diff --git a/eggs.ini b/eggs.ini
index 1c0491984b7..4470e0c103b 100644
--- a/eggs.ini
+++ b/eggs.ini
@@ -26,7 +26,6 @@ pycrypto = 2.5
 pysam = 0.4.2
 pysqlite = 2.5.6
 python_lzo = 1.08_2.03_static
-simplejson = 2.1.1
 threadframe = 0.2
 guppy = 0.1.8
 SQLAlchemy = 0.7.9
diff --git a/lib/galaxy/datatypes/metadata.py b/lib/galaxy/datatypes/metadata.py
index 2bf4de1fcd8..54efe4d2949 100644
--- a/lib/galaxy/datatypes/metadata.py
+++ b/lib/galaxy/datatypes/metadata.py
@@ -2,15 +2,13 @@
 Galaxy Metadata
 
 """
-from galaxy import eggs
-eggs.require("simplejson")
 
 import copy
 import cPickle
+import json
 import logging
 import os
 import shutil
-import simplejson
 import sys
 import tempfile
 import weakref
@@ -130,7 +128,7 @@ class MetadataCollection( object ):
     def from_JSON_dict( self, filename ):
         dataset = self.parent
         log.debug( 'loading metadata from file for: %s %s' % ( dataset.__class__.__name__, dataset.id ) )
-        JSONified_dict = simplejson.load( open( filename ) )
+        JSONified_dict = json.load( open( filename ) )
         for name, spec in self.spec.items():
             if name in JSONified_dict:
                 dataset._metadata[ name ] = spec.param.from_external_value( JSONified_dict[ name ], dataset )
@@ -146,7 +144,7 @@ class MetadataCollection( object ):
         for name, spec in self.spec.items():
             if name in dataset_meta_dict:
                 meta_dict[ name ] = spec.param.to_external_value( dataset_meta_dict[ name ] )
-        simplejson.dump( meta_dict, open( filename, 'wb+' ) )
+        json.dump( meta_dict, open( filename, 'wb+' ) )
 
     def __getstate__( self ):
         return None #cannot pickle a weakref item (self._parent), when data._metadata_collection is None, it will be recreated on demand
@@ -456,7 +454,7 @@ class ListParameter( MetadataParameter ):
 class DictParameter( MetadataParameter ):
 
     def to_string( self, value ):
-        return  simplejson.dumps( value )
+        return  json.dumps( value )
 
 
 class PythonObjectParameter( MetadataParameter ):
@@ -594,7 +592,7 @@ class MetadataTempFile( object ):
     @classmethod
     def cleanup_from_JSON_dict_filename( cls, filename ):
         try:
-            for key, value in simplejson.load( open( filename ) ).items():
+            for key, value in json.load( open( filename ) ).items():
                 if cls.is_JSONified_value( value ):
                     value = cls.from_JSON( value )
                 if isinstance( value, cls ) and os.path.exists( value.file_name ):
@@ -686,10 +684,10 @@ class JobExternalOutputMetadataWrapper( object ):
                 #file to store a 'return code' indicating the results of the set_meta() call
                 #results code is like (True/False - if setting metadata was successful/failed , exception or string of reason of success/failure )
                 metadata_files.filename_results_code = abspath( tempfile.NamedTemporaryFile( dir = tmp_dir, prefix = "metadata_results_%s_" % key ).name )
-                simplejson.dump( ( False, 'External set_meta() not called' ), open( metadata_files.filename_results_code, 'wb+' ) ) # create the file on disk, so it cannot be reused by tempfile (unlikely, but possible)
+                json.dump( ( False, 'External set_meta() not called' ), open( metadata_files.filename_results_code, 'wb+' ) ) # create the file on disk, so it cannot be reused by tempfile (unlikely, but possible)
                 #file to store kwds passed to set_meta()
                 metadata_files.filename_kwds = abspath( tempfile.NamedTemporaryFile( dir = tmp_dir, prefix = "metadata_kwds_%s_" % key ).name )
-                simplejson.dump( kwds, open( metadata_files.filename_kwds, 'wb+' ), ensure_ascii=True )
+                json.dump( kwds, open( metadata_files.filename_kwds, 'wb+' ), ensure_ascii=True )
                 #existing metadata file parameters need to be overridden with cluster-writable file locations
                 metadata_files.filename_override_metadata = abspath( tempfile.NamedTemporaryFile( dir = tmp_dir, prefix = "metadata_override_%s_" % key ).name )
                 open( metadata_files.filename_override_metadata, 'wb+' ) # create the file on disk, so it cannot be reused by tempfile (unlikely, but possible)
@@ -699,7 +697,7 @@ class JobExternalOutputMetadataWrapper( object ):
                         metadata_temp = MetadataTempFile()
                         shutil.copy( dataset.metadata.get( meta_key, None ).file_name, metadata_temp.file_name )
                         override_metadata.append( ( meta_key, metadata_temp.to_JSON() ) )
-                simplejson.dump( override_metadata, open( metadata_files.filename_override_metadata, 'wb+' ) )
+                json.dump( override_metadata, open( metadata_files.filename_override_metadata, 'wb+' ) )
                 #add to session and flush
                 sa_session.add( metadata_files )
                 sa_session.flush()
@@ -711,7 +709,7 @@ class JobExternalOutputMetadataWrapper( object ):
         metadata_files = self.get_output_filenames_by_dataset( dataset, sa_session )
         if not metadata_files:
             return False # this file doesn't exist
-        rval, rstring = simplejson.load( open( metadata_files.filename_results_code ) )
+        rval, rstring = json.load( open( metadata_files.filename_results_code ) )
         if not rval:
             log.debug( 'setting metadata externally failed for %s %s: %s' % ( dataset.__class__.__name__, dataset.id, rstring ) )
         return rval
diff --git a/lib/galaxy/datatypes/sequence.py b/lib/galaxy/datatypes/sequence.py
index f63593a7915..87e3cf0b82a 100644
--- a/lib/galaxy/datatypes/sequence.py
+++ b/lib/galaxy/datatypes/sequence.py
@@ -2,12 +2,14 @@
 Sequence classes
 """
 
-import data
+from . import data
 import gzip
+import json
 import logging
 import os
 import re
 import string
+
 from cgi import escape
 
 from galaxy import eggs, util
@@ -16,8 +18,6 @@ from galaxy.datatypes.checkers import is_gzip
 from galaxy.datatypes.sniff import get_test_fname, get_headers
 from galaxy.datatypes.metadata import MetadataElement
 
-eggs.require("simplejson")
-import simplejson
 
 try:
     eggs.require( "bx-python" )
@@ -44,8 +44,8 @@ class SequenceSplitLocations( data.Text ):
     def set_peek( self, dataset, is_multi_byte=False ):
         if not dataset.dataset.purged:
             try:
-                parsed_data = simplejson.load(open(dataset.file_name))
-                # dataset.peek = simplejson.dumps(data, sort_keys=True, indent=4)
+                parsed_data = json.load(open(dataset.file_name))
+                # dataset.peek = json.dumps(data, sort_keys=True, indent=4)
                 dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
                 dataset.blurb = '%d sections' % len(parsed_data['sections'])
             except Exception, e:
@@ -60,7 +60,7 @@ class SequenceSplitLocations( data.Text ):
     def sniff( self, filename ):
         if os.path.getsize(filename) < 50000:
             try:
-                data = simplejson.load(open(filename))
+                data = json.load(open(filename))
                 sections = data['sections']
                 for section in sections:
                     if 'start' not in section or 'end' not in section or 'sequences' not in section:
@@ -155,7 +155,7 @@ class Sequence( data.Text ):
     do_slow_split = classmethod(do_slow_split)
 
     def do_fast_split( cls, input_datasets, toc_file_datasets, subdir_generator_function, split_params):
-        data = simplejson.load(open(toc_file_datasets[0].file_name))
+        data = json.load(open(toc_file_datasets[0].file_name))
         sections = data['sections']
         total_sequences = long(0)
         for section in sections:
@@ -191,7 +191,7 @@ class Sequence( data.Text ):
                     toc = toc_file_datasets[ds_no]
                     split_data['args']['toc_file'] = toc.file_name
                 f = open(os.path.join(dir, 'split_info_%s.json' % base_name), 'w')
-                simplejson.dump(split_data, f)
+                json.dump(split_data, f)
                 f.close()
             start_sequence += sequences_per_file[part_no]
         return directories
@@ -557,7 +557,7 @@ class Fastq ( Sequence ):
         sequence_count = long(args['num_sequences'])
 
         if 'toc_file' in args:
-            toc_file = simplejson.load(open(args['toc_file'], 'r'))
+            toc_file = json.load(open(args['toc_file'], 'r'))
             commands = Sequence.get_split_commands_with_toc(input_name, output_name, toc_file, start_sequence, sequence_count)
         else:
             commands = Sequence.get_split_commands_sequential(is_gzip(input_name), input_name, output_name, start_sequence, sequence_count)
diff --git a/lib/galaxy/jobs/runners/drmaa.py b/lib/galaxy/jobs/runners/drmaa.py
index 465d5e9f6ad..5e111ca4710 100644
--- a/lib/galaxy/jobs/runners/drmaa.py
+++ b/lib/galaxy/jobs/runners/drmaa.py
@@ -2,13 +2,13 @@
 Job control via the DRMAA API.
 """
 
+import json
+import logging
 import os
+import string
+import subprocess
 import sys
 import time
-import string
-import logging
-import subprocess
-import simplejson as json
 
 from galaxy import eggs
 from galaxy import model
diff --git a/lib/galaxy/jobs/runners/lwr_client/action_mapper.py b/lib/galaxy/jobs/runners/lwr_client/action_mapper.py
index ce09207b38a..3903f515610 100644
--- a/lib/galaxy/jobs/runners/lwr_client/action_mapper.py
+++ b/lib/galaxy/jobs/runners/lwr_client/action_mapper.py
@@ -1,4 +1,4 @@
-from simplejson import load
+from json import load
 from os.path import abspath
 from os.path import dirname
 from os.path import join
diff --git a/lib/galaxy/jobs/runners/lwr_client/client.py b/lib/galaxy/jobs/runners/lwr_client/client.py
index ff45642647a..b29126f0f3d 100644
--- a/lib/galaxy/jobs/runners/lwr_client/client.py
+++ b/lib/galaxy/jobs/runners/lwr_client/client.py
@@ -1,7 +1,6 @@
 import os
 import shutil
-import simplejson
-from simplejson import dumps
+from json import dumps, loads
 from time import sleep
 
 from .destination import submit_params
@@ -16,7 +15,7 @@ class parseJson(object):
     def __call__(self, func):
         def replacement(*args, **kwargs):
             response = func(*args, **kwargs)
-            return simplejson.loads(response)
+            return loads(response)
         return replacement
 
 
diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index 23d9c9e03df..7075562f274 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -6,7 +6,6 @@ the relationship cardinalities are obvious (e.g. prefer Dataset to Data)
 """
 
 from galaxy import eggs
-eggs.require("simplejson")
 eggs.require("pexpect")
 
 import codecs
@@ -15,7 +14,7 @@ import logging
 import operator
 import os
 import pexpect
-import simplejson
+import json
 import socket
 import time
 from string import Template
@@ -2250,7 +2249,7 @@ class LibraryDatasetDatasetAssociation( DatasetInstance ):
             template_data[template.name] = tmp_dict
         return template_data
     def templates_json( self, use_name=False ):
-        return simplejson.dumps( self.templates_dict( use_name=use_name ) )
+        return json.dumps( self.templates_dict( use_name=use_name ) )
 
     def get_display_name( self ):
         """
diff --git a/lib/galaxy/model/custom_types.py b/lib/galaxy/model/custom_types.py
index 183484467f4..0096c7bc405 100644
--- a/lib/galaxy/model/custom_types.py
+++ b/lib/galaxy/model/custom_types.py
@@ -1,8 +1,6 @@
 from sqlalchemy.types import *
 
-import pkg_resources
-pkg_resources.require("simplejson")
-import simplejson
+import json
 import pickle
 import copy
 import uuid
@@ -19,8 +17,8 @@ import logging
 log = logging.getLogger( __name__ )
 
 # Default JSON encoder and decoder
-json_encoder = simplejson.JSONEncoder( sort_keys=True )
-json_decoder = simplejson.JSONDecoder( )
+json_encoder = json.JSONEncoder( sort_keys=True )
+json_decoder = json.JSONDecoder( )
 
 def _sniffnfix_pg9_hex(value):
     """
diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index 565dd009196..6f5f0279e18 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -4,6 +4,7 @@ Classes encapsulating galaxy tools and tool configuration.
 
 import binascii
 import glob
+import json
 import logging
 import os
 import pipes
@@ -19,14 +20,12 @@ import urllib
 from math import isinf
 
 from galaxy import eggs
-eggs.require( "simplejson" )
 eggs.require( "MarkupSafe" ) #MarkupSafe must load before mako
 eggs.require( "Mako" )
 eggs.require( "elementtree" )
 eggs.require( "Paste" )
 eggs.require( "SQLAlchemy >= 0.4" )
 
-import simplejson
 from cgi import FieldStorage
 from elementtree import ElementTree
 from mako.template import Template
@@ -869,7 +868,7 @@ class DefaultToolState( object ):
         value = params_to_strings( tool.inputs, self.inputs, app )
         value["__page__"] = self.page
         value["__rerun_remap_job_id__"] = self.rerun_remap_job_id
-        value = simplejson.dumps( value )
+        value = json.dumps( value )
         # Make it secure
         if secure:
             a = hmac_new( app.config.tool_secret, value )
@@ -888,7 +887,7 @@ class DefaultToolState( object ):
             test = hmac_new( app.config.tool_secret, value )
             assert a == test
         # Restore from string
-        values = json_fix( simplejson.loads( value ) )
+        values = json_fix( json.loads( value ) )
         self.page = values.pop( "__page__" )
         if '__rerun_remap_job_id__' in values:
             self.rerun_remap_job_id = values.pop( "__rerun_remap_job_id__" )
@@ -2921,7 +2920,7 @@ class Tool( object, Dictifiable ):
         try:
             json_file = open( os.path.join( job_working_directory, jobs.TOOL_PROVIDED_JOB_METADATA_FILE ), 'r' )
             for line in json_file:
-                line = simplejson.loads( line )
+                line = json.loads( line )
                 if line.get( 'type' ) == 'new_primary_dataset':
                     new_primary_datasets[ os.path.split( line.get( 'filename' ) )[-1] ] = line
         except Exception:
@@ -3085,7 +3084,7 @@ class OutputParameterJSONTool( Tool ):
             if json_filename is None:
                 json_filename = file_name
         out = open( json_filename, 'w' )
-        out.write( simplejson.dumps( json_params ) )
+        out.write( json.dumps( json_params ) )
         out.close()
 
 class DataSourceTool( OutputParameterJSONTool ):
@@ -3145,7 +3144,7 @@ class DataSourceTool( OutputParameterJSONTool ):
             if json_filename is None:
                 json_filename = file_name
         out = open( json_filename, 'w' )
-        out.write( simplejson.dumps( json_params ) )
+        out.write( json.dumps( json_params ) )
         out.close()
 
 class AsyncDataSourceTool( DataSourceTool ):
diff --git a/lib/galaxy/tools/data_manager/manager.py b/lib/galaxy/tools/data_manager/manager.py
index decee9e1e2b..f5091e1c4ba 100644
--- a/lib/galaxy/tools/data_manager/manager.py
+++ b/lib/galaxy/tools/data_manager/manager.py
@@ -1,9 +1,6 @@
-import pkg_resources
-
-pkg_resources.require( "simplejson" )
-
-import os, errno
-import simplejson
+import errno
+import json
+import os
 
 from galaxy import util
 from galaxy.util.odict import odict
@@ -226,7 +223,7 @@ class DataManager( object ):
         #TODO: fix this merging below
         for output_name, output_dataset in out_data.iteritems():
             try:
-                output_dict = simplejson.loads( open( output_dataset.file_name ).read() )
+                output_dict = json.loads( open( output_dataset.file_name ).read() )
             except Exception, e:
                 log.warning( 'Error reading DataManagerTool json for "%s": %s'  % ( output_name, e ) )
                 continue
diff --git a/lib/galaxy/tools/genome_index/__init__.py b/lib/galaxy/tools/genome_index/__init__.py
index 80b2287fba8..0fb36f7be4a 100644
--- a/lib/galaxy/tools/genome_index/__init__.py
+++ b/lib/galaxy/tools/genome_index/__init__.py
@@ -1,6 +1,11 @@
 from __future__ import with_statement
 
-import os, shutil, logging, tempfile, tarfile
+import json
+import logging
+import os
+import shutil
+import tarfile
+import tempfile
 
 from galaxy import model, util
 from galaxy.web.framework.helpers import to_unicode
@@ -9,9 +14,6 @@ from galaxy.util.json import *
 from galaxy.web.base.controller import UsesHistoryMixin
 from galaxy.tools.data import ToolDataTableManager
 
-import pkg_resources
-pkg_resources.require("simplejson")
-import simplejson
 
 log = logging.getLogger(__name__)
 
@@ -74,7 +76,7 @@ class GenomeIndexToolWrapper( object ):
             fp = open( gitd.dataset.get_file_name(), 'r' )
             deferred = sa_session.query( model.DeferredJob ).filter_by( id=gitd.deferred_job_id ).first()
             try:
-                logloc = simplejson.load( fp )
+                logloc = json.load( fp )
             except ValueError:
                 deferred.state = app.model.DeferredJob.states.ERROR
                 sa_session.add( deferred )
diff --git a/lib/galaxy/tools/genome_index/index_genome.py b/lib/galaxy/tools/genome_index/index_genome.py
index 7c7017a9966..fa10450059c 100644
--- a/lib/galaxy/tools/genome_index/index_genome.py
+++ b/lib/galaxy/tools/genome_index/index_genome.py
@@ -7,11 +7,17 @@ usage: %prog history_attrs dataset_attrs job_attrs out_file
 """
 from __future__ import with_statement
 
-import optparse, sys, os, tempfile, time, subprocess, shlex, tarfile, shutil
+import json
+import optparse
+import os
+import shlex
+import shutil
+import subprocess
+import sys
+import tarfile
+import tempfile
+import time
 
