.py
@@ -262,9 +262,8 @@ def db_next_hid( self ):
 
 History._next_hid = db_next_hid
     
-def init( file_path, url, **kwargs ):
+def init( file_path, url, engine_options, create_tables=False ):
     """Connect mappings to the database"""
-    create_tables = kwargs.pop( 'create_tables', False )
     # Connect dataset to the file path
     Dataset.file_path = file_path
     # MySQL hacking, doesn't support passive defaults for anything but TIMESTAMP
@@ -274,7 +273,7 @@ def init( file_path, url, **kwargs ):
                 table.columns['create_time'].type = TIMESTAMP()
             if table.columns.has_key( "update_time" ):
                 table.columns['update_time'].type = TIMESTAMP()
-        metadata.connect( url, **kwargs )
+        metadata.connect( url, **engine_options )
     # Connect the metadata to the database. 
     elif url.startswith( "postgresql:///" ): 
         import psycopg
@@ -290,9 +289,10 @@ def init( file_path, url, **kwargs ):
             metadata.connect( engine )
         except:
             log.exception( "error connecting to database using connection: '%s'." % url )
-            metadata.connect( url, **kwargs )
+            metadata.connect( url, **engine_options )
     else:
-        metadata.connect( url, **kwargs )
+        engine = create_engine( url, **engine_options )
+        metadata.connect( engine )
     ## metadata.engine.echo = True
     # Create tables if needed
     if create_tables: