Merge branch 'testing' of github.com:genenetwork/genenetwork2 into reaper_bootstrap_fix

64 files changed, 1548 insertions, 1593 deletions

diff --git a/wqflask/wqflask/__init__.py b/wqflask/wqflask/__init__.py
index 7ed9c7b8..274c3d82 100644
--- a/wqflask/wqflask/__init__.py
+++ b/wqflask/wqflask/__init__.py
@@ -1,8 +1,8 @@
-from __future__ import absolute_import, division, print_function
-
 import sys
+import time
 import jinja2
 
+from flask import g
 from flask import Flask
 from utility import formatting
 
@@ -19,6 +19,13 @@ app.jinja_env.globals.update(
     undefined=jinja2.StrictUndefined,
     numify=formatting.numify)
 
+
+@app.before_request
+def before_request():
+   g.request_start_time = time.time()
+   g.request_time = lambda: "%.5fs" % (time.time() - g.request_start_time)
+
+
 from wqflask.api import router
 from wqflask import group_manager
 from wqflask import resource_manager
diff --git a/wqflask/wqflask/api/correlation.py b/wqflask/wqflask/api/correlation.py
index 7f5312c1..f5b50dcd 100644
--- a/wqflask/wqflask/api/correlation.py
+++ b/wqflask/wqflask/api/correlation.py
@@ -1,10 +1,8 @@
-from __future__ import absolute_import, division, print_function
-
 import collections
 
 import scipy
 
-from MySQLdb import escape_string as escape
+from utility.db_tools import escape
 
 from flask import g
 
@@ -36,7 +34,7 @@ def do_correlation(start_vars):
     #corr_results = collections.OrderedDict(sorted(corr_results.items(), key=lambda t: -abs(t[1][0])))
 
     final_results = []
-    for _trait_counter, trait in enumerate(corr_results.keys()[:corr_params['return_count']]):
+    for _trait_counter, trait in enumerate(list(corr_results.keys())[:corr_params['return_count']]):
         if corr_params['type'] == "tissue":
             [sample_r, num_overlap, sample_p, symbol] = corr_results[trait]
             result_dict = {
@@ -76,20 +74,20 @@ def calculate_results(this_trait, this_dataset, target_dataset, corr_params):
     if corr_params['type'] == "tissue":
         trait_symbol_dict = this_dataset.retrieve_genes("Symbol")
         corr_results = do_tissue_correlation_for_all_traits(this_trait, trait_symbol_dict, corr_params)
-        sorted_results = collections.OrderedDict(sorted(corr_results.items(),
+        sorted_results = collections.OrderedDict(sorted(list(corr_results.items()),
                                                         key=lambda t: -abs(t[1][1])))
     elif corr_params['type'] == "literature" or corr_params['type'] == "lit": #ZS: Just so a user can use either "lit" or "literature"
         trait_geneid_dict = this_dataset.retrieve_genes("GeneId")
         corr_results = do_literature_correlation_for_all_traits(this_trait, this_dataset, trait_geneid_dict, corr_params)
-        sorted_results = collections.OrderedDict(sorted(corr_results.items(),
+        sorted_results = collections.OrderedDict(sorted(list(corr_results.items()),
                                                  key=lambda t: -abs(t[1][1])))
     else:
-        for target_trait, target_vals in target_dataset.trait_data.iteritems():
+        for target_trait, target_vals in list(target_dataset.trait_data.items()):
             result = get_sample_r_and_p_values(this_trait, this_dataset, target_vals, target_dataset, corr_params['type'])
             if result is not None:
                 corr_results[target_trait] = result
 
-        sorted_results = collections.OrderedDict(sorted(corr_results.items(), key=lambda t: -abs(t[1][0])))
+        sorted_results = collections.OrderedDict(sorted(list(corr_results.items()), key=lambda t: -abs(t[1][0])))
 
     return sorted_results
 
@@ -100,10 +98,10 @@ def do_tissue_correlation_for_all_traits(this_trait, trait_symbol_dict, corr_par
     if this_trait.symbol.lower() in primary_trait_tissue_vals_dict:
         primary_trait_tissue_values = primary_trait_tissue_vals_dict[this_trait.symbol.lower()]
 
-        corr_result_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values(symbol_list=trait_symbol_dict.values())
+        corr_result_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values(symbol_list=list(trait_symbol_dict.values()))
 
         tissue_corr_data = {}
-        for trait, symbol in trait_symbol_dict.iteritems():
+        for trait, symbol in list(trait_symbol_dict.items()):
             if symbol and symbol.lower() in corr_result_tissue_vals_dict:
                 this_trait_tissue_values = corr_result_tissue_vals_dict[symbol.lower()]
 
@@ -119,7 +117,7 @@ def do_literature_correlation_for_all_traits(this_trait, target_dataset, trait_g
     input_trait_mouse_gene_id = convert_to_mouse_gene_id(target_dataset.group.species.lower(), this_trait.geneid)
 
     lit_corr_data = {}
-    for trait, gene_id in trait_geneid_dict.iteritems():
+    for trait, gene_id in list(trait_geneid_dict.items()):
         mouse_gene_id = convert_to_mouse_gene_id(target_dataset.group.species.lower(), gene_id)
 
         if mouse_gene_id and str(mouse_gene_id).find(";") == -1:
@@ -234,4 +232,4 @@ def init_corr_params(start_vars):
         'return_count' : return_count
     }
 
-    return corr_params
\ No newline at end of file
+    return corr_params
diff --git a/wqflask/wqflask/api/gen_menu.py b/wqflask/wqflask/api/gen_menu.py
index fedf3e0b..1dcafe1f 100644
--- a/wqflask/wqflask/api/gen_menu.py
+++ b/wqflask/wqflask/api/gen_menu.py
@@ -1,5 +1,3 @@
-from __future__ import print_function, division
-
 from flask import g
 
 
@@ -61,7 +59,7 @@ def get_types(groups):
     """Build types list"""
     types = {}
 
-    for species, group_dict in groups.iteritems():
+    for species, group_dict in list(groups.items()):
         types[species] = {}
         for group_name, _group_full_name, _family_name in group_dict:
             if phenotypes_exist(group_name):
@@ -136,9 +134,9 @@ def build_types(species, group):
 def get_datasets(types):
     """Build datasets list"""
     datasets = {}
-    for species, group_dict in types.iteritems():
+    for species, group_dict in list(types.items()):
         datasets[species] = {}
-        for group, type_list in group_dict.iteritems():
+        for group, type_list in list(group_dict.items()):
             datasets[species][group] = {}
             for type_name in type_list:
                 these_datasets = build_datasets(species, group, type_name[0])
diff --git a/wqflask/wqflask/api/mapping.py b/wqflask/wqflask/api/mapping.py
index 92c27c9b..d59a69df 100644
--- a/wqflask/wqflask/api/mapping.py
+++ b/wqflask/wqflask/api/mapping.py
@@ -1,5 +1,3 @@
-from __future__ import absolute_import, division, print_function
-
 import string
 
 from base import data_set
diff --git a/wqflask/wqflask/api/router.py b/wqflask/wqflask/api/router.py
index 6324cabe..8e59ef27 100644
--- a/wqflask/wqflask/api/router.py
+++ b/wqflask/wqflask/api/router.py
@@ -1,16 +1,21 @@
 # GN2 API
 
-from __future__ import absolute_import, division, print_function
+import os
+import io
+import csv
+import json
+import datetime
+import requests
 
-import os, io, csv, json, datetime, requests, yaml
-import zlib
 from zipfile import ZipFile, ZIP_DEFLATED
 
-import StringIO
 
 import flask
-from flask import g, Response, request, make_response, render_template, send_from_directory, jsonify, redirect, send_file
-import sqlalchemy
+from flask import g
+from flask import request
+from flask import make_response
+from flask import send_file
+
 from wqflask import app
 
 from wqflask.api import correlation, mapping, gen_menu
@@ -308,7 +313,7 @@ def fetch_traits(dataset_name, file_format = "json"):
         else:
             filename = dataset_name + "_trait_ids.csv"
 
-            si = StringIO.StringIO()
+            si = io.StringIO()
             csv_writer = csv.writer(si)
             csv_writer.writerows([[trait_id] for trait_id in trait_ids])
             output = make_response(si.getvalue())
@@ -322,7 +327,7 @@ def fetch_traits(dataset_name, file_format = "json"):
         else:
             filename = dataset_name + "_trait_names.csv"
 
-            si = StringIO.StringIO()
+            si = io.StringIO()
             csv_writer = csv.writer(si)
             csv_writer.writerows([[trait_name] for trait_name in trait_names])
             output = make_response(si.getvalue())
@@ -413,7 +418,7 @@ def fetch_traits(dataset_name, file_format = "json"):
                 for result in g.db.execute(final_query).fetchall():
                     results_list.append(result)
 
-                si = StringIO.StringIO()
+                si = io.StringIO()
                 csv_writer = csv.writer(si)
                 csv_writer.writerows(results_list)
                 output = make_response(si.getvalue())
@@ -517,9 +522,9 @@ def all_sample_data(dataset_name, file_format = "csv"):
                         line_list.append("x")
                 results_list.append(line_list)
 
-            results_list = map(list, zip(*results_list))
+            results_list = list(map(list, zip(*results_list)))
 
-            si = StringIO.StringIO()
+            si = io.StringIO()
             csv_writer = csv.writer(si)
             csv_writer.writerows(results_list)
             output = make_response(si.getvalue())
@@ -558,10 +563,10 @@ def trait_sample_data(dataset_name, trait_name, file_format = "json"):
         sample_list = []
         for sample in sample_data:
             sample_dict = {
-              "sample_name"   : sample[0],
-              "sample_name_2" : sample[1],
-              "value"         : sample[2],
-              "data_id"       : sample[3],
+              "sample_name": sample[0],
+              "sample_name_2": sample[1],
+              "value": sample[2],
+              "data_id": sample[3],
             }
             if sample[4]:
                 sample_dict["se"] = sample[4]
@@ -706,7 +711,7 @@ def get_mapping_results():
         if format == "csv":
             filename = "mapping_" + datetime.datetime.utcnow().strftime("%b_%d_%Y_%I:%M%p") + ".csv"
 
-            si = StringIO.StringIO()
+            si = io.StringIO()
             csv_writer = csv.writer(si)
             csv_writer.writerows(results)
             output = make_response(si.getvalue())
@@ -732,7 +737,7 @@ def get_genotypes(group_name, file_format="csv", dataset_name=None):
         if request.args['limit_to'].isdigit():
             limit_num = int(request.args['limit_to'])
 
-    si = StringIO.StringIO()
+    si = io.StringIO()
     if file_format == "csv" or file_format == "geno":
         filename = group_name + ".geno"
 
@@ -966,4 +971,4 @@ def get_group_id(group_name):
     if group_id:
         return group_id[0]
     else:
-        return None
\ No newline at end of file
+        return None
diff --git a/wqflask/wqflask/collect.py b/wqflask/wqflask/collect.py
index 4c558bfe..e074a3d8 100644
--- a/wqflask/wqflask/collect.py
+++ b/wqflask/wqflask/collect.py
@@ -1,5 +1,4 @@
-from __future__ import print_function, division, absolute_import
-
+import hashlib
 import datetime
 import simplejson as json
 
@@ -27,7 +26,9 @@ Redis = get_redis_conn()
 
 
 def process_traits(unprocessed_traits):
-    if isinstance(unprocessed_traits, basestring):
+    if isinstance(unprocessed_traits, bytes):
+        unprocessed_traits = unprocessed_traits.decode('utf-8').split(",")
+    else:  # It's a string
         unprocessed_traits = unprocessed_traits.split(",")
     traits = set()
     for trait in unprocessed_traits:
@@ -114,7 +115,8 @@ def collections_new():
         g.user_session.add_traits_to_collection(collection_id, traits)
         return redirect(url_for('view_collection', uc_id=collection_id))
     else:
-        CauseAnError
+        # CauseAnError
+        pass
 
 def create_new(collection_name):
     params = request.args
@@ -182,7 +184,7 @@ def view_collection():
     params = request.args
 
     uc_id = params['uc_id']
-    uc = (collection for collection in g.user_session.user_collections if collection["id"] == uc_id).next()
+    uc = next((collection for collection in g.user_session.user_collections if collection["id"] == uc_id))
     traits = uc["members"]
 
     trait_obs = []
diff --git a/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py b/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py
index 09d6b9cc..92de6073 100644
--- a/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py
+++ b/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py
@@ -18,35 +18,16 @@
 #
 # This module is used by GeneNetwork project (www.genenetwork.org)
 
-from __future__ import absolute_import, print_function, division
-
-import sys
-# sys.path.append(".")   Never do this in a webserver!
-
-import string
-import cPickle
-import os
-import time
-import pp
-import math
-import collections
-import resource
-
-
 from pprint import pformat as pf
 
 from base.trait import create_trait
 from base import data_set
 from utility import webqtlUtil, helper_functions, corr_result_helpers
-from db import webqtlDatabaseFunction
 import utility.webqtlUtil #this is for parallel computing only.
 from wqflask.correlation import correlation_functions
-from utility.benchmark import Bench
 
 from MySQLdb import escape_string as escape
 
-from pprint import pformat as pf
-
 from flask import Flask, g
 
 
diff --git a/wqflask/wqflask/correlation/corr_scatter_plot.py b/wqflask/wqflask/correlation/corr_scatter_plot.py
index 0f3d455c..6ab8c3d8 100644
--- a/wqflask/wqflask/correlation/corr_scatter_plot.py
+++ b/wqflask/wqflask/correlation/corr_scatter_plot.py
@@ -1,5 +1,3 @@
-from __future__ import absolute_import, print_function, division
-
 import math
 
 from flask import g
@@ -43,13 +41,13 @@ class CorrScatterPlot(object):
         samples_1, samples_2, num_overlap = corr_result_helpers.normalize_values_with_samples(self.trait_1.data, self.trait_2.data)
 
         self.data = []
-        self.indIDs = samples_1.keys()
+        self.indIDs = list(samples_1.keys())
         vals_1 = []
-        for sample in samples_1.keys():
+        for sample in list(samples_1.keys()):
             vals_1.append(samples_1[sample].value)
         self.data.append(vals_1)
         vals_2 = []
-        for sample in samples_2.keys():
+        for sample in list(samples_2.keys()):
             vals_2.append(samples_2[sample].value)
         self.data.append(vals_2)
 
@@ -137,4 +135,4 @@ def get_intercept_coords(slope, intercept, x_range, y_range):
     intercept_coords.append([x1, y1])
     intercept_coords.append([x2, y2])
 
-    return intercept_coords
\ No newline at end of file
+    return intercept_coords
diff --git a/wqflask/wqflask/correlation/correlation_functions.py b/wqflask/wqflask/correlation/correlation_functions.py
index 06dec795..b883e361 100644
--- a/wqflask/wqflask/correlation/correlation_functions.py
+++ b/wqflask/wqflask/correlation/correlation_functions.py
@@ -24,8 +24,6 @@
 #
 # Last updated by NL 2011/03/23
 
-from __future__ import absolute_import, print_function, division
-
 import math
 import rpy2.robjects
 import string
@@ -50,12 +48,12 @@ from flask import Flask, g
 
 def cal_zero_order_corr_for_tiss (primaryValue=[], targetValue=[], method='pearson'):
 
-    R_primary = rpy2.robjects.FloatVector(range(len(primaryValue)))
+    R_primary = rpy2.robjects.FloatVector(list(range(len(primaryValue))))
     N = len(primaryValue)
     for i in range(len(primaryValue)):
         R_primary[i] = primaryValue[i]
 
-    R_target = rpy2.robjects.FloatVector(range(len(targetValue)))
+    R_target = rpy2.robjects.FloatVector(list(range(len(targetValue))))
     for i in range(len(targetValue)):
         R_target[i]=targetValue[i]
 
@@ -114,4 +112,4 @@ def get_trait_symbol_and_tissue_values(symbol_list=None):
     tissue_data = MrnaAssayTissueData(gene_symbols=symbol_list)
 
     if len(tissue_data.gene_symbols):
-        return tissue_data.get_symbol_values_pairs()
\ No newline at end of file
+        return tissue_data.get_symbol_values_pairs()
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index de7a1c0c..e710bacd 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -18,51 +18,36 @@
 #
 # This module is used by GeneNetwork project (www.genenetwork.org)
 
-from __future__ import absolute_import, print_function, division
-
-import sys
-
-import string
-import cPickle
-import os
-import time
-import pp
-import math
 import collections
-import resource
 import json
-
 import scipy
 import numpy
 import rpy2.robjects as ro                    # R Objects
-import rpy2.rinterface as ri
+import utility.logger
+import utility.webqtlUtil
 
-from rpy2.robjects.packages import importr
-utils = importr("utils")
+from base.trait import create_trait
 
-from pprint import pformat as pf
+from rpy2.robjects.packages import importr
 
-from base import webqtlConfig
-from utility.THCell import THCell
-from utility.TDCell import TDCell
-from base.trait import create_trait
 from base import data_set
-from utility import webqtlUtil, helper_functions, corr_result_helpers, hmac
-from db import webqtlDatabaseFunction
-import utility.webqtlUtil #this is for parallel computing only.
+from utility import helper_functions
+from utility import corr_result_helpers
+from utility import hmac
+
 from wqflask.correlation import correlation_functions
 from utility.benchmark import Bench
-import utility.webqtlUtil
-from utility.type_checking import is_float, is_int, is_str, get_float, get_int, get_string
 
-from MySQLdb import escape_string as escape
+from utility.type_checking import is_str
+from utility.type_checking import get_float
+from utility.type_checking import get_int
+from utility.type_checking import get_string
+from utility.db_tools import escape
 
-from pprint import pformat as pf
+from flask import g
 
-from flask import Flask, g
-
-import utility.logger
-logger = utility.logger.getLogger(__name__ )
+utils = importr("utils")
+logger = utility.logger.getLogger(__name__)
 
 METHOD_LIT = "3"
 METHOD_TISSUE_PEARSON = "4"
@@ -72,6 +57,7 @@ TISSUE_METHODS = [METHOD_TISSUE_PEARSON, METHOD_TISSUE_RANK]
 
 TISSUE_MOUSE_DB = 1
 
+
 class CorrelationResults(object):
     def __init__(self, start_vars):
         # get trait list from db (database name)
@@ -108,17 +94,17 @@ class CorrelationResults(object):
             self.sample_data = {}
             self.corr_type = start_vars['corr_type']
             self.corr_method = start_vars['corr_sample_method']
-            self.min_expr = get_float(start_vars,'min_expr')
-            self.p_range_lower = get_float(start_vars,'p_range_lower',-1.0)
-            self.p_range_upper = get_float(start_vars,'p_range_upper',1.0)
+            self.min_expr = get_float(start_vars, 'min_expr')
+            self.p_range_lower = get_float(start_vars, 'p_range_lower', -1.0)
+            self.p_range_upper = get_float(start_vars, 'p_range_upper', 1.0)
 
             if ('loc_chr' in start_vars and
                 'min_loc_mb' in start_vars and
                 'max_loc_mb' in start_vars):
 
-                self.location_chr = get_string(start_vars,'loc_chr')
-                self.min_location_mb = get_int(start_vars,'min_loc_mb')
-                self.max_location_mb = get_int(start_vars,'max_loc_mb')
+                self.location_chr = get_string(start_vars, 'loc_chr')
+                self.min_location_mb = get_int(start_vars, 'min_loc_mb')
+                self.max_location_mb = get_int(start_vars, 'max_loc_mb')
             else:
                 self.location_chr = self.min_location_mb = self.max_location_mb = None
 
@@ -145,10 +131,10 @@ class CorrelationResults(object):
                 if corr_samples_group == 'samples_other':
                     primary_samples = [x for x in primary_samples if x not in (
                                     self.dataset.group.parlist + self.dataset.group.f1list)]
-                self.process_samples(start_vars, self.this_trait.data.keys(), primary_samples)
+                self.process_samples(start_vars, list(self.this_trait.data.keys()), primary_samples)
 
             self.target_dataset = data_set.create_dataset(start_vars['corr_dataset'])
-            self.target_dataset.get_trait_data(self.sample_data.keys())
+            self.target_dataset.get_trait_data(list(self.sample_data.keys()))
 
             self.header_fields = get_header_fields(self.target_dataset.type, self.corr_method)
 
@@ -168,41 +154,41 @@ class CorrelationResults(object):
 
                 tissue_corr_data = self.do_tissue_correlation_for_all_traits()
                 if tissue_corr_data != None:
-                    for trait in tissue_corr_data.keys()[:self.return_number]:
+                    for trait in list(tissue_corr_data.keys())[:self.return_number]:
                         self.get_sample_r_and_p_values(trait, self.target_dataset.trait_data[trait])
                 else:
-                    for trait, values in self.target_dataset.trait_data.iteritems():
+                    for trait, values in list(self.target_dataset.trait_data.items()):
                         self.get_sample_r_and_p_values(trait, values)
 
             elif self.corr_type == "lit":
                 self.trait_geneid_dict = self.dataset.retrieve_genes("GeneId")
                 lit_corr_data = self.do_lit_correlation_for_all_traits()
 
-                for trait in lit_corr_data.keys()[:self.return_number]:
+                for trait in list(lit_corr_data.keys())[:self.return_number]:
                     self.get_sample_r_and_p_values(trait, self.target_dataset.trait_data[trait])
 
             elif self.corr_type == "sample":
-                for trait, values in self.target_dataset.trait_data.iteritems():
+                for trait, values in list(self.target_dataset.trait_data.items()):
                     self.get_sample_r_and_p_values(trait, values)
 
-            self.correlation_data = collections.OrderedDict(sorted(self.correlation_data.items(),
+            self.correlation_data = collections.OrderedDict(sorted(list(self.correlation_data.items()),
                                                                    key=lambda t: -abs(t[1][0])))
 
             if self.target_dataset.type == "ProbeSet" or self.target_dataset.type == "Geno":
                 #ZS: Convert min/max chromosome to an int for the location range option
                 range_chr_as_int = None
-                for order_id, chr_info in self.dataset.species.chromosomes.chromosomes.iteritems():
+                for order_id, chr_info in list(self.dataset.species.chromosomes.chromosomes.items()):
                     if 'loc_chr' in start_vars:
                         if chr_info.name == self.location_chr:
                             range_chr_as_int = order_id
 
-            for _trait_counter, trait in enumerate(self.correlation_data.keys()[:self.return_number]):
+            for _trait_counter, trait in enumerate(list(self.correlation_data.keys())[:self.return_number]):
                 trait_object = create_trait(dataset=self.target_dataset, name=trait, get_qtl_info=True, get_sample_info=False)
 
                 if self.target_dataset.type == "ProbeSet" or self.target_dataset.type == "Geno":
                     #ZS: Convert trait chromosome to an int for the location range option
                     chr_as_int = 0
-                    for order_id, chr_info in self.dataset.species.chromosomes.chromosomes.iteritems():
+                    for order_id, chr_info in list(self.dataset.species.chromosomes.chromosomes.items()):
                         if chr_info.name == trait_object.chr:
                             chr_as_int = order_id
 
@@ -297,14 +283,14 @@ class CorrelationResults(object):
 
             #print("trait_gene_symbols: ", pf(trait_gene_symbols.values()))
             corr_result_tissue_vals_dict= correlation_functions.get_trait_symbol_and_tissue_values(
-                                                    symbol_list=self.trait_symbol_dict.values())
+                                                    symbol_list=list(self.trait_symbol_dict.values()))
 
             #print("corr_result_tissue_vals: ", pf(corr_result_tissue_vals_dict))
 
             #print("trait_gene_symbols: ", pf(trait_gene_symbols))
 
             tissue_corr_data = {}
-            for trait, symbol in self.trait_symbol_dict.iteritems():
+            for trait, symbol in list(self.trait_symbol_dict.items()):
                 if symbol and symbol.lower() in corr_result_tissue_vals_dict:
                     this_trait_tissue_values = corr_result_tissue_vals_dict[symbol.lower()]
 
@@ -314,7 +300,7 @@ class CorrelationResults(object):
 
                     tissue_corr_data[trait] = [symbol, result[0], result[2]]
 
-            tissue_corr_data = collections.OrderedDict(sorted(tissue_corr_data.items(),
+            tissue_corr_data = collections.OrderedDict(sorted(list(tissue_corr_data.items()),
                                                            key=lambda t: -abs(t[1][1])))
 
             return tissue_corr_data
@@ -359,7 +345,7 @@ class CorrelationResults(object):
         input_trait_mouse_gene_id = self.convert_to_mouse_gene_id(self.dataset.group.species.lower(), self.this_trait.geneid)
 
         lit_corr_data = {}
-        for trait, gene_id in self.trait_geneid_dict.iteritems():
+        for trait, gene_id in list(self.trait_geneid_dict.items()):
             mouse_gene_id = self.convert_to_mouse_gene_id(self.dataset.group.species.lower(), gene_id)
 
             if mouse_gene_id and str(mouse_gene_id).find(";") == -1:
@@ -387,7 +373,7 @@ class CorrelationResults(object):
             else:
                 lit_corr_data[trait] = [gene_id, 0]
 
-        lit_corr_data = collections.OrderedDict(sorted(lit_corr_data.items(),
+        lit_corr_data = collections.OrderedDict(sorted(list(lit_corr_data.items()),
                                                            key=lambda t: -abs(t[1][1])))
 
         return lit_corr_data
@@ -648,4 +634,4 @@ def get_header_fields(data_type, corr_method):
                                 'N',
                                 'Sample p(r)']
 
-    return header_fields
\ No newline at end of file
+    return header_fields
diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
index 3beee84f..a394f548 100644
--- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
+++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
@@ -18,52 +18,29 @@
 #
 # This module is used by GeneNetwork project (www.genenetwork.org)
 
-from __future__ import absolute_import, print_function, division
-
-import sys
-# sys.path.append(".")   Never do this in a webserver!
-
-import string
-import cPickle
-import os
 import datetime
-import time
-import pp
 import math
-import collections
-import resource
-
 import numpy as np
 import scipy
-
-from rpy2.robjects.packages import importr
 import rpy2.robjects as robjects
+import utility.webqtlUtil  # this is for parallel computing only.
+import utility.logger
 
-from pprint import pformat as pf
-
-from utility.redis_tools import get_redis_conn
-Redis = get_redis_conn()
-THIRTY_DAYS = 60 * 60 * 24 * 30
-
-from utility.THCell import THCell
-from utility.TDCell import TDCell
-from base.trait import GeneralTrait
 from base import data_set
-from utility import webqtlUtil, helper_functions, corr_result_helpers
-
-from db import webqtlDatabaseFunction
-import utility.webqtlUtil #this is for parallel computing only.
-from wqflask.correlation import correlation_functions
-from utility.benchmark import Bench
+from functools import reduce
+from functools import cmp_to_key
+from rpy2.robjects.packages import importr
 
-from MySQLdb import escape_string as escape
+from utility import webqtlUtil
+from utility import helper_functions
+from utility import corr_result_helpers
+from utility.redis_tools import get_redis_conn
 
-from pprint import pformat as pf
+logger = utility.logger.getLogger(__name__)
 
-from flask import Flask, g, url_for
+Redis = get_redis_conn()
+THIRTY_DAYS = 60 * 60 * 24 * 30
 
-import utility.logger
-logger = utility.logger.getLogger(__name__ )
 
 class CorrelationMatrix(object):
 
@@ -190,7 +167,7 @@ class CorrelationMatrix(object):
                 if self.do_PCA == True:
                     self.pca_works = "True"
                     self.pca_trait_ids = []
-                    pca = self.calculate_pca(range(len(self.traits)), corr_eigen_value, corr_eigen_vectors)
+                    pca = self.calculate_pca(list(range(len(self.traits))), corr_eigen_value, corr_eigen_vectors)
                     self.loadings_array = self.process_loadings()
                 else:
                     self.pca_works = "False"
@@ -199,8 +176,8 @@ class CorrelationMatrix(object):
 
             self.js_data = dict(traits = [trait.name for trait in self.traits],
                                 groups = groups,
-                                cols = range(len(self.traits)),
-                                rows = range(len(self.traits)),
+                                cols = list(range(len(self.traits))),
+                                rows = list(range(len(self.traits))),
                                 samples = self.all_sample_list,
                                 sample_data = self.sample_data,)
             #                    corr_results = [result[1] for result in result_row for result_row in self.corr_results])
@@ -271,14 +248,14 @@ def zScore(trait_data_array):
         i = 0
         for data in trait_data_array:
             N = len(data)
-            S = reduce(lambda x,y: x+y, data, 0.)
-            SS = reduce(lambda x,y: x+y*y, data, 0.)
+            S = reduce(lambda x, y: x+y, data, 0.)
+            SS = reduce(lambda x, y: x+y*y, data, 0.)
             mean = S/N
             var = SS - S*S/N
             stdev = math.sqrt(var/(N-1))
             if stdev == 0:
                 stdev = 1e-100
-            data2 = map(lambda x:(x-mean)/stdev,data)
+            data2 = [(x-mean)/stdev for x in data]
             trait_data_array[i] = data2
             i += 1
         return trait_data_array
@@ -290,16 +267,16 @@ def sortEigenVectors(vector):
         combines = []
         i = 0
         for item in eigenValues:
-            combines.append([eigenValues[i],eigenVectors[i]])
+            combines.append([eigenValues[i], eigenVectors[i]])
             i += 1
-        combines.sort(webqtlUtil.cmpEigenValue)
+        sorted(combines, key=cmp_to_key(webqtlUtil.cmpEigenValue))
         A = []
         B = []
         for item in combines:
             A.append(item[0])
             B.append(item[1])
-        sum = reduce(lambda x,y: x+y, A, 0.0)
-        A = map(lambda x:x*100.0/sum, A) 
+        sum = reduce(lambda x, y: x+y, A, 0.0)
+        A = [x*100.0/sum for x in A] 
         return [A, B]
     except:
-        return []
\ No newline at end of file
+        return []
diff --git a/wqflask/wqflask/ctl/ctl_analysis.py b/wqflask/wqflask/ctl/ctl_analysis.py
index 35067036..72b4f3a3 100644
--- a/wqflask/wqflask/ctl/ctl_analysis.py
+++ b/wqflask/wqflask/ctl/ctl_analysis.py
@@ -125,7 +125,7 @@ class CTL(object):
             gt = create_trait(name = ts[0], dataset_name = ts[1])
             gt = retrieve_sample_data(gt, dataset, individuals)
             for ind in individuals:
-              if ind in gt.data.keys():
+              if ind in list(gt.data.keys()):
                 traits.append(gt.data[ind].value)
               else:
                 traits.append("-999")
@@ -143,7 +143,7 @@ class CTL(object):
         #r_write_table(rPheno, "~/outputGN/pheno.csv")
 
         # Perform the CTL scan
-        res = self.r_CTLscan(rGeno, rPheno, strategy = strategy, nperm = nperm, parametric = parametric, ncores = 6)
+        res = self.r_CTLscan(rGeno, rPheno, strategy = strategy, nperm = nperm, parametric = parametric, nthreads=6)
 
         # Get significant interactions
         significant = self.r_CTLsignificant(res, significance = significance)
@@ -175,7 +175,7 @@ class CTL(object):
         sys.stdout.flush()
 
         # Create the interactive graph for cytoscape visualization (Nodes and Edges)
-        if not type(significant) == ri.RNULLType:
+        if not isinstance(significant, ri.RNULLType):
           for x in range(len(significant[0])):
             logger.debug(significant[0][x], significant[1][x], significant[2][x])     # Debug to console
             tsS = significant[0][x].split(':')                                        # Source
@@ -186,15 +186,15 @@ class CTL(object):
             self.addNode(gtT)
             self.addEdge(gtS, gtT, significant, x)
 
-            significant[0][x] = gtS.symbol + " (" + gtS.name + ")"                    # Update the trait name for the displayed table
-            significant[2][x] = gtT.symbol + " (" + gtT.name + ")"                    # Update the trait name for the displayed table
+            significant[0][x] = "{} ({})".format(gtS.symbol, gtS.name)                    # Update the trait name for the displayed table
+            significant[2][x] = "{} ({})".format(gtT.symbol, gtT.name)                    # Update the trait name for the displayed table
 
         self.elements = json.dumps(self.nodes_list + self.edges_list)
 
     def loadImage(self, path, name):
         imgfile = open(self.results[path], 'rb')
         imgdata = imgfile.read()
-        imgB64 = imgdata.encode("base64")
+        imgB64 = base64.b64encode(imgdata)
         bytesarray = array.array('B', imgB64)
         self.results[name] = bytesarray
 
diff --git a/wqflask/wqflask/db_info.py b/wqflask/wqflask/db_info.py
index f04e38bf..f420b472 100644
--- a/wqflask/wqflask/db_info.py
+++ b/wqflask/wqflask/db_info.py
@@ -1,127 +1,138 @@
-import httplib, urllib2

-import re

-

-from flask import Flask, g

-

-from utility.logger import getLogger

-logger = getLogger(__name__ )

-

-class InfoPage(object):

-    def __init__(self, start_vars):

-        self.info = None

-        self.gn_accession_id = None

-        if 'gn_accession_id' in start_vars:

-            self.gn_accession_id = start_vars['gn_accession_id']

-        self.info_page_name = start_vars['info_page_name']

-

-        self.get_info()

-        self.get_datasets_list()

-

-    def get_info(self, create=False):

-        query_base = ("SELECT InfoPageName, GN_AccesionId, Species.MenuName, Species.TaxonomyId, Tissue.Name, InbredSet.Name, " +

-                      "GeneChip.GeneChipName, GeneChip.GeoPlatform, AvgMethod.Name, Datasets.DatasetName, Datasets.GeoSeries, " +

-                      "Datasets.PublicationTitle, DatasetStatus.DatasetStatusName, Datasets.Summary, Datasets.AboutCases, " +

-                      "Datasets.AboutTissue, Datasets.AboutDataProcessing, Datasets.Acknowledgment, Datasets.ExperimentDesign, " +

-                      "Datasets.Contributors, Datasets.Citation, Datasets.Notes, Investigators.FirstName, Investigators.LastName, " +

-                      "Investigators.Address, Investigators.City, Investigators.State, Investigators.ZipCode, Investigators.Country, " +

-                      "Investigators.Phone, Investigators.Email, Investigators.Url, Organizations.OrganizationName, " +

-                      "InvestigatorId, DatasetId, DatasetStatusId, Datasets.AboutPlatform, InfoFileTitle, Specifics " +

-                      "FROM InfoFiles " +

-                      "LEFT JOIN Species USING (SpeciesId) " +

-                      "LEFT JOIN Tissue USING (TissueId) " +

-                      "LEFT JOIN InbredSet USING (InbredSetId) " +

-                      "LEFT JOIN GeneChip USING (GeneChipId) " +

-                      "LEFT JOIN AvgMethod USING (AvgMethodId) " +

-                      "LEFT JOIN Datasets USING (DatasetId) " +

-                      "LEFT JOIN Investigators USING (InvestigatorId) " +

-                      "LEFT JOIN Organizations USING (OrganizationId) " +

-                      "LEFT JOIN DatasetStatus USING (DatasetStatusId) WHERE ")

-

-        if self.gn_accession_id:

-            final_query = query_base + "GN_AccesionId = {}".format(self.gn_accession_id)

-            results = g.db.execute(final_query).fetchone()

-            if self.info_page_name and not results:

-				final_query = query_base + "InfoPageName={}".format(self.info_page_name)

-        elif self.info_page_name:

-            final_query = query_base + "InfoPageName={}".format(self.info_page_name)

-            results = g.db.execute(final_query).fetchone()

-        else:

-            raise 'No correct parameter found'

-

-        if results:

-            self.info = process_query_results(results)

-

-        if (not results or len(results) < 1) and self.info_page_name and create:

-            insert_sql = "INSERT INTO InfoFiles SET InfoFiles.InfoPageName={}".format(self.info_page_name)

-            return self.get_info()

-

-        if not self.gn_accession_id and self.info:

-            self.gn_accession_id = self.info['accession_id']

-        if not self.info_page_name and self.info:

-            self.info_page_name = self.info['info_page_name'] 

-

-    def get_datasets_list(self):

-        self.filelist = []

-        try:

-            response = urllib2.urlopen("http://datafiles.genenetwork.org/download/GN%s" % self.gn_accession_id)

-            data = response.read()

-

-            matches = re.findall(r"<tr>.+?</tr>", data, re.DOTALL)

-            for i, match in enumerate(matches):

-                if i == 0:

-                    continue

-                cells = re.findall(r"<td.+?>.+?</td>", match, re.DOTALL)

-                full_filename = re.search(r"<a href=\"(.+?)\"", cells[1], re.DOTALL).group(1).strip()

-                filename = full_filename.split("/")[-1]

-                filesize = re.search(r">(.+?)<", cells[2]).group(1).strip()

-                filedate = "N/A" #ZS: Since we can't get it for now

-

-                self.filelist.append([filename, filedate, filesize])

-        except Exception, e:

-            pass

-

-def process_query_results(results):

-    info_ob = {

-        'info_page_name': results[0],

-        'accession_id': results[1],

-        'menu_name': results[2],

-        'taxonomy_id': results[3],

-        'tissue_name': results[4],

-        'group_name': results[5],

-        'gene_chip_name': results[6],

-        'geo_platform': results[7],

-        'avg_method_name': results[8],

-        'dataset_name': results[9],

-        'geo_series': results[10],

-        'publication_title': results[11],

-        'dataset_status_name': results[12],

-        'dataset_summary': results[13],

-        'about_cases': results[14],

-        'about_tissue': results[15],

-        'about_data_processing': results[16],

-        'acknowledgement': results[17],

-        'experiment_design': results[18],

-        'contributors': results[19],

-        'citation': results[20],

-        'notes': results[21],

-        'investigator_firstname': results[22],

-        'investigator_lastname': results[23],

-        'investigator_address': results[24],

-        'investigator_city': results[25],

-        'investigator_state': results[26],

-        'investigator_zipcode': results[27],

-        'investigator_country': results[28],

-        'investigator_phone': results[29],

-        'investigator_email': results[30],

-        'investigator_url': results[31],

-        'organization_name': results[32],

-        'investigator_id': results[33],

-        'dataset_id': results[34],

-        'dataset_status_is': results[35],

-        'about_platform': results[36],

-        'info_file_title': results[37],

-        'specifics': results[38]

-    }

-

-    return info_ob

-        
\ No newline at end of file
+import http.client
+import urllib.request
+import urllib.error
+import urllib.parse
+import re
+
+from flask import Flask, g
+
+from utility.logger import getLogger
+logger = getLogger(__name__)
+
+
+class InfoPage(object):
+    def __init__(self, start_vars):
+        self.info = None
+        self.gn_accession_id = None
+        if 'gn_accession_id' in start_vars:
+            self.gn_accession_id = start_vars['gn_accession_id']
+        self.info_page_name = start_vars['info_page_name']
+
+        self.get_info()
+        self.get_datasets_list()
+
+    def get_info(self, create=False):
+        query_base = ("SELECT InfoPageName, GN_AccesionId, Species.MenuName, Species.TaxonomyId, Tissue.Name, InbredSet.Name, " +
+                      "GeneChip.GeneChipName, GeneChip.GeoPlatform, AvgMethod.Name, Datasets.DatasetName, Datasets.GeoSeries, " +
+                      "Datasets.PublicationTitle, DatasetStatus.DatasetStatusName, Datasets.Summary, Datasets.AboutCases, " +
+                      "Datasets.AboutTissue, Datasets.AboutDataProcessing, Datasets.Acknowledgment, Datasets.ExperimentDesign, " +
+                      "Datasets.Contributors, Datasets.Citation, Datasets.Notes, Investigators.FirstName, Investigators.LastName, " +
+                      "Investigators.Address, Investigators.City, Investigators.State, Investigators.ZipCode, Investigators.Country, " +
+                      "Investigators.Phone, Investigators.Email, Investigators.Url, Organizations.OrganizationName, " +
+                      "InvestigatorId, DatasetId, DatasetStatusId, Datasets.AboutPlatform, InfoFileTitle, Specifics " +
+                      "FROM InfoFiles " +
+                      "LEFT JOIN Species USING (SpeciesId) " +
+                      "LEFT JOIN Tissue USING (TissueId) " +
+                      "LEFT JOIN InbredSet USING (InbredSetId) " +
+                      "LEFT JOIN GeneChip USING (GeneChipId) " +
+                      "LEFT JOIN AvgMethod USING (AvgMethodId) " +
+                      "LEFT JOIN Datasets USING (DatasetId) " +
+                      "LEFT JOIN Investigators USING (InvestigatorId) " +
+                      "LEFT JOIN Organizations USING (OrganizationId) " +
+                      "LEFT JOIN DatasetStatus USING (DatasetStatusId) WHERE ")
+
+        if self.gn_accession_id:
+            final_query = query_base + \
+                "GN_AccesionId = {}".format(self.gn_accession_id)
+            results = g.db.execute(final_query).fetchone()
+            if self.info_page_name and not results:
+                final_query = query_base + \
+                    "InfoPageName={}".format(self.info_page_name)
+        elif self.info_page_name:
+            final_query = query_base + \
+                "InfoPageName={}".format(self.info_page_name)
+            results = g.db.execute(final_query).fetchone()
+        else:
+            raise 'No correct parameter found'
+
+        if results:
+            self.info = process_query_results(results)
+
+        if (not results or len(results) < 1) and self.info_page_name and create:
+            insert_sql = "INSERT INTO InfoFiles SET InfoFiles.InfoPageName={}".format(
+                self.info_page_name)
+            return self.get_info()
+
+        if not self.gn_accession_id and self.info:
+            self.gn_accession_id = self.info['accession_id']
+        if not self.info_page_name and self.info:
+            self.info_page_name = self.info['info_page_name']
+
+    def get_datasets_list(self):
+        self.filelist = []
+        try:
+            response = urllib.request.urlopen(
+                "http://datafiles.genenetwork.org/download/GN%s" % self.gn_accession_id)
+            data = response.read()
+
+            matches = re.findall(r"<tr>.+?</tr>", data, re.DOTALL)
+            for i, match in enumerate(matches):
+                if i == 0:
+                    continue
+                cells = re.findall(r"<td.+?>.+?</td>", match, re.DOTALL)
+                full_filename = re.search(
+                    r"<a href=\"(.+?)\"", cells[1], re.DOTALL).group(1).strip()
+                filename = full_filename.split("/")[-1]
+                filesize = re.search(r">(.+?)<", cells[2]).group(1).strip()
+                filedate = "N/A"  # ZS: Since we can't get it for now
+
+                self.filelist.append([filename, filedate, filesize])
+        except Exception as e:
+            pass
+
+def process_query_results(results):
+    info_ob = {
+        'info_page_name': results[0],
+        'accession_id': results[1],
+        'menu_name': results[2],
+        'taxonomy_id': results[3],
+        'tissue_name': results[4],
+        'group_name': results[5],
+        'gene_chip_name': results[6],
+        'geo_platform': results[7],
+        'avg_method_name': results[8],
+        'dataset_name': results[9],
+        'geo_series': results[10],
+        'publication_title': results[11],
+        'dataset_status_name': results[12],
+        'dataset_summary': results[13],
+        'about_cases': results[14],
+        'about_tissue': results[15],
+        'about_data_processing': results[16],
+        'acknowledgement': results[17],
+        'experiment_design': results[18],
+        'contributors': results[19],
+        'citation': results[20],
+        'notes': results[21],
+        'investigator_firstname': results[22],
+        'investigator_lastname': results[23],
+        'investigator_address': results[24],
+        'investigator_city': results[25],
+        'investigator_state': results[26],
+        'investigator_zipcode': results[27],
+        'investigator_country': results[28],
+        'investigator_phone': results[29],
+        'investigator_email': results[30],
+        'investigator_url': results[31],
+        'organization_name': results[32],
+        'investigator_id': results[33],
+        'dataset_id': results[34],
+        'dataset_status_is': results[35],
+        'about_platform': results[36],
+        'info_file_title': results[37],
+        'specifics': results[38]
+    }
+
+    return info_ob
+
+
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py
index 1e15d28f..00636563 100644
--- a/wqflask/wqflask/do_search.py
+++ b/wqflask/wqflask/do_search.py
@@ -1,16 +1,13 @@
-from __future__ import print_function, division
-
 import string
 import requests
 import json
 
 from flask import Flask, g
 
-from MySQLdb import escape_string as escape
+from utility.db_tools import escape
 from pprint import pformat as pf
 
 import sys
-# sys.path.append("..") Never in a running webserver
 
 from db import webqtlDatabaseFunction
 from utility.tools import GN2_BASE_URL
@@ -19,6 +16,7 @@ import logging
 from utility.logger import getLogger
 logger = getLogger(__name__)
 
+
 class DoSearch(object):
     """Parent class containing parameters/functions used for all searches"""
 
@@ -46,8 +44,8 @@ class DoSearch(object):
 
     def handle_wildcard(self, str):
         keyword = str.strip()
-        keyword = keyword.replace("*",".*")
-        keyword = keyword.replace("?",".")
+        keyword = keyword.replace("*", ".*")
+        keyword = keyword.replace("?", ".")
 
         return keyword
 
diff --git a/wqflask/wqflask/docs.py b/wqflask/wqflask/docs.py
index 9fad1cf1..d653c269 100644
--- a/wqflask/wqflask/docs.py
+++ b/wqflask/wqflask/docs.py
@@ -1,5 +1,3 @@
-from __future__ import absolute_import, print_function, division
-
 import codecs
 
 from flask import g
@@ -42,4 +40,4 @@ def update_text(start_vars):
             sql = "UPDATE Docs SET content='{0}' WHERE entry='{1}';".format(content, start_vars['entry_type'])
             g.db.execute(sql)
     except:
-        pass
\ No newline at end of file
+        pass
diff --git a/wqflask/wqflask/export_traits.py b/wqflask/wqflask/export_traits.py
index 3272c03d..3a886537 100644
--- a/wqflask/wqflask/export_traits.py
+++ b/wqflask/wqflask/export_traits.py
@@ -1,8 +1,6 @@
-from __future__ import print_function, division
-
 import csv
 import xlsxwriter
-import StringIO 
+import io 
 import datetime
 import itertools
 
@@ -61,9 +59,9 @@ def export_search_results_csv(targs):
     traits_by_group = sort_traits_by_group(trait_list)
 
     file_list = []
-    for group in traits_by_group.keys():
+    for group in list(traits_by_group.keys()):
         group_traits = traits_by_group[group]
-        buff = StringIO.StringIO()
+        buff = io.StringIO()
         writer = csv.writer(buff)
         csv_rows = []
 
@@ -122,7 +120,7 @@ def export_search_results_csv(targs):
 
             csv_rows.append(row_contents)
 
-        csv_rows = map(list, itertools.izip_longest(*[row for row in csv_rows]))
+        csv_rows = list(map(list, itertools.zip_longest(*[row for row in csv_rows])))
         writer.writerows(csv_rows)
         csv_data = buff.getvalue()
         buff.close()
@@ -135,9 +133,9 @@ def export_search_results_csv(targs):
 def sort_traits_by_group(trait_list=[]):
     traits_by_group = {}
     for trait in trait_list:
-        if trait.dataset.group.name not in traits_by_group.keys():
+        if trait.dataset.group.name not in list(traits_by_group.keys()):
             traits_by_group[trait.dataset.group.name] = []
 
         traits_by_group[trait.dataset.group.name].append(trait)
 
-    return traits_by_group
\ No newline at end of file
+    return traits_by_group
diff --git a/wqflask/wqflask/external_tools/send_to_bnw.py b/wqflask/wqflask/external_tools/send_to_bnw.py
index 68efd10d..efa17f05 100644
--- a/wqflask/wqflask/external_tools/send_to_bnw.py
+++ b/wqflask/wqflask/external_tools/send_to_bnw.py
@@ -18,8 +18,6 @@
 #
 # This module is used by GeneNetwork project (www.genenetwork.org)
 
-from __future__ import absolute_import, print_function, division
-
 from base.trait import GeneralTrait
 from utility import helper_functions, corr_result_helpers
 
@@ -69,4 +67,4 @@ class SendToBNW(object):
             if has_none:
                 continue
             self.form_value += ",".join(str(cell) for cell in row)
-            self.form_value += ";"
\ No newline at end of file
+            self.form_value += ";"
diff --git a/wqflask/wqflask/external_tools/send_to_geneweaver.py b/wqflask/wqflask/external_tools/send_to_geneweaver.py
index 7a5dba73..4c958a88 100644
--- a/wqflask/wqflask/external_tools/send_to_geneweaver.py
+++ b/wqflask/wqflask/external_tools/send_to_geneweaver.py
@@ -18,8 +18,6 @@
 #
 # This module is used by GeneNetwork project (www.genenetwork.org)
 
-from __future__ import absolute_import, print_function, division
-
 import string
 
 from flask import Flask, g
@@ -54,10 +52,10 @@ class SendToGeneWeaver(object):
             trait_name_list = get_trait_name_list(self.trait_list)
 
             self.hidden_vars = {
-                                 'client'                     : "genenetwork",
-                                 'species'                    : species_name,
-                                 'idtype'                     : self.chip_name,
-                                 'list'                       : string.join(trait_name_list, ","),
+                                 'client': "genenetwork",
+                                 'species': species_name,
+                                 'idtype': self.chip_name,
+                                 'list': ",".join(trait_name_list),
                                }
 
 def get_trait_name_list(trait_list):
@@ -109,4 +107,4 @@ def test_chip(trait_list):
                 chip_name = '%s_NA' % result[0]
                 return chip_name
 
-    return chip_name
\ No newline at end of file
+    return chip_name
diff --git a/wqflask/wqflask/external_tools/send_to_webgestalt.py b/wqflask/wqflask/external_tools/send_to_webgestalt.py
index 30ca024f..2f068792 100644
--- a/wqflask/wqflask/external_tools/send_to_webgestalt.py
+++ b/wqflask/wqflask/external_tools/send_to_webgestalt.py
@@ -18,8 +18,6 @@
 #
 # This module is used by GeneNetwork project (www.genenetwork.org)
 
-from __future__ import absolute_import, print_function, division
-
 import string
 
 from flask import Flask, g
@@ -49,7 +47,7 @@ class SendToWebGestalt(object):
             id_type = "entrezgene"
 
             self.hidden_vars = { 
-                             'gene_list'                  : string.join(gene_id_list, "\n"),
+                             'gene_list'                  : "\n".join(gene_id_list),
                              'id_type'                    : "entrezgene",
                              'ref_set'                    : "genome",
                              'enriched_database_category' : "geneontology",
@@ -123,4 +121,4 @@ def gen_gene_id_list(trait_list):
         trait_name_list.append(trait.name)
         retrieve_trait_info(trait, trait.dataset)
         gene_id_list.append(str(trait.geneid))
-    return trait_name_list, gene_id_list
\ No newline at end of file
+    return trait_name_list, gene_id_list
diff --git a/wqflask/wqflask/group_manager.py b/wqflask/wqflask/group_manager.py
index 99d5db26..69ee9623 100644
--- a/wqflask/wqflask/group_manager.py
+++ b/wqflask/wqflask/group_manager.py
@@ -1,6 +1,3 @@
-
-from __future__ import print_function, division, absolute_import
-
 import random, string
 
 from flask import (Flask, g, render_template, url_for, request, make_response,
@@ -155,4 +152,4 @@ def send_group_invites(group_id, user_email_list = [], user_type="members"):
          save_user(user_details, user_details['user_id'])
          send_invitation_email(user_email, temp_password)
 
-#@app.route()
\ No newline at end of file
+#@app.route()
diff --git a/wqflask/wqflask/gsearch.py b/wqflask/wqflask/gsearch.py
index c65a1415..9e46c0c5 100644
--- a/wqflask/wqflask/gsearch.py
+++ b/wqflask/wqflask/gsearch.py
@@ -1,5 +1,3 @@
-from __future__ import absolute_import, print_function, division
-
 import json
 
 from flask import Flask, g
@@ -37,7 +35,7 @@ class GSearch(object):
                 ProbeSetFreeze.FullName AS probesetfreeze_fullname,
                 ProbeSet.Name AS probeset_name,
                 ProbeSet.Symbol AS probeset_symbol,
-                ProbeSet.`description` AS probeset_description,
+                CAST(ProbeSet.`description` AS BINARY) AS probeset_description,
                 ProbeSet.Chr AS chr,
                 ProbeSet.Mb AS mb,
                 ProbeSetXRef.Mean AS mean,
@@ -137,8 +135,8 @@ class GSearch(object):
                 PublishFreeze.`Name`,
                 PublishFreeze.`FullName`,
                 PublishXRef.`Id`,
-                Phenotype.`Pre_publication_description`,
-                Phenotype.`Post_publication_description`,
+                CAST(Phenotype.`Pre_publication_description` AS BINARY),
+                CAST(Phenotype.`Post_publication_description` AS BINARY),
                 Publication.`Authors`,
                 Publication.`Year`,
                 Publication.`PubMed_ID`,
diff --git a/wqflask/wqflask/heatmap/heatmap.py b/wqflask/wqflask/heatmap/heatmap.py
index 5098a184..cca5a4fc 100644
--- a/wqflask/wqflask/heatmap/heatmap.py
+++ b/wqflask/wqflask/heatmap/heatmap.py
@@ -1,46 +1,17 @@
-from __future__ import absolute_import, print_function, division
-
-import sys
-# sys.path.append(".") Never in a running webserver
-
 import string
-import cPickle
 import os
-import datetime
-import time
-import pp
-import math
 import random
-import collections
-import resource
-
-import scipy
-import numpy as np
-
-from pprint import pformat as pf
-
-from base.trait import GeneralTrait
-from base import data_set
 from base import species
 from base import webqtlConfig
 from utility import helper_functions
-from utility import Plot, Bunch
-from utility import temp_data
-from utility.tools import flat_files, REAPER_COMMAND, TEMPDIR
-
-from MySQLdb import escape_string as escape
-
-import cPickle as pickle
-import simplejson as json
-
-from pprint import pformat as pf
 
+from utility.tools import flat_files, REAPER_COMMAND, TEMPDIR
 from redis import Redis
-Redis = Redis()
-
 from flask import Flask, g
-
 from utility.logger import getLogger
+
+Redis = Redis()
+
 logger = getLogger(__name__ )
 
 class Heatmap(object):
@@ -60,7 +31,7 @@ class Heatmap(object):
 
         chrnames = []
         self.species = species.TheSpecies(dataset=self.trait_list[0][1])
-        for key in self.species.chromosomes.chromosomes.keys():
+        for key in list(self.species.chromosomes.chromosomes.keys()):
             chrnames.append([self.species.chromosomes.chromosomes[key].name, self.species.chromosomes.chromosomes[key].mb_length])
 
         for trait_db in self.trait_list:
@@ -93,7 +64,7 @@ class Heatmap(object):
         pos = []
         markernames = []
 
-        for trait in self.trait_results.keys():
+        for trait in list(self.trait_results.keys()):
             lodnames.append(trait)
 
         self.dataset.group.get_markers()
@@ -205,4 +176,4 @@ def parse_reaper_output(gwa_filename):
                 marker['additive'] = float(line.split("\t")[6])
                 marker_obs.append(marker)
 
-    return marker_obs
\ No newline at end of file
+    return marker_obs
diff --git a/wqflask/wqflask/interval_analyst/GeneUtil.py b/wqflask/wqflask/interval_analyst/GeneUtil.py
index 2c60dd70..d0dd7aea 100644
--- a/wqflask/wqflask/interval_analyst/GeneUtil.py
+++ b/wqflask/wqflask/interval_analyst/GeneUtil.py
@@ -1,5 +1,3 @@
-from __future__ import absolute_import, print_function, division
-
 import string
 
 from flask import Flask, g
@@ -24,7 +22,7 @@ def loadGenes(chrName, diffCol, startMb, endMb, species='mouse'):
 	
 	##List current Species and other Species
 	speciesId = speciesDict[species]
-	otherSpecies = map(lambda X: [X, speciesDict[X]], speciesDict.keys())
+	otherSpecies = [[X, speciesDict[X]] for X in list(speciesDict.keys())]
 	otherSpecies.remove([species, speciesId])
 
 	results = g.db.execute("""
@@ -33,7 +31,7 @@ def loadGenes(chrName, diffCol, startMb, endMb, species='mouse'):
                       Chromosome = '%s' AND
 					  ((TxStart > %f and TxStart <= %f) OR (TxEnd > %f and TxEnd <= %f))
 				ORDER BY txStart
-                """ % (string.join(fetchFields, ", "),
+                """ % (", ".join(fetchFields),
                        speciesId, chrName,
                        startMb, endMb,
                        startMb, endMb)).fetchall()
@@ -68,7 +66,7 @@ def loadGenes(chrName, diffCol, startMb, endMb, species='mouse'):
 				othSpec, othSpecId = item
 				newdict2 = {}
 				
-				resultsOther = g.db.execute("SELECT %s FROM GeneList WHERE SpeciesId = %d AND geneSymbol= '%s' LIMIT 1" % (string.join(fetchFields, ", "),
+				resultsOther = g.db.execute("SELECT %s FROM GeneList WHERE SpeciesId = %d AND geneSymbol= '%s' LIMIT 1" % (", ".join(fetchFields),
                                                                                                                            othSpecId,
                                                                                                                            newdict["GeneSymbol"])).fetchone()
 
diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py
index de751907..2fc633aa 100644
--- a/wqflask/wqflask/marker_regression/display_mapping_results.py
+++ b/wqflask/wqflask/marker_regression/display_mapping_results.py
@@ -35,7 +35,7 @@ import json
 
 from flask import Flask, g
 
-from htmlgen import HTMLgen2 as HT
+import htmlgen as HT
 
 from base import webqtlConfig
 from base.GeneralObject import GeneralObject
@@ -47,7 +47,11 @@ from base.webqtlConfig import GENERATED_IMAGE_DIR
 from utility.pillow_utils import draw_rotated_text, draw_open_polygon
 
 import utility.logger
-logger = utility.logger.getLogger(__name__)
+try:  # Only import this for Python3
+    from functools import reduce
+except:
+    pass
+logger = utility.logger.getLogger(__name__ )
 
 RED = ImageColor.getrgb("red")
 BLUE = ImageColor.getrgb("blue")
@@ -84,35 +88,60 @@ class HtmlGenWrapper:
     """Wrapper Methods for HTML gen"""
     @staticmethod
     def create_image_tag(**kwargs):
-        return HT.Image(**kwargs)
+        image = HT.Image("", "")
+        for key, value in list(kwargs.items()):
+            image.set_attribute(key, value)
+        return image
 
     @staticmethod
     def create_form_tag(**kwargs):
-        return HT.Form(**kwargs)
+        form = HT.Form("POST", "")  # Default method is POST
+
+        for key, value in list(kwargs.items()):
+            if key == "submit":
+                form.append(value)
+                continue
+            form.set_attribute(key.replace("cgi", "action"), str(value))
+        return form
 
     @staticmethod
     def create_p_tag(**kwargs):
-        return HT.Paragraph(**kwargs)
+        paragraph = HT.Paragraph()
+        for key, value in list(kwargs.items()):
+            paragraph.set_attribute(key, value)
+        return paragraph
 
     @staticmethod
     def create_br_tag():
-        return HT.BR()
+        return HT.VoidElement("br")
 
     @staticmethod
     def create_input_tag(**kwargs):
-        return HT.Input(**kwargs)
+        input_ = HT.Input()
+        for key, value in list(kwargs.items()):
+            input_.set_attribute(key.lower().replace("_", ""), value)
+        return input_
 
     @staticmethod
     def create_area_tag(**kwargs):
-        return HT.Area(**kwargs)
+        area = HT.VoidElement("area")
+        for key, value in list(kwargs.items()):
+            area.set_attribute(key, value)
+        return area
 
     @staticmethod
     def create_link_tag(href, content, **kwargs):
-        return HT.Href(href, content, **kwargs)
+        link = HT.Link(href, content)
+        for key, value in list(kwargs.items()):
+            link.set_attribute(key, value)
+        return link
 
     @staticmethod
     def create_map_tag(**kwargs):
-        return HT.Map(**kwargs)
+        map_ = HT.Element("map")
+        for key, value in list(kwargs.items()):
+            map_.set_attribute(key, value)
+        return map_
 
 
 class DisplayMappingResults(object):
@@ -265,7 +294,7 @@ class DisplayMappingResults(object):
 
         self.manhattan_plot = start_vars['manhattan_plot']
 
-        if 'permCheck' in start_vars.keys():
+        if 'permCheck' in list(start_vars.keys()):
             self.permChecked = start_vars['permCheck']
         else:
             self.permChecked = False
@@ -278,46 +307,46 @@ class DisplayMappingResults(object):
         else:
             self.nperm = 0
 
-        if 'bootCheck' in start_vars.keys():
+        if 'bootCheck' in list(start_vars.keys()):
             self.bootChecked = start_vars['bootCheck']
         else:
             self.bootChecked = False
-        if 'num_bootstrap' in start_vars.keys():
+        if 'num_bootstrap' in list(start_vars.keys()):
             self.nboot = int(start_vars['num_bootstrap'])
         else:
             self.nboot = 0
-        if 'bootstrap_results' in start_vars.keys():
+        if 'bootstrap_results' in list(start_vars.keys()):
             self.bootResult = start_vars['bootstrap_results']
         else:
             self.bootResult = []
 
-        if 'do_control' in start_vars.keys():
+        if 'do_control' in list(start_vars.keys()):
             self.doControl = start_vars['do_control']
         else:
             self.doControl = "false"
-        if 'control_marker' in start_vars.keys():
+        if 'control_marker' in list(start_vars.keys()):
             self.controlLocus = start_vars['control_marker']
         else:
             self.controlLocus = ""
-        if 'covariates' in start_vars.keys():
+        if 'covariates' in list(start_vars.keys()):
             self.covariates = start_vars['covariates']
-        if 'maf' in start_vars.keys():
+        if 'maf' in list(start_vars.keys()):
             self.maf = start_vars['maf']
         else:
             self.maf = ""
-        if 'output_files' in start_vars.keys():
+        if 'output_files' in list(start_vars.keys()):
             self.output_files = start_vars['output_files']
-        if 'use_loco' in start_vars.keys() and self.mapping_method == "gemma":
+        if 'use_loco' in list(start_vars.keys()) and self.mapping_method == "gemma":
             self.use_loco = start_vars['use_loco']
 
-        if 'reaper_version' in start_vars.keys() and self.mapping_method == "reaper":
+        if 'reaper_version' in list(start_vars.keys()) and self.mapping_method == "reaper":
             self.reaper_version = start_vars['reaper_version']
             if 'output_files' in start_vars:
                 self.output_files = ",".join(start_vars['output_files'])
 
         self.categorical_vars = ""
         self.perm_strata = ""
-        if 'perm_strata' in start_vars.keys() and 'categorical_vars' in start_vars.keys():
+        if 'perm_strata' in list(start_vars.keys()) and 'categorical_vars' in list(start_vars.keys()):
             self.categorical_vars = start_vars['categorical_vars']
             self.perm_strata = start_vars['perm_strata']
 
@@ -359,7 +388,7 @@ class DisplayMappingResults(object):
                self.graphWidth  = self.MULT_GRAPH_DEFAULT_WIDTH
 
 ## BEGIN HaplotypeAnalyst
-        if 'haplotypeAnalystCheck' in start_vars.keys():
+        if 'haplotypeAnalystCheck' in list(start_vars.keys()):
             self.haplotypeAnalystChecked = start_vars['haplotypeAnalystCheck']
         else:
             self.haplotypeAnalystChecked = False
@@ -367,25 +396,25 @@ class DisplayMappingResults(object):
 
         self.graphHeight = self.GRAPH_DEFAULT_HEIGHT
         self.dominanceChecked = False
-        if 'LRSCheck' in start_vars.keys():
+        if 'LRSCheck' in list(start_vars.keys()):
             self.LRS_LOD = start_vars['LRSCheck']
         else:
             self.LRS_LOD = start_vars['score_type']
         self.intervalAnalystChecked = True
         self.draw2X = False
-        if 'additiveCheck' in start_vars.keys():
+        if 'additiveCheck' in list(start_vars.keys()):
             self.additiveChecked = start_vars['additiveCheck']
         else:
             self.additiveChecked = False
-        if 'viewLegend' in start_vars.keys():
+        if 'viewLegend' in list(start_vars.keys()):
             self.legendChecked = start_vars['viewLegend']
         else:
             self.legendChecked = False
-        if 'showSNP' in start_vars.keys():
+        if 'showSNP' in list(start_vars.keys()):
             self.SNPChecked = start_vars['showSNP']
         else:
             self.SNPChecked = False
-        if 'showGenes' in start_vars.keys():
+        if 'showGenes' in list(start_vars.keys()):
             self.geneChecked = start_vars['showGenes']
         else:
             self.geneChecked = False
@@ -425,9 +454,9 @@ class DisplayMappingResults(object):
                         Chr_Length.Name in (%s)
                 Order by
                         Chr_Length.OrderId
-                """ % (self.dataset.group.name, string.join(map(lambda X: "'%s'" % X[0], self.ChrList[1:]), ", ")))
+                """ % (self.dataset.group.name, ", ".join(["'%s'" % X[0] for X in self.ChrList[1:]])))
 
-        self.ChrLengthMbList = map(lambda x: x[0]/1000000.0, self.ChrLengthMbList)
+        self.ChrLengthMbList = [x[0]/1000000.0 for x in self.ChrLengthMbList]
         self.ChrLengthMbSum = reduce(lambda x, y:x+y, self.ChrLengthMbList, 0.0)
         if self.ChrLengthMbList:
             self.MbGraphInterval = self.ChrLengthMbSum/(len(self.ChrLengthMbList)*12) #Empirical Mb interval
@@ -458,7 +487,7 @@ class DisplayMappingResults(object):
                 else:
                     continue
             samplelist = list(self.genotype.prgy)
-            for j,_geno in enumerate (self.genotype[0][1].genotype):
+            for j, _geno in enumerate (self.genotype[0][1].genotype):
                 for item in smd:
                     if item.name == samplelist[j]:
                         self.NR_INDIVIDUALS = self.NR_INDIVIDUALS + 1
@@ -550,11 +579,10 @@ class DisplayMappingResults(object):
             src="/image/{}.png".format(self.filename),
             border="0", usemap='#WebQTLImageMap'
         )
-        self.intImg = intImg
 
         #Scales plot differently for high resolution
         if self.draw2X:
-            intCanvasX2 = Image.new("RGBA", size=(self.graphWidth*2,self.graphHeight*2))
+            intCanvasX2 = Image.new("RGBA", size=(self.graphWidth*2, self.graphHeight*2))
             gifmapX2 = self.plotIntMapping(intCanvasX2, startMb = self.startMb, endMb = self.endMb, showLocusForm= showLocusForm, zoom=2)
             intCanvasX2.save(
                 "{}.png".format(
@@ -571,12 +599,12 @@ class DisplayMappingResults(object):
                 cgi=os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE),
                 enctype='multipart/form-data',
                 name=showLocusForm,
-                submit=HtmlGenWrapper.create_input_tag(type='hidden'))
+                submit=HtmlGenWrapper.create_input_tag(type_='hidden'))
 
             hddn = {'FormID':'showDatabase', 'ProbeSetID':'_','database':fd.RISet+"Geno",'CellID':'_', 'RISet':fd.RISet, 'incparentsf1':'ON'}
             for key in hddn.keys():
                 showLocusForm.append(HtmlGenWrapper.create_input_tag(
-                    name=key, value=hddn[key], type='hidden'))
+                    name=key, value=hddn[key], type_='hidden'))
             showLocusForm.append(intImg)
         else:
             showLocusForm = intImg
@@ -791,17 +819,17 @@ class DisplayMappingResults(object):
         bootScale = bootScale[:-1] + [highestPercent]
 
         bootOffset = 50*fontZoom
-        bootScaleFont=ImageFont.truetype(font=VERDANA_FILE,size=13*fontZoom)
+        bootScaleFont=ImageFont.truetype(font=VERDANA_FILE, size=13*fontZoom)
         im_drawer.rectangle(
             xy=((canvas.size[0]-bootOffset, yZero-bootHeightThresh),
-                (canvas.size[0]-bootOffset-15*zoom,yZero)),
+                (canvas.size[0]-bootOffset-15*zoom, yZero)),
             fill = YELLOW, outline=BLACK)
         im_drawer.line(
             xy=((canvas.size[0]-bootOffset+4, yZero),
                 (canvas.size[0]-bootOffset, yZero)),
             fill=BLACK)
         TEXT_Y_DISPLACEMENT = -8
-        im_drawer.text(xy=(canvas.size[0]-bootOffset+10,yZero+TEXT_Y_DISPLACEMENT), text='0%',
+        im_drawer.text(xy=(canvas.size[0]-bootOffset+10, yZero+TEXT_Y_DISPLACEMENT), text='0%',
                        font=bootScaleFont, fill=BLACK)
 
         for item in bootScale:
@@ -809,10 +837,10 @@ class DisplayMappingResults(object):
                 continue
             bootY = yZero-bootHeightThresh*item/highestPercent
             im_drawer.line(
-                xy=((canvas.size[0]-bootOffset+4,bootY),
-                 (canvas.size[0]-bootOffset,bootY)),
+                xy=((canvas.size[0]-bootOffset+4, bootY),
+                 (canvas.size[0]-bootOffset, bootY)),
                 fill=BLACK)
-            im_drawer.text(xy=(canvas.size[0]-bootOffset+10,bootY+TEXT_Y_DISPLACEMENT),
+            im_drawer.text(xy=(canvas.size[0]-bootOffset+10, bootY+TEXT_Y_DISPLACEMENT),
                            text='%2.1f'%item, font=bootScaleFont, fill=BLACK)
 
         if self.legendChecked:
@@ -821,7 +849,7 @@ class DisplayMappingResults(object):
             smallLabelFont = ImageFont.truetype(font=TREBUC_FILE, size=12*fontZoom)
             leftOffset = xLeftOffset+(nCol-1)*200
             im_drawer.rectangle(
-                xy=((leftOffset,startPosY-6), (leftOffset+12,startPosY+6)),
+                xy=((leftOffset, startPosY-6), (leftOffset+12, startPosY+6)),
                 fill=YELLOW, outline=BLACK)
             im_drawer.text(xy=(leftOffset+ 20, startPosY+TEXT_Y_DISPLACEMENT),
                            text='Frequency of the Peak LRS',
@@ -918,7 +946,7 @@ class DisplayMappingResults(object):
             TEXT_Y_DISPLACEMENT = -8
             im_drawer.text(
                 text="Sequence Site",
-                xy=(leftOffset+15,startPosY+TEXT_Y_DISPLACEMENT), font=smallLabelFont,
+                xy=(leftOffset+15, startPosY+TEXT_Y_DISPLACEMENT), font=smallLabelFont,
                 fill=self.TOP_RIGHT_INFO_COLOR)
 
     def drawSNPTrackNew(self, canvas, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None):
@@ -968,7 +996,7 @@ class DisplayMappingResults(object):
     def drawMultiTraitName(self, fd, canvas, gifmap, showLocusForm, offset= (40, 120, 80, 10), zoom = 1):
         nameWidths = []
         yPaddingTop = 10
-        colorFont=ImageFont.truetype(font=TREBUC_FILE,size=12)
+        colorFont=ImageFont.truetype(font=TREBUC_FILE, size=12)
         if len(self.qtlresults) >20 and self.selectedChr > -1:
             rightShift = 20
             rightShiftStep = 60
@@ -987,21 +1015,21 @@ class DisplayMappingResults(object):
                 rightShift += rightShiftStep
 
             name = thisTrait.displayName()
-            nameWidth, nameHeight = im_drawer.textsize(name,font=colorFont)
+            nameWidth, nameHeight = im_drawer.textsize(name, font=colorFont)
             nameWidths.append(nameWidth)
 
             im_drawer.rectangle(
-                xy=((rightShift,yPaddingTop+kstep*15),
-                    (rectWidth+rightShift,yPaddingTop+10+kstep*15)),
+                xy=((rightShift, yPaddingTop+kstep*15),
+                    (rectWidth+rightShift, yPaddingTop+10+kstep*15)),
                 fill=thisLRSColor, outline=BLACK)
             im_drawer.text(
-                text=name,xy=(rectWidth+2+rightShift,yPaddingTop+10+kstep*15),
-                font=colorFont,fill=BLACK)
+                text=name, xy=(rectWidth+2+rightShift, yPaddingTop+10+kstep*15),
+                font=colorFont, fill=BLACK)
             if thisTrait.db:
-                COORDS = "%d,%d,%d,%d" %(rectWidth+2+rightShift,yPaddingTop+kstep*15,rectWidth+2+rightShift+nameWidth,yPaddingTop+10+kstep*15,)
+                COORDS = "%d,%d,%d,%d" %(rectWidth+2+rightShift, yPaddingTop+kstep*15, rectWidth+2+rightShift+nameWidth, yPaddingTop+10+kstep*15,)
                 HREF= "javascript:showDatabase3('%s','%s','%s','');" % (showLocusForm, thisTrait.db.name, thisTrait.name)
-                Areas = HtmlGenWrapper.create_area_tag(shape='rect',coords=COORDS,href=HREF)
-                gifmap.areas.append(Areas) ### TODO
+                Areas = HtmlGenWrapper.create_area_tag(shape='rect', coords=COORDS, href=HREF)
+                gifmap.append(Areas) ### TODO
 
     def drawLegendPanel(self, canvas, offset= (40, 120, 80, 10), zoom = 1):
         im_drawer = ImageDraw.Draw(canvas)
@@ -1014,80 +1042,80 @@ class DisplayMappingResults(object):
         if zoom == 2:
             fontZoom = 1.5
 
-        labelFont=ImageFont.truetype(font=TREBUC_FILE,size=12*fontZoom)
+        labelFont=ImageFont.truetype(font=TREBUC_FILE, size=12*fontZoom)
         startPosY = 15
         stepPosY = 12*fontZoom
         if self.manhattan_plot != True:
             im_drawer.line(
-                xy=((xLeftOffset,startPosY),(xLeftOffset+32,startPosY)),
+                xy=((xLeftOffset, startPosY), (xLeftOffset+32, startPosY)),
                 fill=self.LRS_COLOR, width=2)
             im_drawer.text(
-                text=self.LRS_LOD, xy=(xLeftOffset+40,startPosY+TEXT_Y_DISPLACEMENT),
-                font=labelFont,fill=BLACK)
+                text=self.LRS_LOD, xy=(xLeftOffset+40, startPosY+TEXT_Y_DISPLACEMENT),
+                font=labelFont, fill=BLACK)
             startPosY += stepPosY
 
         if self.additiveChecked:
             startPosX = xLeftOffset
             im_drawer.line(
-                xy=((startPosX,startPosY),(startPosX+17,startPosY)),
+                xy=((startPosX, startPosY), (startPosX+17, startPosY)),
                 fill=self.ADDITIVE_COLOR_POSITIVE, width=2)
             im_drawer.line(
-                xy=((startPosX+18,startPosY),(startPosX+32,startPosY)),
+                xy=((startPosX+18, startPosY), (startPosX+32, startPosY)),
                 fill=self.ADDITIVE_COLOR_NEGATIVE, width=2)
             im_drawer.text(
-                text='Additive Effect',xy=(startPosX+40,startPosY+TEXT_Y_DISPLACEMENT),
-                font=labelFont,fill=BLACK)
+                text='Additive Effect', xy=(startPosX+40, startPosY+TEXT_Y_DISPLACEMENT),
+                font=labelFont, fill=BLACK)
 
         if self.genotype.type == 'intercross' and self.dominanceChecked:
             startPosX = xLeftOffset
             startPosY += stepPosY
             im_drawer.line(
-                xy=((startPosX,startPosY),(startPosX+17,startPosY)),
+                xy=((startPosX, startPosY), (startPosX+17, startPosY)),
                 fill=self.DOMINANCE_COLOR_POSITIVE, width=4)
             im_drawer.line(
-                xy=((startPosX+18,startPosY),(startPosX+35,startPosY)),
+                xy=((startPosX+18, startPosY), (startPosX+35, startPosY)),
                 fill=self.DOMINANCE_COLOR_NEGATIVE, width=4)
             im_drawer.text(
-                text='Dominance Effect', xy=(startPosX+42,startPosY+5),
-                font=labelFont,fill=BLACK)
+                text='Dominance Effect', xy=(startPosX+42, startPosY+5),
+                font=labelFont, fill=BLACK)
 
         if self.haplotypeAnalystChecked:
             startPosY += stepPosY
             startPosX = xLeftOffset
             im_drawer.line(
-                xy=((startPosX,startPosY),(startPosX+17,startPosY)),
+                xy=((startPosX, startPosY), (startPosX+17, startPosY)),
                 fill=self.HAPLOTYPE_POSITIVE, width=4)
             im_drawer.line(
-                xy=((startPosX+18,startPosY),(startPosX+35,startPosY)),
+                xy=((startPosX+18, startPosY), (startPosX+35, startPosY)),
                 fill=self.HAPLOTYPE_NEGATIVE, width=4)
             im_drawer.line(
-                xy=((startPosX+36,startPosY),(startPosX+53,startPosY)),
+                xy=((startPosX+36, startPosY), (startPosX+53, startPosY)),
                 fill=self.HAPLOTYPE_HETEROZYGOUS, width=4)
             im_drawer.line(
-                xy=((startPosX+54,startPosY),(startPosX+67,startPosY)),
+                xy=((startPosX+54, startPosY), (startPosX+67, startPosY)),
                 fill=self.HAPLOTYPE_RECOMBINATION, width=4)
             im_drawer.text(
                 text='Haplotypes (Pat, Mat, Het, Unk)',
-                xy=(startPosX+76,startPosY+5),font=labelFont,fill=BLACK)
+                xy=(startPosX+76, startPosY+5), font=labelFont, fill=BLACK)
 
         if self.permChecked and self.nperm > 0:
             startPosY += stepPosY
             startPosX = xLeftOffset
             im_drawer.line(
-                xy=((startPosX, startPosY),( startPosX + 32, startPosY)),
+                xy=((startPosX, startPosY), ( startPosX + 32, startPosY)),
                 fill=self.SIGNIFICANT_COLOR, width=self.SIGNIFICANT_WIDTH)
             im_drawer.line(
-                xy=((startPosX, startPosY + stepPosY),( startPosX + 32, startPosY + stepPosY)),
+                xy=((startPosX, startPosY + stepPosY), ( startPosX + 32, startPosY + stepPosY)),
                 fill=self.SUGGESTIVE_COLOR, width=self.SUGGESTIVE_WIDTH)
             im_drawer.text(
-                text='Significant %s = %2.2f' % (self.LRS_LOD,self.significant),
-                xy=(xLeftOffset+42,startPosY+TEXT_Y_DISPLACEMENT),font=labelFont,fill=BLACK)
+                text='Significant %s = %2.2f' % (self.LRS_LOD, self.significant),
+                xy=(xLeftOffset+42, startPosY+TEXT_Y_DISPLACEMENT), font=labelFont, fill=BLACK)
             im_drawer.text(
                 text='Suggestive %s = %2.2f' % (self.LRS_LOD, self.suggestive),
-                xy=(xLeftOffset+42,startPosY + TEXT_Y_DISPLACEMENT +stepPosY),font=labelFont,
+                xy=(xLeftOffset+42, startPosY + TEXT_Y_DISPLACEMENT +stepPosY), font=labelFont,
                 fill=BLACK)
 
-        labelFont = ImageFont.truetype(font=VERDANA_FILE,size=12*fontZoom)
+        labelFont = ImageFont.truetype(font=VERDANA_FILE, size=12*fontZoom)
         labelColor = BLACK
         if self.dataset.type == "Publish" or self.dataset.type == "Geno":
             dataset_label = self.dataset.fullname
@@ -1155,22 +1183,22 @@ class DisplayMappingResults(object):
                 im_drawer.textsize(string2, font=labelFont)[0])
             im_drawer.text(
                 text=identification,
-                xy=(canvas.size[0] - xRightOffset-d,20*fontZoom),font=labelFont,
+                xy=(canvas.size[0] - xRightOffset-d, 20*fontZoom), font=labelFont,
                 fill=labelColor)
         else:
             d = 4+ max(
                 im_drawer.textsize(string1, font=labelFont)[0],
                 im_drawer.textsize(string2, font=labelFont)[0])
         im_drawer.text(
-            text=string1,xy=(canvas.size[0] - xRightOffset-d,35*fontZoom),
-            font=labelFont,fill=labelColor)
+            text=string1, xy=(canvas.size[0] - xRightOffset-d, 35*fontZoom),
+            font=labelFont, fill=labelColor)
         im_drawer.text(
-            text=string2,xy=(canvas.size[0] - xRightOffset-d,50*fontZoom),
-            font=labelFont,fill=labelColor)
+            text=string2, xy=(canvas.size[0] - xRightOffset-d, 50*fontZoom),
+            font=labelFont, fill=labelColor)
         if string3 != '':
             im_drawer.text(
-                text=string3,xy=(canvas.size[0] - xRightOffset-d,65*fontZoom),
-                font=labelFont,fill=labelColor)
+                text=string3, xy=(canvas.size[0] - xRightOffset-d, 65*fontZoom),
+                font=labelFont, fill=labelColor)
 
 
     def drawGeneBand(self, canvas, gifmap, plotXScale, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None):
@@ -1197,8 +1225,8 @@ class DisplayMappingResults(object):
                 tenPercentLength = geneLength*0.0001
                 SNPdensity = theGO["snpCount"]/geneLength
 
-                exonStarts = map(float, theGO['exonStarts'].split(",")[:-1])
-                exonEnds = map(float, theGO['exonEnds'].split(",")[:-1])
+                exonStarts = list(map(float, theGO['exonStarts'].split(",")[:-1]))
+                exonEnds = list(map(float, theGO['exonEnds'].split(",")[:-1]))
                 cdsStart = theGO['cdsStart']
                 cdsEnd = theGO['cdsEnd']
                 accession = theGO['NM_ID']
@@ -1391,7 +1419,7 @@ class DisplayMappingResults(object):
                             labelText = "3'"
                             im_drawer.text(
                                 text=labelText,
-                                xy=(utrEndPix+2,geneYLocation+self.EACH_GENE_HEIGHT),
+                                xy=(utrEndPix+2, geneYLocation+self.EACH_GENE_HEIGHT),
                                 font=ImageFont.truetype(font=ARIAL_FILE, size=2))
 
             #draw the genes as rectangles
@@ -1403,7 +1431,7 @@ class DisplayMappingResults(object):
 
             COORDS = "%d, %d, %d, %d" %(geneStartPix, geneYLocation, geneEndPix, (geneYLocation + self.EACH_GENE_HEIGHT))
             # NL: 06-02-2011 Rob required to display NCBI info in a new window
-            gifmap.areas.append(
+            gifmap.append(
                 HtmlGenWrapper.create_area_tag(
                     shape='rect',
                     coords=COORDS,
@@ -1544,7 +1572,7 @@ class DisplayMappingResults(object):
                                         counter = counter + 1
                                         if item.name == samplelist[k]:
                                             ind = counter
-                                    maxind=max(ind,maxind)
+                                    maxind=max(ind, maxind)
 
                                     # lines
                                     if (oldgeno[k] == -1 and _geno == -1):
@@ -1577,7 +1605,7 @@ class DisplayMappingResults(object):
                                     COORDS = "%d, %d, %d, %d" %(geneStartPix, geneYLocation+ind*self.EACH_GENE_HEIGHT, geneEndPix+1, (geneYLocation + ind*self.EACH_GENE_HEIGHT))
                                     TITLE = "Strain: %s, marker (%s) \n Position  %2.3f Mb." % (samplelist[k], _chr[j].name, float(txStart))
                                     HREF = ''
-                                    gifmap.areas.append(
+                                    gifmap.append(
                                         HtmlGenWrapper.create_area_tag(
                                             shape='rect',
                                             coords=COORDS,
@@ -1698,7 +1726,7 @@ class DisplayMappingResults(object):
                 WEBQTL_HREF = "javascript:rangeView('%s', %f, %f)" % (self.selectedChr - 1, max(0, (calBase-webqtlZoomWidth))/1000000.0, (calBase+webqtlZoomWidth)/1000000.0)
 