-import pkg_resources
-pkg_resources.require("simplejson")
-import simplejson
 
 class ManagedIndexer():
     def __init__( self, output_file, infile, workingdir, rsync_url, tooldata ):
@@ -76,7 +82,7 @@ class ManagedIndexer():
         return result
 
     def _flush_files( self ):
-        simplejson.dump( self.locations, self.outfile )
+        json.dump( self.locations, self.outfile )
         self.outfile.close()
         self.logfile.close()
 
@@ -318,4 +324,4 @@ if __name__ == "__main__":
     returncode = idxobj.run_indexer( indexer )
     if not returncode:
         exit(1)
-    exit(0)
\ No newline at end of file
+    exit(0)
diff --git a/lib/galaxy/tools/imp_exp/__init__.py b/lib/galaxy/tools/imp_exp/__init__.py
index 2639a3fa78d..6b7f8a954bb 100644
--- a/lib/galaxy/tools/imp_exp/__init__.py
+++ b/lib/galaxy/tools/imp_exp/__init__.py
@@ -1,4 +1,4 @@
-import os, shutil, logging, tempfile, simplejson
+import os, shutil, logging, tempfile, json
 from galaxy import model
 from galaxy.tools.parameters.basic import UnvalidatedValue
 from galaxy.web.framework.helpers import to_unicode
@@ -226,13 +226,13 @@ class JobImportHistoryArchiveWrapper( object, UsesHistoryMixin, UsesAnnotations
                     self.sa_session.add( imported_job )
                     self.sa_session.flush()
 
-                    class HistoryDatasetAssociationIDEncoder( simplejson.JSONEncoder ):
+                    class HistoryDatasetAssociationIDEncoder( json.JSONEncoder ):
                         """ Custom JSONEncoder for a HistoryDatasetAssociation that encodes an HDA as its ID. """
                         def default( self, obj ):
                             """ Encode an HDA, default encoding for everything else. """
                             if isinstance( obj, model.HistoryDatasetAssociation ):
                                 return obj.id
-                            return simplejson.JSONEncoder.default( self, obj )
+                            return json.JSONEncoder.default( self, obj )
 
                     # Set parameters. May be useful to look at metadata.py for creating parameters.
                     # TODO: there may be a better way to set parameters, e.g.:
@@ -311,7 +311,7 @@ class JobExportHistoryArchiveWrapper( object, UsesHistoryMixin, UsesAnnotations
                     del metadata[ name ]
             return metadata
 
-        class HistoryDatasetAssociationEncoder( simplejson.JSONEncoder ):
+        class HistoryDatasetAssociationEncoder( json.JSONEncoder ):
             """ Custom JSONEncoder for a HistoryDatasetAssociation. """
             def default( self, obj ):
                 """ Encode an HDA, default encoding for everything else. """
@@ -337,7 +337,7 @@ class JobExportHistoryArchiveWrapper( object, UsesHistoryMixin, UsesAnnotations
                     }
                 if isinstance( obj, UnvalidatedValue ):
                     return obj.__str__()
-                return simplejson.JSONEncoder.default( self, obj )
+                return json.JSONEncoder.default( self, obj )
 
         #
         # Create attributes/metadata files for export.
diff --git a/lib/galaxy/util/__init__.py b/lib/galaxy/util/__init__.py
index 2d116466d3e..1790a92e19a 100644
--- a/lib/galaxy/util/__init__.py
+++ b/lib/galaxy/util/__init__.py
@@ -2,7 +2,26 @@
 Utility functions used systemwide.
 
 """
-import binascii, errno, grp, logging, os, pickle, random, re, shutil, smtplib, stat, string, sys, tempfile, threading
+
+from __future__ import absolute_import
+
+import binascii
+import errno
+import grp
+import json
+import logging
+import os
+import pickle
+import random
+import re
+import shutil
+import smtplib
+import stat
+import string
+import sys
+import tempfile
+import threading
+
 from email.MIMEText import MIMEText
 
 from os.path import relpath
@@ -21,12 +40,9 @@ from elementtree import ElementTree, ElementInclude
 eggs.require( "wchartype" )
 import wchartype
 
-from inflection import Inflector, English
+from .inflection import Inflector, English
 inflector = Inflector(English)
 
-eggs.require( "simplejson" )
-import simplejson
-
 log   = logging.getLogger(__name__)
 _lock = threading.RLock()
 
@@ -292,8 +308,8 @@ def shrink_string_by_size( value, size, join_by="..", left_larger=True, beginnin
 
 def pretty_print_json(json_data, is_json_string=False):
     if is_json_string:
-        json_data = simplejson.loads(json_data)
-    return simplejson.dumps(json_data, sort_keys=True, indent=4 * ' ')
+        json_data = json.loads(json_data)
+    return json.dumps(json_data, sort_keys=True, indent=4 * ' ')
 
 # characters that are valid
 valid_chars  = set(string.letters + string.digits + " -=_.()/+*^,:?!")
diff --git a/lib/galaxy/util/json.py b/lib/galaxy/util/json.py
index 5219a44f52a..7e7d5ba2368 100644
--- a/lib/galaxy/util/json.py
+++ b/lib/galaxy/util/json.py
@@ -1,16 +1,15 @@
+from __future__ import absolute_import
 
 __all__ = [ "to_json_string", "from_json_string", "json_fix", "validate_jsonrpc_request", "validate_jsonrpc_response", "jsonrpc_request", "jsonrpc_response" ]
 
-import random, string, logging
+import json
+import logging
+import random
 import socket
+import string
 
-import pkg_resources
-pkg_resources.require( "simplejson" )
-
-import simplejson
-
-to_json_string = simplejson.dumps
-from_json_string = simplejson.loads
+to_json_string = json.dumps
+from_json_string = json.loads
 
 log = logging.getLogger( __name__ )
 
diff --git a/lib/galaxy/visualization/data_providers/phyloviz/baseparser.py b/lib/galaxy/visualization/data_providers/phyloviz/baseparser.py
index 0abcafd2f6d..f44d3606a17 100644
--- a/lib/galaxy/visualization/data_providers/phyloviz/baseparser.py
+++ b/lib/galaxy/visualization/data_providers/phyloviz/baseparser.py
@@ -1,6 +1,4 @@
-import pkg_resources
-pkg_resources.require("simplejson")
-import simplejson
+import json
 
 class Node(object):
     """Node class of PhyloTree, which represents a CLAUDE in a phylogenetic tree"""
@@ -118,7 +116,7 @@ class Base_Parser(object):
 
     def toJson(self, jsonDict):
         """Convenience method to get a json string from a python json dict"""
-        return simplejson.dumps(jsonDict)
+        return json.dumps(jsonDict)
 
     def _writeJsonToFile(self, filepath, json):
         """Writes the file out to the system"""
diff --git a/lib/galaxy/web/framework/__init__.py b/lib/galaxy/web/framework/__init__.py
index 7a019b7efcd..4432d743924 100644
--- a/lib/galaxy/web/framework/__init__.py
+++ b/lib/galaxy/web/framework/__init__.py
@@ -2,6 +2,7 @@
 Galaxy web application framework
 """
 
+import hashlib
 import inspect
 import os
 import pkg_resources
@@ -9,27 +10,24 @@ import random
 import socket
 import string
 import time
-import hashlib
-from Cookie import CookieError
 
+from functools import wraps
+from Cookie import CookieError
 
 pkg_resources.require( "Cheetah" )
 from Cheetah.Template import Template
+
+#TODO: Relative imports to be removed
 import base
-from functools import wraps
-from galaxy import util
-from galaxy.exceptions import MessageException
-from galaxy.util.json import to_json_string, from_json_string
-from galaxy.util.backports.importlib import import_module
-from galaxy.util.sanitize_html import sanitize_html
-from galaxy.util import safe_str_cmp
-
-pkg_resources.require( "simplejson" )
-import simplejson
-
 import helpers
 
+from galaxy import util
+from galaxy.exceptions import MessageException
 from galaxy.util import asbool
+from galaxy.util import safe_str_cmp
+from galaxy.util.backports.importlib import import_module
+from galaxy.util.json import from_json_string, to_json_string
+from galaxy.util.sanitize_html import sanitize_html
 
 import paste.httpexceptions
 
@@ -76,7 +74,7 @@ def json( func ):
     @wraps(func)
     def decorator( self, trans, *args, **kwargs ):
         trans.response.set_content_type( "text/javascript" )
-        return simplejson.dumps( func( self, trans, *args, **kwargs ) )
+        return to_json_string( func( self, trans, *args, **kwargs ) )
     if not hasattr(func, '_orig'):
         decorator._orig = func
     decorator.exposed = True
@@ -86,7 +84,7 @@ def json_pretty( func ):
     @wraps(func)
     def decorator( self, trans, *args, **kwargs ):
         trans.response.set_content_type( "text/javascript" )
-        return simplejson.dumps( func( self, trans, *args, **kwargs ), indent=4, sort_keys=True )
+        return to_json_string( func( self, trans, *args, **kwargs ), indent=4, sort_keys=True )
     if not hasattr(func, '_orig'):
         decorator._orig = func
     decorator.exposed = True
@@ -158,7 +156,7 @@ def expose_api( func, to_json=True, user_required=True ):
                     for k, v in payload.iteritems():
                         if isinstance(v, (str, unicode)):
                             try:
-                                payload[k] = simplejson.loads(v)
+                                payload[k] = from_json_string(v)
                             except:
                                 # may not actually be json, just continue
                                 pass
@@ -167,7 +165,7 @@ def expose_api( func, to_json=True, user_required=True ):
                     # Assume application/json content type and parse request body manually, since wsgi won't do it. However, the order of this check
                     # should ideally be in reverse, with the if clause being a check for application/json and the else clause assuming a standard encoding
                     # such as multipart/form-data. Leaving it as is for backward compatibility, just in case.
-                    payload = util.recursively_stringify_dictionary_keys( simplejson.loads( trans.request.body ) )
+                    payload = util.recursively_stringify_dictionary_keys( from_json_string( trans.request.body ) )
                 return payload
             try:
                 kwargs['payload'] = extract_payload_from_request(trans, func, kwargs)
@@ -198,9 +196,9 @@ def expose_api( func, to_json=True, user_required=True ):
         try:
             rval = func( self, trans, *args, **kwargs)
             if to_json and trans.debug:
-                rval = simplejson.dumps( rval, indent=4, sort_keys=True )
+                rval = to_json_string( rval, indent=4, sort_keys=True )
             elif to_json:
-                rval = simplejson.dumps( rval )
+                rval = to_json_string( rval )
             return rval
         except paste.httpexceptions.HTTPException:
             raise # handled
diff --git a/lib/galaxy/webapps/demo_sequencer/framework/__init__.py b/lib/galaxy/webapps/demo_sequencer/framework/__init__.py
index 54cc7e121cf..b2d563fca00 100644
--- a/lib/galaxy/webapps/demo_sequencer/framework/__init__.py
+++ b/lib/galaxy/webapps/demo_sequencer/framework/__init__.py
@@ -2,9 +2,15 @@
 Demo sequencer web application framework
 """
 
+import json
+import os
 import pkg_resources
+import random
+import socket
+import string
+import sys
+import time
 
-import os, sys, time, socket, random, string
 pkg_resources.require( "Cheetah" )
 from Cheetah.Template import Template
 
@@ -19,9 +25,6 @@ import galaxy.web.framework.base
 
 from galaxy.util import asbool
 
-pkg_resources.require( "simplejson" )
-import simplejson
-
 pkg_resources.require( "Mako" )
 import mako.template
 import mako.lookup
diff --git a/lib/galaxy/webapps/galaxy/controllers/data_admin.py b/lib/galaxy/webapps/galaxy/controllers/data_admin.py
index 82762f1d068..59f36f2c808 100644
--- a/lib/galaxy/webapps/galaxy/controllers/data_admin.py
+++ b/lib/galaxy/webapps/galaxy/controllers/data_admin.py
@@ -1,14 +1,13 @@
-import sys, ftplib
+import ftplib
+import json
+import sys
 from galaxy import model, util
 from galaxy.jobs import transfer_manager
-from galaxy.web.base.controller import *
-from galaxy.web.framework.helpers import time_ago, iff, grids
 from galaxy.model.orm import *
+from galaxy.web.base.controller import *
+from galaxy.web.framework.helpers import grids, iff, time_ago
 from library_common import get_comptypes, lucene_search, whoosh_search
 
-import pkg_resources
-pkg_resources.require("simplejson")
-import simplejson
 
 # Older py compatibility
 try:
@@ -161,7 +160,7 @@ class DataAdmin( BaseUIController ):
         gname = deferred.params[ 'intname' ]
         indexers = ', '.join( deferred.params[ 'indexes' ] )
         jobs = self._get_jobs( deferred, trans )
-        jsonjobs = simplejson.dumps( jobs )
+        jsonjobs = json.dumps( jobs )
         return trans.fill_template( '/admin/data_admin/download_status.mako', name=gname, indexers=indexers, mainjob=jobid, jobs=jobs, jsonjobs=jsonjobs )
 
     @web.expose
@@ -173,7 +172,7 @@ class DataAdmin( BaseUIController ):
         jobid = params.get( 'jobid', '' )
         job = sa_session.query( model.DeferredJob ).filter_by( id=jobid ).first()
         jobs = self._get_jobs( job, trans )
-        return trans.fill_template( '/admin/data_admin/ajax_status.mako', json=simplejson.dumps( jobs ) )
+        return trans.fill_template( '/admin/data_admin/ajax_status.mako', json=json.dumps( jobs ) )
 
     def _get_job( self, jobid, jobtype, trans ):
         sa = trans.app.model.context.current
@@ -297,4 +296,4 @@ def build_param_dict( params, trans ):
 
     params = dict( status='ok', dbkey=dbkey, datatype='fasta', url=url, user=trans.user.id, liftover=newlift, longname=longname, indexers=indexers )
 
-    return params
\ No newline at end of file
+    return params
diff --git a/lib/galaxy/webapps/galaxy/controllers/root.py b/lib/galaxy/webapps/galaxy/controllers/root.py
index 3a4ac83bc45..78468b9f33b 100644
--- a/lib/galaxy/webapps/galaxy/controllers/root.py
+++ b/lib/galaxy/webapps/galaxy/controllers/root.py
@@ -508,7 +508,7 @@ class RootController( BaseUIController, UsesHistoryMixin, UsesHistoryDatasetAsso
         Attempts to parse values passed as boolean, float, then int. Defaults
         to string. Non-recursive (will not parse lists).
         """
-        #TODO: use simplejson or json
+        #TODO: use json
         rval = {}
         for k in kwd:
             rval[ k ] = kwd[k]
diff --git a/lib/galaxy/webapps/galaxy/controllers/workflow.py b/lib/galaxy/webapps/galaxy/controllers/workflow.py
index c4477535f7e..14b1ab0345a 100644
--- a/lib/galaxy/webapps/galaxy/controllers/workflow.py
+++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py
@@ -1,13 +1,12 @@
 import pkg_resources
-pkg_resources.require( "simplejson" )
 pkg_resources.require( "SVGFig" )
 
 import base64
 import httplib
+import json
 import math
 import os
 import sgmllib
-import simplejson
 import svgfig
 import urllib2
 
@@ -20,17 +19,17 @@ from galaxy import util
 from galaxy import web
 from galaxy.datatypes.data import Data
 from galaxy.jobs.actions.post import ActionBox
+from galaxy.model.item_attrs import UsesAnnotations, UsesItemRatings
 from galaxy.model.mapping import desc
 from galaxy.tools.parameters import RuntimeValue, visit_input_values
 from galaxy.tools.parameters.basic import DataToolParameter, DrillDownSelectToolParameter, SelectToolParameter, UnvalidatedValue
 from galaxy.tools.parameters.grouping import Conditional, Repeat
-from galaxy.util.odict import odict
 from galaxy.util.json import to_json_string
+from galaxy.util.odict import odict
 from galaxy.util.sanitize_html import sanitize_html
 from galaxy.util.topsort import CycleError, topsort, topsort_levels
 from galaxy.web import error, url_for
 from galaxy.web.base.controller import BaseUIController, SharableMixin, UsesStoredWorkflowMixin
-from galaxy.model.item_attrs import UsesAnnotations, UsesItemRatings
 from galaxy.web.framework import form
 from galaxy.web.framework.helpers import grids, time_ago
 from galaxy.web.framework.helpers import to_unicode
@@ -812,7 +811,7 @@ class WorkflowController( BaseUIController, SharableMixin, UsesStoredWorkflowMix
         # Put parameters in workflow mode
         trans.workflow_building_mode = True
         # Convert incoming workflow data from json
-        data = simplejson.loads( workflow_data )
+        data = json.loads( workflow_data )
         # Create new workflow from incoming data
         workflow = model.Workflow()
         # Just keep the last name (user can rename later)
@@ -920,7 +919,7 @@ class WorkflowController( BaseUIController, SharableMixin, UsesStoredWorkflowMix
         #
 
         # Create workflow content JSON.
-        workflow_content = simplejson.dumps( workflow_dict, indent=4, sort_keys=True )
+        workflow_content = json.dumps( workflow_dict, indent=4, sort_keys=True )
 
         # Create myExperiment request.
         request_raw = trans.fill_template( "workflow/myexp_export.mako", \
@@ -1073,7 +1072,7 @@ class WorkflowController( BaseUIController, SharableMixin, UsesStoredWorkflowMix
             if workflow_data:
                 # Convert incoming workflow data from json
                 try:
-                    data = simplejson.loads( workflow_data )
+                    data = json.loads( workflow_data )
                 except Exception, e:
                     data = None
                     message = "The data content does not appear to be a Galaxy workflow.<br/>Exception: %s" % str( e )
@@ -1294,7 +1293,7 @@ class WorkflowController( BaseUIController, SharableMixin, UsesStoredWorkflowMix
         # It is possible for a workflow to have 0 steps
         if len( workflow.steps ) == 0:
             error( "Workflow cannot be run because it does not have any steps" )
-        #workflow = Workflow.from_simple( simplejson.loads( stored.encoded_value ), trans.app )
+        #workflow = Workflow.from_simple( json.loads( stored.encoded_value ), trans.app )
         if workflow.has_cycles:
             error( "Workflow cannot be run because it contains cycles" )
         if workflow.has_errors:
diff --git a/lib/tool_shed/scripts/api/common.py b/lib/tool_shed/scripts/api/common.py
index 56f42de4298..9ed77d7c5aa 100644
--- a/lib/tool_shed/scripts/api/common.py
+++ b/lib/tool_shed/scripts/api/common.py
@@ -1,4 +1,8 @@
-import os, sys, urllib, urllib2
+import json
+import os
+import sys
+import urllib
+import urllib2
 
 new_path = [ os.path.join( os.path.dirname( __file__ ), '..', '..', '..', '..', 'lib' ) ]
 new_path.extend( sys.path[ 1: ] )
@@ -7,9 +11,6 @@ sys.path = new_path
 from galaxy import eggs
 import pkg_resources
 
-pkg_resources.require( "simplejson" )
-import simplejson
-
 pkg_resources.require( "pycrypto" )
 from Crypto.Cipher import Blowfish
 from Crypto.Util.randpool import RandomPool
@@ -29,9 +30,9 @@ def delete( api_key, url, data, return_formatted=True ):
     # Sends an API DELETE request and acts as a generic formatter for the JSON response - 'data' will become the JSON payload read by Galaxy.
     try:
         url = make_url( api_key, url )
-        req = urllib2.Request( url, headers = { 'Content-Type': 'application/json' }, data = simplejson.dumps( data ))
+        req = urllib2.Request( url, headers = { 'Content-Type': 'application/json' }, data = json.dumps( data ))
         req.get_method = lambda: 'DELETE'
-        r = simplejson.loads( urllib2.urlopen( req ).read() )
+        r = json.loads( urllib2.urlopen( req ).read() )
     except urllib2.HTTPError, e:
         if return_formatted:
             print e
@@ -86,8 +87,8 @@ def get( url, api_key=None ):
     # Do the actual GET.
     url = make_url( url, api_key=api_key )
     try:
-        return simplejson.loads( urllib2.urlopen( url ).read() )
-    except simplejson.decoder.JSONDecodeError, e:
+        return json.loads( urllib2.urlopen( url ).read() )
+    except ValueError, e:
         print "URL did not return JSON data"
         sys.exit(1)
 
@@ -106,15 +107,15 @@ def make_url( url, api_key=None, args=None ):
 def post( url, data, api_key=None ):
     # Do the actual POST.
     url = make_url( url, api_key=api_key )
-    req = urllib2.Request( url, headers = { 'Content-Type': 'application/json' }, data = simplejson.dumps( data ) )
-    return simplejson.loads( urllib2.urlopen( req ).read() )
+    req = urllib2.Request( url, headers = { 'Content-Type': 'application/json' }, data = json.dumps( data ) )
+    return json.loads( urllib2.urlopen( req ).read() )
 
 def put( url, data, api_key=None ):
     # Do the actual PUT.
     url = make_url( url, api_key=api_key )
-    req = urllib2.Request( url, headers = { 'Content-Type': 'application/json' }, data = simplejson.dumps( data ))
+    req = urllib2.Request( url, headers = { 'Content-Type': 'application/json' }, data = json.dumps( data ))
     req.get_method = lambda: 'PUT'
-    return simplejson.loads( urllib2.urlopen( req ).read() )
+    return json.loads( urllib2.urlopen( req ).read() )
 
 def submit( url, data, api_key=None, return_formatted=True ):
     # Sends an API POST request and acts as a generic formatter for the JSON response - 'data' will become the JSON payload read by Galaxy.
diff --git a/lib/tool_shed/scripts/api/tool_shed_repository_revision_update.py b/lib/tool_shed/scripts/api/tool_shed_repository_revision_update.py
index 16a38bd65b2..322027aaa02 100755
--- a/lib/tool_shed/scripts/api/tool_shed_repository_revision_update.py
+++ b/lib/tool_shed/scripts/api/tool_shed_repository_revision_update.py
@@ -5,17 +5,16 @@ PUT/update script to update appropriate values in a repository_metadata table re
 usage: tool_shed_repository_revision_update.py key url key1=value1 key2=value2 ...
 """
 
-import os, sys
+import json
+import os
+import sys
+
 sys.path.insert( 0, os.path.dirname( __file__ ) )
 from common import update
 
-import pkg_resources
-pkg_resources.require( "simplejson" )
 
-import simplejson
-
-to_json_string = simplejson.dumps
-from_json_string = simplejson.loads
+to_json_string = json.dumps
+from_json_string = json.loads
 
 data = {}
 for key, value in [ kwarg.split( '=', 1 ) for kwarg in sys.argv[ 3: ] ]:
diff --git a/lib/tool_shed/util/encoding_util.py b/lib/tool_shed/util/encoding_util.py
index 6b7c12c1ff9..92e53a21e0e 100644
--- a/lib/tool_shed/util/encoding_util.py
+++ b/lib/tool_shed/util/encoding_util.py
@@ -1,14 +1,10 @@
 import binascii
+import json
 import logging
 from galaxy import eggs
 from galaxy.util.hash_util import hmac_new
 from galaxy.util.json import json_fix
 
-import pkg_resources
-
-pkg_resources.require( "simplejson" )
-import simplejson
-
 log = logging.getLogger( __name__ )
 
 encoding_sep = '__esep__'
@@ -23,7 +19,7 @@ def tool_shed_decode( value ):
     # Restore from string
     values = None
     try:
-        values = simplejson.loads( value )
+        values = json.loads( value )
     except Exception, e:
         #log.debug( "Decoding json value from tool shed for value '%s' threw exception: %s" % ( str( value ), str( e ) ) )
         pass
@@ -39,7 +35,7 @@ def tool_shed_decode( value ):
 
 def tool_shed_encode( val ):
     if isinstance( val, dict ):
-        value = simplejson.dumps( val )
+        value = json.dumps( val )
     else:
         value = val
     a = hmac_new( 'ToolShedAndGalaxyMustHaveThisSameKey', value )
diff --git a/scripts/api/common.py b/scripts/api/common.py
index b39a0b136a2..fd240a5d0cf 100644
--- a/scripts/api/common.py
+++ b/scripts/api/common.py
@@ -1,3 +1,4 @@
+import json
 import logging
 import os
 import sys
@@ -10,9 +11,6 @@ sys.path = new_path
 from galaxy import eggs
 import pkg_resources
 
-pkg_resources.require( "simplejson" )
-import simplejson
-
 pkg_resources.require( "pycrypto" )
 from Crypto.Cipher import Blowfish
 from Crypto.Util.randpool import RandomPool
@@ -35,30 +33,30 @@ def get( api_key, url ):
     # Do the actual GET.
     url = make_url( api_key, url )
     try:
-        return simplejson.loads( urllib2.urlopen( url ).read() )
-    except simplejson.decoder.JSONDecodeError, e:
+        return json.loads( urllib2.urlopen( url ).read() )
+    except json.decoder.JSONDecodeError, e:
         print "URL did not return JSON data"
         sys.exit(1)
 
 def post( api_key, url, data ):
     # Do the actual POST.
     url = make_url( api_key, url )
-    req = urllib2.Request( url, headers = { 'Content-Type': 'application/json' }, data = simplejson.dumps( data ) )
-    return simplejson.loads( urllib2.urlopen( req ).read() )
+    req = urllib2.Request( url, headers = { 'Content-Type': 'application/json' }, data = json.dumps( data ) )
+    return json.loads( urllib2.urlopen( req ).read() )
 
 def put( api_key, url, data ):
     # Do the actual PUT
     url = make_url( api_key, url )
-    req = urllib2.Request( url, headers = { 'Content-Type': 'application/json' }, data = simplejson.dumps( data ))
+    req = urllib2.Request( url, headers = { 'Content-Type': 'application/json' }, data = json.dumps( data ))
     req.get_method = lambda: 'PUT'
-    return simplejson.loads( urllib2.urlopen( req ).read() )
+    return json.loads( urllib2.urlopen( req ).read() )
 
 def __del( api_key, url, data ):
     # Do the actual DELETE
     url = make_url( api_key, url )
-    req = urllib2.Request( url, headers = { 'Content-Type': 'application/json' }, data = simplejson.dumps( data ))
+    req = urllib2.Request( url, headers = { 'Content-Type': 'application/json' }, data = json.dumps( data ))
     req.get_method = lambda: 'DELETE'
-    return simplejson.loads( urllib2.urlopen( req ).read() )
+    return json.loads( urllib2.urlopen( req ).read() )
 
 
 def display( api_key, url, return_formatted=True ):
diff --git a/scripts/api/workflow_import_from_file_rpark.py b/scripts/api/workflow_import_from_file_rpark.py
index 3443d3989fa..d1c8ad0af6a 100644
--- a/scripts/api/workflow_import_from_file_rpark.py
+++ b/scripts/api/workflow_import_from_file_rpark.py
@@ -11,11 +11,11 @@ sys.path.insert( 0, os.path.dirname( __file__ ) )
 from common import submit
 
 ### Rpark edit ###
-import simplejson
+import json
 
 def openWorkflow(in_file):        
     with open(in_file) as f:
-        temp_data = simplejson.load(f)
+        temp_data = json.load(f)
     return temp_data;
 
 
diff --git a/scripts/drmaa_external_killer.py b/scripts/drmaa_external_killer.py
index 98320ce2540..37c7ebe004f 100755
--- a/scripts/drmaa_external_killer.py
+++ b/scripts/drmaa_external_killer.py
@@ -4,10 +4,11 @@
 Terminates a DRMAA job if given a job id and (appropriate) user id.
 """
 
-import os
-import sys
 import errno
+import json
+import os
 import pwd
+import sys
 #import drmaa
 new_path = [ os.path.join( os.getcwd(), "lib" ) ]
 new_path.extend( sys.path[1:] ) # remove scripts/ from the path
@@ -15,8 +16,6 @@ sys.path = new_path
 
 from galaxy import eggs
 import pkg_resources
-pkg_resources.require("simplejson")
-import simplejson as json
 pkg_resources.require("drmaa")
 import drmaa
 
diff --git a/scripts/drmaa_external_runner.py b/scripts/drmaa_external_runner.py
index bead083fdf5..7653654a1c1 100755
--- a/scripts/drmaa_external_runner.py
+++ b/scripts/drmaa_external_runner.py
@@ -10,8 +10,8 @@ import os
 import sys
 import errno
 import pwd
+import json
 
-#import simplejson as json
 #import drmaa
 new_path = [ os.path.join( os.getcwd(), "lib" ) ]
 new_path.extend( sys.path[1:] )  # remove scripts/ from the path
@@ -19,8 +19,6 @@ sys.path = new_path
 
 from galaxy import eggs
 import pkg_resources
-pkg_resources.require("simplejson")
-import simplejson as json
 pkg_resources.require("drmaa")
 import drmaa
 
diff --git a/scripts/external_chown_script.py b/scripts/external_chown_script.py
index ce0e268a454..b53c97ea457 100755
--- a/scripts/external_chown_script.py
+++ b/scripts/external_chown_script.py
@@ -1,17 +1,17 @@
 #!/usr/bin/env python
-import os
-import sys
 import errno
+import json
+import os
 import pwd
+import sys
 #import drmaa
+
 new_path = [ os.path.join( os.getcwd(), "lib" ) ]
 new_path.extend( sys.path[1:] ) # remove scripts/ from the path
 sys.path = new_path
 
 from galaxy import eggs
 import pkg_resources
-pkg_resources.require("simplejson")
-import simplejson as json
 pkg_resources.require("drmaa")
 import drmaa
 
diff --git a/scripts/extract_dataset_part.py b/scripts/extract_dataset_part.py
index 862cb8f40cb..05c57cf5ef6 100644
--- a/scripts/extract_dataset_part.py
+++ b/scripts/extract_dataset_part.py
@@ -6,9 +6,10 @@ Used by jobs that split large files into pieces to be processed concurrently
 on a gid in a scatter-gather mode. This does part of the scatter.
 
 """
+import json
+import logging
 import os
 import sys
-import logging
 logging.basicConfig()
 log = logging.getLogger( __name__ )
 
@@ -16,11 +17,6 @@ new_path = [ os.path.join( os.getcwd(), "lib" ) ]
 new_path.extend( sys.path[1:] ) # remove scripts/ from the path
 sys.path = new_path
 
-from galaxy import eggs
-import pkg_resources
-pkg_resources.require("simplejson")
-import simplejson
-
 # This junk is here to prevent loading errors
 import galaxy.model.mapping #need to load this before we unpickle, in order to setup properties assigned by the mappers
 galaxy.model.Job() #this looks REAL stupid, but it is REQUIRED in order for SA to insert parameters into the classes defined by the mappers --> it appears that instantiating ANY mapper'ed class would suffice here
@@ -33,7 +29,7 @@ def __main__():
     if not os.path.isfile(file_path):
         #Nothing to do - some splitters don't write a JSON file
         sys.exit(0)
-    data = simplejson.load(open(file_path, 'r'))
+    data = json.load(open(file_path, 'r'))
     try:
         class_name_parts = data['class_name'].split('.')
         module_name = '.'.join(class_name_parts[:-1])
diff --git a/scripts/galaxy_messaging/server/data_transfer.py b/scripts/galaxy_messaging/server/data_transfer.py
index 619100a676d..6eb90b95348 100755
--- a/scripts/galaxy_messaging/server/data_transfer.py
+++ b/scripts/galaxy_messaging/server/data_transfer.py
@@ -13,12 +13,21 @@ python data_transfer.py <config_file>
 
 """
 import ConfigParser
-import sys, os, time, traceback
+import cookielib
+import datetime
+import logging
 import optparse
-import urllib,urllib2, cookielib, shutil
-import logging, time, datetime
+import os
+import shutil
+import sys
+import time
+import time
+import traceback
+import urllib
+import urllib2
 import xml.dom.minidom
 
+
 from xml_helper import get_value, get_value_index
 
 log = logging.getLogger( "datatx_" + str( os.getpid() ) )
@@ -39,14 +48,11 @@ new_path.extend( sys.path[1:] ) # remove scripts/ from the path
 sys.path = new_path
 
 from galaxy import eggs
-from galaxy.util.json import from_json_string, to_json_string
 from galaxy.model import SampleDataset
 from galaxy.web.api.samples import SamplesAPIController
 import pkg_resources
 pkg_resources.require( "pexpect" )
 import pexpect
-pkg_resources.require( "simplejson" )
-import simplejson
 
 log.debug(str(dir(api)))
 
diff --git a/scripts/set_metadata.py b/scripts/set_metadata.py
index fdeb2b0da09..711b02f3de5 100644
--- a/scripts/set_metadata.py
+++ b/scripts/set_metadata.py
@@ -10,9 +10,11 @@ import logging
 logging.basicConfig()
 log = logging.getLogger( __name__ )
 
+import cPickle
+import json
 import os
 import sys
-import cPickle
+
 # ensure supported version
 from check_python import check_python
 try:
@@ -26,8 +28,6 @@ sys.path = new_path
 
 from galaxy import eggs
 import pkg_resources
-pkg_resources.require("simplejson")
-import simplejson
 import galaxy.model.mapping  # need to load this before we unpickle, in order to setup properties assigned by the mappers
 galaxy.model.Job()  # this looks REAL stupid, but it is REQUIRED in order for SA to insert parameters into the classes defined by the mappers --> it appears that instantiating ANY mapper'ed class would suffice here
 from galaxy.util import stringify_dictionary_keys
@@ -107,17 +107,17 @@ def __main__():
                 dataset.extension = ext_override[ dataset.dataset.id ]
             # Metadata FileParameter types may not be writable on a cluster node, and are therefore temporarily substituted with MetadataTempFiles
             if override_metadata:
-                override_metadata = simplejson.load( open( override_metadata ) )
+                override_metadata = json.load( open( override_metadata ) )
                 for metadata_name, metadata_file_override in override_metadata:
                     if galaxy.datatypes.metadata.MetadataTempFile.is_JSONified_value( metadata_file_override ):
                         metadata_file_override = galaxy.datatypes.metadata.MetadataTempFile.from_JSON( metadata_file_override )
                     setattr( dataset.metadata, metadata_name, metadata_file_override )
-            kwds = stringify_dictionary_keys( simplejson.load( open( filename_kwds ) ) )  # load kwds; need to ensure our keywords are not unicode
+            kwds = stringify_dictionary_keys( json.load( open( filename_kwds ) ) )  # load kwds; need to ensure our keywords are not unicode
             dataset.datatype.set_meta( dataset, **kwds )
             dataset.metadata.to_JSON_dict( filename_out )  # write out results of set_meta
-            simplejson.dump( ( True, 'Metadata has been set successfully' ), open( filename_results_code, 'wb+' ) )  # setting metadata has succeeded
+            json.dump( ( True, 'Metadata has been set successfully' ), open( filename_results_code, 'wb+' ) )  # setting metadata has succeeded
         except Exception, e:
-            simplejson.dump( ( False, str( e ) ), open( filename_results_code, 'wb+' ) )  # setting metadata has failed somehow
+            json.dump( ( False, str( e ) ), open( filename_results_code, 'wb+' ) )  # setting metadata has failed somehow
     clear_mappers()
     # Shut down any additional threads that might have been created via the ObjectStore
     object_store.shutdown()
diff --git a/test/base/interactor.py b/test/base/interactor.py
index 9e8b9acebb8..95b3ca20656 100644
--- a/test/base/interactor.py
+++ b/test/base/interactor.py
@@ -5,7 +5,7 @@ from galaxy.util.odict import odict
 import galaxy.model
 from galaxy.model.orm import and_, desc
 from base.test_db_util import sa_session
-from simplejson import dumps, loads
+from json import dumps, loads
 
 from logging import getLogger
 log = getLogger( __name__ )
diff --git a/test/functional/test_workflow.py b/test/functional/test_workflow.py
index 93ce0e02afe..db2c88d292b 100644
--- a/test/functional/test_workflow.py
+++ b/test/functional/test_workflow.py
@@ -5,7 +5,7 @@ from base.interactor import GalaxyInteractorApi, stage_data_in_history
 
 from galaxy.util import parse_xml
 from galaxy.tools.test import parse_param_elem, require_file, test_data_iter, parse_output_elems
-from simplejson import load, dumps
+from json import load, dumps
 
 from logging import getLogger
 log = getLogger( __name__ )
diff --git a/test/tool_shed/base/twilltestcase.py b/test/tool_shed/base/twilltestcase.py
index f73419b23a8..4e282e6b215 100644
--- a/test/tool_shed/base/twilltestcase.py
+++ b/test/tool_shed/base/twilltestcase.py
@@ -3,7 +3,6 @@ import string
 import os
 import re
 import test_db_util
-import simplejson
 import shutil
 import logging
 import time
diff --git a/tools/filters/join.py b/tools/filters/join.py
index f2fa82cd076..db29cdca8c9 100644
--- a/tools/filters/join.py
+++ b/tools/filters/join.py
@@ -8,20 +8,15 @@ User can also opt to have have non-joining rows of file1 echoed.
 
 """
 
-import optparse, os, sys, tempfile, struct
+import json
+import optparse
+import os
 import psyco_full
-
-try:
-    simple_json_exception = None
-    from galaxy import eggs
-    from galaxy.util.bunch import Bunch
-    from galaxy.util import stringify_dictionary_keys
-    import pkg_resources
-    pkg_resources.require("simplejson")
-    import simplejson
-except Exception, e:
-    simplejson_exception = e
-    simplejson = None
+import struct
+import sys
+import tempfile
+from galaxy.util.bunch import Bunch
+from galaxy.util import stringify_dictionary_keys
 
 
 class OffsetList:
@@ -337,11 +332,9 @@ def main():
     fill_options = None
     if options.fill_options_file is not None:
         try:
-            if simplejson is None:
-                raise simplejson_exception
-            fill_options = Bunch( **stringify_dictionary_keys( simplejson.load( open( options.fill_options_file ) ) ) ) #simplejson.load( open( options.fill_options_file ) )
+            fill_options = Bunch( **stringify_dictionary_keys( json.load( open( options.fill_options_file ) ) ) ) #json.load( open( options.fill_options_file ) )
         except Exception, e:
-            print "Warning: Ignoring fill options due to simplejson error (%s)." % e
+            print "Warning: Ignoring fill options due to json error (%s)." % e
     if fill_options is None:
         fill_options = Bunch()
     if 'fill_unjoined_only' not in fill_options:
diff --git a/tools/filters/joiner.xml b/tools/filters/joiner.xml
index 757965118c0..953145f4594 100644
--- a/tools/filters/joiner.xml
+++ b/tools/filters/joiner.xml
@@ -51,7 +51,7 @@
   </inputs>
   <configfiles>
     <configfile name="fill_options_file">&lt;%
-import simplejson
+import json
 %&gt;
 #set $__fill_options = {}
 #if $fill_empty_columns['fill_empty_columns_switch'] == 'fill_empty':
@@ -72,7 +72,7 @@ import simplejson
         #end for
     #end if
 #end if
-${simplejson.dumps( __fill_options )}
+${json.dumps( __fill_options )}
     </configfile>
   </configfiles>
   <outputs>
diff --git a/tools/genomespace/genomespace_exporter.py b/tools/genomespace/genomespace_exporter.py
index 2ebebcf5a61..fc2a2a09ab1 100644
--- a/tools/genomespace/genomespace_exporter.py
+++ b/tools/genomespace/genomespace_exporter.py
@@ -1,12 +1,16 @@
 #Dan Blankenberg
 
-import optparse, os, urllib2, urllib, cookielib, hashlib, base64, cgi, binascii, logging
-
-from galaxy import eggs
-import pkg_resources
-
-pkg_resources.require( "simplejson" )
-import simplejson
+import base64
+import binascii
+import cgi
+import cookielib
+import hashlib
+import json
+import logging
+import optparse
+import os
+import urllib
+import urllib2
 
 log = logging.getLogger( "tools.genomespace.genomespace_exporter" )#( __name__ )
 
@@ -58,7 +62,7 @@ def get_directory( url_opener, dm_url, path ):
         dir_request = urllib2.Request( url, headers = { 'Content-Type': 'application/json', 'Accept': 'application/json' } )
         dir_request.get_method = lambda: 'GET'
         try:
-            dir_dict = simplejson.loads( url_opener.open( dir_request ).read() )
+            dir_dict = json.loads( url_opener.open( dir_request ).read() )
         except urllib2.HTTPError, e:
             #print "e", e, url #punting, assuming lack of permissions at this low of a level...
             continue
@@ -81,16 +85,16 @@ def create_directory( url_opener, directory_dict, new_dir, dm_url ):
         if dir_slice in ( '', '/', None ):
             continue
         url = '/'.join( ( directory_dict['url'], urllib.quote( dir_slice.replace( '/', '_' ), safe='' ) ) )
-        new_dir_request = urllib2.Request( url, headers = { 'Content-Type': 'application/json', 'Accept': 'application/json' }, data = simplejson.dumps( payload ) )
+        new_dir_request = urllib2.Request( url, headers = { 'Content-Type': 'application/json', 'Accept': 'application/json' }, data = json.dumps( payload ) )
         new_dir_request.get_method = lambda: 'PUT'
-        directory_dict = simplejson.loads( url_opener.open( new_dir_request ).read() )
+        directory_dict = json.loads( url_opener.open( new_dir_request ).read() )
     return directory_dict
 
 def get_genome_space_launch_apps( atm_url, url_opener, file_url, file_type ):
     gs_request = urllib2.Request( "%s/%s/webtool/descriptor" % ( atm_url, GENOMESPACE_API_VERSION_STRING ) )
     gs_request.get_method = lambda: 'GET'
     opened_gs_request = url_opener.open( gs_request )
-    webtool_descriptors = simplejson.loads( opened_gs_request.read() )
+    webtool_descriptors = json.loads( opened_gs_request.read() )
     webtools = []
     for webtool in webtool_descriptors:
         webtool_name = webtool.get( 'name' )
@@ -125,7 +129,7 @@ def galaxy_code_get_genomespace_folders( genomespace_site='prod', trans=None, va
         except urllib2.HTTPError, e:
             log.debug( 'GenomeSpace export tool failed reading a directory "%s": %s' % ( url, e ) )
             return #bad url, go to next
-        cur_directory = simplejson.loads( cur_directory )
+        cur_directory = json.loads( cur_directory )
         directory = cur_directory.get( 'directory', {} )
         contents = cur_directory.get( 'contents', [] )
         if directory.get( 'isDirectory', False ):
diff --git a/tools/genomespace/genomespace_file_browser.py b/tools/genomespace/genomespace_file_browser.py
index 002b72d90b9..7b1ce406ef0 100644
--- a/tools/genomespace/genomespace_file_browser.py
+++ b/tools/genomespace/genomespace_file_browser.py
@@ -1,12 +1,13 @@
 #Dan Blankenberg
 
-import optparse, os, urllib, urllib2, urlparse, cookielib
+import cookielib
+import json
+import optparse
+import os
+import urllib
+import urllib2
+import urlparse
 
-from galaxy import eggs
-import pkg_resources
-
-pkg_resources.require( "simplejson" )
-import simplejson
 
 GENOMESPACE_API_VERSION_STRING = "v1.0"
 GENOMESPACE_SERVER_URL_PROPERTIES = "https://dm.genomespace.org/config/%s/serverurl.properties" % ( GENOMESPACE_API_VERSION_STRING )
@@ -87,12 +88,12 @@ def set_genomespace_format_identifiers( url_opener, dm_site ):
     gs_request = urllib2.Request( "%s/%s/dataformat/list" % ( dm_site, GENOMESPACE_API_VERSION_STRING ) )
     gs_request.get_method = lambda: 'GET'
     opened_gs_request = url_opener.open( gs_request )
-    genomespace_formats = simplejson.loads( opened_gs_request.read() )
+    genomespace_formats = json.loads( opened_gs_request.read() )
     for format in genomespace_formats:
         GENOMESPACE_FORMAT_IDENTIFIER_TO_GENOMESPACE_EXT[ format['url'] ] = format['name']
 
 def download_from_genomespace_file_browser( json_parameter_file, genomespace_site ):
-    json_params = simplejson.loads( open( json_parameter_file, 'r' ).read() )
+    json_params = json.loads( open( json_parameter_file, 'r' ).read() )
     datasource_params = json_params.get( 'param_dict' )
     username = datasource_params.get( "gs-username", None )
     token = datasource_params.get( "gs-token", None )
@@ -150,14 +151,14 @@ def download_from_genomespace_file_browser( json_parameter_file, genomespace_sit
                 filename = "-%s" % filename
             used_filenames.append( filename )
             output_filename = os.path.join( datasource_params['__new_file_path__'],  'primary_%i_%s_visible_%s' % ( hda_id, filename, galaxy_ext ) )
-            metadata_parameter_file.write( "%s\n" % simplejson.dumps( dict( type = 'new_primary_dataset',
+            metadata_parameter_file.write( "%s\n" % json.dumps( dict( type = 'new_primary_dataset',
                                      base_dataset_id = dataset_id,
                                      ext = galaxy_ext,
                                      filename = output_filename,
                                      name = "GenomeSpace import on %s" % ( original_filename ) ) ) )
         else:
             if dataset_id is not None:
-               metadata_parameter_file.write( "%s\n" % simplejson.dumps( dict( type = 'dataset',
+               metadata_parameter_file.write( "%s\n" % json.dumps( dict( type = 'dataset',
                                      dataset_id = dataset_id,
                                      ext = galaxy_ext,
                                      name = "GenomeSpace import on %s" % ( filename ) ) ) )
diff --git a/tools/genomespace/genomespace_importer.py b/tools/genomespace/genomespace_importer.py
index 75977fc7363..ef467ff2469 100644
--- a/tools/genomespace/genomespace_importer.py
+++ b/tools/genomespace/genomespace_importer.py
@@ -1,12 +1,14 @@
 #Dan Blankenberg
 
-import optparse, os, urllib2, urllib, cookielib, urlparse, tempfile, shutil
-
-from galaxy import eggs
-import pkg_resources
-
-pkg_resources.require( "simplejson" )
-import simplejson
+import cookielib
+import json
+import optparse
+import os
+import shutil
+import tempfile
+import urllib
+import urllib2
+import urlparse
 
 import galaxy.model # need to import model before sniff to resolve a circular import dependency
 from galaxy.datatypes import sniff
@@ -91,12 +93,12 @@ def set_genomespace_format_identifiers( url_opener, dm_site ):
     gs_request = urllib2.Request( "%s/%s/dataformat/list" % ( dm_site, GENOMESPACE_API_VERSION_STRING ) )
     gs_request.get_method = lambda: 'GET'
     opened_gs_request = url_opener.open( gs_request )
-    genomespace_formats = simplejson.loads( opened_gs_request.read() )
+    genomespace_formats = json.loads( opened_gs_request.read() )
     for format in genomespace_formats:
         GENOMESPACE_FORMAT_IDENTIFIER_TO_GENOMESPACE_EXT[ format['url'] ] = format['name']
 
 def download_from_genomespace_importer( username, token, json_parameter_file, genomespace_site ):
-    json_params = simplejson.loads( open( json_parameter_file, 'r' ).read() )
+    json_params = json.loads( open( json_parameter_file, 'r' ).read() )
     datasource_params = json_params.get( 'param_dict' )
     assert None not in [ username, token ], "Missing GenomeSpace username or token."
     output_filename = datasource_params.get( "output_file1", None )
@@ -152,7 +154,7 @@ def download_from_genomespace_importer( username, token, json_parameter_file, ge
                 metadata_request = urllib2.Request( "%s/%s/filemetadata/%s" % ( genomespace_site_dict['dmServer'], GENOMESPACE_API_VERSION_STRING, download_file_path ) )
                 metadata_request.get_method = lambda: 'GET'
                 metadata_url = url_opener.open( metadata_request )
-                file_metadata_dict = simplejson.loads( metadata_url.read() )
+                file_metadata_dict = json.loads( metadata_url.read() )
                 metadata_url.close()
                 file_type = file_metadata_dict.get( 'dataFormat', None )
                 if file_type and file_type.get( 'url' ):
@@ -176,7 +178,7 @@ def download_from_genomespace_importer( username, token, json_parameter_file, ge
         
         #save json info for single primary dataset
         if dataset_id is not None:
-           metadata_parameter_file.write( "%s\n" % simplejson.dumps( dict( type = 'dataset',
+           metadata_parameter_file.write( "%s\n" % json.dumps( dict( type = 'dataset',
                                  dataset_id = dataset_id,
                                  ext = file_type,
                                  name = "GenomeSpace importer on %s" % ( filename ) ) ) )
@@ -189,7 +191,7 @@ def download_from_genomespace_importer( username, token, json_parameter_file, ge
             used_filenames.append( filename )
             target_output_filename = os.path.join( datasource_params['__new_file_path__'],  'primary_%i_%s_visible_%s' % ( hda_id, filename, file_type ) )
             shutil.move( output_filename, target_output_filename )
-            metadata_parameter_file.write( "%s\n" % simplejson.dumps( dict( type = 'new_primary_dataset',
+            metadata_parameter_file.write( "%s\n" % json.dumps( dict( type = 'new_primary_dataset',
                                      base_dataset_id = base_dataset_id,
                                      ext = file_type,
                                      filename = target_output_filename,
diff --git a/tools/new_operations/column_join.py b/tools/new_operations/column_join.py
index e7e025c8866..aa1624e06fd 100644
--- a/tools/new_operations/column_join.py
+++ b/tools/new_operations/column_join.py
@@ -13,19 +13,16 @@ usage: %prog -o output -1 input1 -2 input2 -c column1[,column2[,column3[,...]]]
     other_inputs: the other input files to join
 """
 
-import optparse, os, re, struct, sys, tempfile
+import json
+import optparse
+import os
+import re
+import struct
+import sys
+import tempfile
 
-try:
-    simple_json_exception = None
-    from galaxy import eggs
-    from galaxy.util.bunch import Bunch
-    from galaxy.util import stringify_dictionary_keys
-    import pkg_resources
-    pkg_resources.require("simplejson")
-    import simplejson
-except Exception, e:
-    simplejson_exception = e
-    simplejson = None
+from galaxy.util.bunch import Bunch
+from galaxy.util import stringify_dictionary_keys
 
 def stop_err( msg ):
     sys.stderr.write( msg )
@@ -162,11 +159,9 @@ def __main__():
     fill_options = None
     if options.fill_options_file != 'None' and options.fill_options_file is not None:
         try:
-            if simplejson is None:
-                raise simplejson_exception
-            fill_options = Bunch( **stringify_dictionary_keys( simplejson.load( open( options.fill_options_file ) ) ) )
+            fill_options = Bunch( **stringify_dictionary_keys( json.load( open( options.fill_options_file ) ) ) )
         except Exception, e:
-            print 'Warning: Ignoring fill options due to simplejson error (%s).' % e
+            print 'Warning: Ignoring fill options due to json error (%s).' % e
     if fill_options is None:
         fill_options = Bunch()
     if 'file1_columns' not in fill_options:
diff --git a/tools/new_operations/column_join.xml b/tools/new_operations/column_join.xml
index 79c890b111e..c194babfbf3 100644
--- a/tools/new_operations/column_join.xml
+++ b/tools/new_operations/column_join.xml
@@ -49,7 +49,7 @@
   </inputs>
   <configfiles>
     <configfile name="fill_options_file">&lt;%
-import simplejson
+import json
 %&gt;
 #set $__fill_options = {}
 #if $fill_empty_columns['fill_empty_columns_switch'] == 'fill_empty':
@@ -65,7 +65,7 @@ import simplejson
         #end for
     #end if
 #end if
-${simplejson.dumps( __fill_options )}
+${json.dumps( __fill_options )}
     </configfile>
   </configfiles>
   <outputs>
diff --git a/tools/peak_calling/macs_wrapper.py b/tools/peak_calling/macs_wrapper.py
index 0487239eff7..710f573ad06 100644
--- a/tools/peak_calling/macs_wrapper.py
+++ b/tools/peak_calling/macs_wrapper.py
@@ -1,8 +1,12 @@
-import sys, subprocess, tempfile, shutil, glob, os, os.path, gzip
-from galaxy import eggs
-import pkg_resources
-pkg_resources.require( "simplejson" )
-import simplejson
+import glob
+import gzip
+import json
+import os
+import os.path
+import shutil
+import subprocess
+import sys
+import tempfile
 
 CHUNK_SIZE = 1024
 
@@ -42,7 +46,7 @@ def xls_to_interval( xls_file, interval_file, header = None ):
     out.close()
 
 def main():
-    options = simplejson.load( open( sys.argv[1] ) )
+    options = json.load( open( sys.argv[1] ) )
     output_bed = sys.argv[2]
     output_extra_html = sys.argv[3]
     output_extra_path = sys.argv[4]
diff --git a/tools/peak_calling/macs_wrapper.xml b/tools/peak_calling/macs_wrapper.xml
index 6601102b306..504c7bef60d 100644
--- a/tools/peak_calling/macs_wrapper.xml
+++ b/tools/peak_calling/macs_wrapper.xml
@@ -93,7 +93,7 @@
   </outputs>
   <configfiles>
     <configfile name="options_file">&lt;%
-import simplejson
+import json
 %&gt;
 #set $__options = { 'experiment_name':str( $experiment_name ), 'gsize':int( float( str( $gsize ) ) ), 'tsize':str( $tsize ), 'bw':str( $bw ), 'pvalue':str( $pvalue ), 'mfold':str( $mfold ), 'nolambda':str( $nolambda ), 'lambdaset': str( $lambdaset ), 'futurefdr':str( $futurefdr ) }
 #if str( $xls_to_interval ) == 'create':
@@ -135,7 +135,7 @@ import simplejson
 #if $diag_type['diag_type_selector'] == 'diag':
 #set $__options['diag'] = { 'fe-min':str( $diag_type['fe-min'] ), 'fe-max':str( $diag_type['fe-max'] ), 'fe-step':str( $diag_type['fe-step'] ) }
 #end if
-${ simplejson.dumps( __options ) }
+${ json.dumps( __options ) }
     </configfile>
   </configfiles>
   <tests>