                 WEBQTL_TITLE = "Click to view this section of the genome in WebQTL"
-                gifmap.areas.append(
+                gifmap.append(
                     HtmlGenWrapper.create_area_tag(
                         shape='rect',
                         coords=WEBQTL_COORDS,
@@ -1710,7 +1738,7 @@ class DisplayMappingResults(object):
                     outline=self.CLICKABLE_WEBQTL_REGION_COLOR,
                     fill=self.CLICKABLE_WEBQTL_REGION_COLOR)
                 im_drawer.line(
-                    xy=((xBrowse1, paddingTop),( xBrowse1, (paddingTop + self.BAND_HEIGHT))),
+                    xy=((xBrowse1, paddingTop), ( xBrowse1, (paddingTop + self.BAND_HEIGHT))),
                     fill=self.CLICKABLE_WEBQTL_REGION_OUTLINE_COLOR)
 
                 if self.dataset.group.species == "mouse" or self.dataset.group.species == "rat":
@@ -1720,7 +1748,7 @@ class DisplayMappingResults(object):
                     else:
                         PHENOGEN_HREF = "https://phenogen.org/gene.jsp?speciesCB=Mm&auto=Y&geneTxt=chr%s:%d-%d&genomeVer=mm10" % (self.selectedChr, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases)
                     PHENOGEN_TITLE = "Click to view this section of the genome in PhenoGen"
-                    gifmap.areas.append(
+                    gifmap.append(
                         HtmlGenWrapper.create_area_tag(
                             shape='rect',
                             coords=PHENOGEN_COORDS,
@@ -1732,7 +1760,7 @@ class DisplayMappingResults(object):
                         outline=self.CLICKABLE_PHENOGEN_REGION_COLOR,
                         fill=self.CLICKABLE_PHENOGEN_REGION_COLOR)
                     im_drawer.line(
-                        xy=((xBrowse1, phenogenPaddingTop),( xBrowse1, (phenogenPaddingTop+self.BAND_HEIGHT))),
+                        xy=((xBrowse1, phenogenPaddingTop), ( xBrowse1, (phenogenPaddingTop+self.BAND_HEIGHT))),
                         fill=self.CLICKABLE_PHENOGEN_REGION_OUTLINE_COLOR)
 
                 UCSC_COORDS = "%d, %d, %d, %d" %(xBrowse1, ucscPaddingTop, xBrowse2, (ucscPaddingTop+self.BAND_HEIGHT))
@@ -1741,7 +1769,7 @@ class DisplayMappingResults(object):
                 else:
                     UCSC_HREF = "http://genome.ucsc.edu/cgi-bin/hgTracks?db=%s&position=chr%s:%d-%d" % (self._ucscDb, self.selectedChr, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases)
                 UCSC_TITLE = "Click to view this section of the genome in the UCSC Genome Browser"
-                gifmap.areas.append(
+                gifmap.append(
                     HtmlGenWrapper.create_area_tag(
                         shape='rect',
                         coords=UCSC_COORDS,
@@ -1763,7 +1791,7 @@ class DisplayMappingResults(object):
                 else:
                     ENSEMBL_HREF = "http://www.ensembl.org/Rattus_norvegicus/contigview?chr=%s&start=%d&end=%d" % (self.selectedChr, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases)
                 ENSEMBL_TITLE = "Click to view this section of the genome in the Ensembl Genome Browser"
-                gifmap.areas.append(HtmlGenWrapper.create_area_tag(
+                gifmap.append(HtmlGenWrapper.create_area_tag(
                     shape='rect',
                     coords=ENSEMBL_COORDS,
                     href=ENSEMBL_HREF,
@@ -1864,8 +1892,8 @@ class DisplayMappingResults(object):
                         continue
                     Xc = xLeftOffset + plotXScale*(_Mb - startMb)
                     if counter % NUM_MINOR_TICKS == 0: # Draw a MAJOR mark, not just a minor tick mark
-                        im_drawer.line(xy=((Xc,yZero),
-                                           (Xc,yZero+xMajorTickHeight)),
+                        im_drawer.line(xy=((Xc, yZero),
+                                           (Xc, yZero+xMajorTickHeight)),
                                        fill=xAxisTickMarkColor,
                                        width=X_MAJOR_TICK_THICKNESS) # Draw the MAJOR tick mark
                         labelStr = str(formatStr % _Mb) # What Mbase location to put on the label
@@ -1875,8 +1903,8 @@ class DisplayMappingResults(object):
                                        text=labelStr, font=MBLabelFont,
                                        fill=xAxisLabelColor)
                     else:
-                        im_drawer.line(xy=((Xc,yZero),
-                                          (Xc,yZero+xMinorTickHeight)),
+                        im_drawer.line(xy=((Xc, yZero),
+                                          (Xc, yZero+xMinorTickHeight)),
                                        fill=xAxisTickMarkColor,
                                        width=X_MINOR_TICK_THICKNESS) # Draw the MINOR tick mark
 
@@ -1909,7 +1937,7 @@ class DisplayMappingResults(object):
                 text="Megabases",
                 xy=(
                     xLeftOffset+(plotWidth-im_drawer.textsize(
-                        "Megabases",font=megabaseLabelFont)[0])/2,
+                        "Megabases", font=megabaseLabelFont)[0])/2,
                     strYLoc+MBLabelFont.font.height+10*(zoom%2)),
                 font=megabaseLabelFont, fill=BLACK)
             pass
@@ -1964,7 +1992,7 @@ class DisplayMappingResults(object):
             for j, ChrInfo in enumerate(ChrAInfo):
                 preLpos = -1
                 for i, item in enumerate(ChrInfo):
-                    Lname,Lpos = item
+                    Lname, Lpos = item
                     if Lpos != preLpos:
                         offsetA += stepA
                         differ = 1
@@ -1978,17 +2006,17 @@ class DisplayMappingResults(object):
                         Zorder = 0
                     if differ:
                         im_drawer.line(
-                            xy=((startPosX+Lpos,yZero),(xLeftOffset+offsetA,\
+                            xy=((startPosX+Lpos, yZero), (xLeftOffset+offsetA,\
                         yZero+25)),
                             fill=lineColor)
                         im_drawer.line(
-                            xy=((xLeftOffset+offsetA,yZero+25),(xLeftOffset+offsetA,\
+                            xy=((xLeftOffset+offsetA, yZero+25), (xLeftOffset+offsetA,\
                         yZero+40+Zorder*(LRectWidth+3))),
                             fill=lineColor)
                         rectColor = ORANGE
                     else:
                         im_drawer.line(
-                            xy=((xLeftOffset+offsetA, yZero+40+Zorder*(LRectWidth+3)-3),(\
+                            xy=((xLeftOffset+offsetA, yZero+40+Zorder*(LRectWidth+3)-3), (\
                         xLeftOffset+offsetA, yZero+40+Zorder*(LRectWidth+3))),
                             fill=lineColor)
                         rectColor = DEEPPINK
@@ -1996,7 +2024,7 @@ class DisplayMappingResults(object):
                         xy=((xLeftOffset+offsetA, yZero+40+Zorder*(LRectWidth+3)),
                             (xLeftOffset+offsetA-LRectHeight,
                              yZero+40+Zorder*(LRectWidth+3)+LRectWidth)),
-                        outline=rectColor,fill=rectColor,width = 0)
+                        outline=rectColor, fill=rectColor, width = 0)
                     COORDS="%d,%d,%d,%d"%(xLeftOffset+offsetA-LRectHeight, yZero+40+Zorder*(LRectWidth+3),\
                             xLeftOffset+offsetA,yZero+40+Zorder*(LRectWidth+3)+LRectWidth)
                     HREF = "/show_trait?trait_id=%s&dataset=%s" % (Lname, self.dataset.group.name+"Geno")
@@ -2007,11 +2035,11 @@ class DisplayMappingResults(object):
                         href=HREF,
                         target="_blank",
                         title="Locus : {}".format(Lname))
-                    gifmap.areas.append(Areas)
+                    gifmap.append(Areas)
                 ##piddle bug
                 if j == 0:
                     im_drawer.line(
-                        xy=((startPosX,yZero),(startPosX,yZero+40)),
+                        xy=((startPosX, yZero), (startPosX, yZero+40)),
                         fill=lineColor)
                 startPosX += (self.ChrLengthDistList[j]+self.GraphInterval)*plotXScale
 
@@ -2023,7 +2051,7 @@ class DisplayMappingResults(object):
                     strYLoc + MBLabelFont.font.height+ 10*(zoom%2)),
                 font=centimorganLabelFont, fill=BLACK)
 
-        im_drawer.line(xy=((xLeftOffset,yZero), (xLeftOffset+plotWidth,yZero)),
+        im_drawer.line(xy=((xLeftOffset, yZero), (xLeftOffset+plotWidth, yZero)),
                        fill=BLACK, width=X_AXIS_THICKNESS) # Draw the X axis itself
 
 
@@ -2125,7 +2153,7 @@ class DisplayMappingResults(object):
         #ZS: Convert to int if all axis values are whole numbers
         all_int = True
         for item in LRSAxisList:
-            if item.is_integer():
+            if isinstance(item, int):
                 continue
             else:
                 all_int = False
@@ -2163,7 +2191,7 @@ class DisplayMappingResults(object):
                 LRS_LOD_Max = 0.000001
             yTopOffset + 30*(zoom - 1)
             yLRS = yZero - (item/LRS_LOD_Max) * LRSHeightThresh
-            im_drawer.line(xy=((xLeftOffset,yLRS), (xLeftOffset-4,yLRS)),
+            im_drawer.line(xy=((xLeftOffset, yLRS), (xLeftOffset-4, yLRS)),
                            fill=self.LRS_COLOR, width=1*zoom)
             if all_int:
                 scaleStr = "%d" % item
@@ -2219,8 +2247,8 @@ class DisplayMappingResults(object):
                     shape='rect',
                     coords=sig_coords,
                     title=sig_title)
-                gifmap.areas.append(Areas1)
-                gifmap.areas.append(Areas2)
+                gifmap.append(Areas1)
+                gifmap.append(Areas2)
 
                 start_pos_x +=  (chr_length_dist+self.GraphInterval)*plotXScale
                 return start_pos_x
@@ -2239,7 +2267,7 @@ class DisplayMappingResults(object):
             lrsEdgeWidth = 1
         else:
             if self.additiveChecked:
-                additiveMax = max(map(lambda X : abs(X['additive']), self.qtlresults))
+                additiveMax = max([abs(X['additive']) for X in self.qtlresults])
             lrsEdgeWidth = 3
 
         if zoom == 2:
@@ -2406,7 +2434,7 @@ class DisplayMappingResults(object):
                     im_drawer.text(
                         text="5",
                         xy=(
-                            Xc-im_drawer.textsize("5",font=symbolFont)[0]/2+1,
+                            Xc-im_drawer.textsize("5", font=symbolFont)[0]/2+1,
                             Yc-4),
                         fill=point_color, font=symbolFont)
                 else:
@@ -2473,8 +2501,8 @@ class DisplayMappingResults(object):
                             )
                         else:
                             im_drawer.line(
-                                xy=((Xc0,yZero-(Yc0-yZero)),
-                                    (Xc,yZero-(Yc-yZero))),
+                                xy=((Xc0, yZero-(Yc0-yZero)),
+                                    (Xc, yZero-(Yc-yZero))),
                                 fill=minusColor, width=lineWidth
                                 #, clipX=(xLeftOffset, xLeftOffset + plotWidth)
                             )
@@ -2561,8 +2589,8 @@ class DisplayMappingResults(object):
 
         ###draw additive scale
         if not self.multipleInterval and self.additiveChecked:
-            additiveScaleFont=ImageFont.truetype(font=VERDANA_FILE,size=16*zoom)
-            additiveScale = Plot.detScaleOld(0,additiveMax)
+            additiveScaleFont=ImageFont.truetype(font=VERDANA_FILE, size=16*zoom)
+            additiveScale = Plot.detScaleOld(0, additiveMax)
             additiveStep = (additiveScale[1]-additiveScale[0])/additiveScale[2]
             additiveAxisList = Plot.frange(0, additiveScale[1], additiveStep)
             addPlotScale = AdditiveHeightThresh/additiveMax
@@ -2572,18 +2600,18 @@ class DisplayMappingResults(object):
             for item in additiveAxisList:
                 additiveY = yZero - item*addPlotScale
                 im_drawer.line(
-                    xy=((xLeftOffset + plotWidth,additiveY),
-                        (xLeftOffset+4+ plotWidth,additiveY)),
+                    xy=((xLeftOffset + plotWidth, additiveY),
+                        (xLeftOffset+4+ plotWidth, additiveY)),
                     fill=self.ADDITIVE_COLOR_POSITIVE, width=1*zoom)
                 scaleStr = "%2.3f" % item
                 im_drawer.text(
                     text=scaleStr,
-                    xy=(xLeftOffset + plotWidth +6,additiveY+TEXT_Y_DISPLACEMENT),
-                    font=additiveScaleFont,fill=self.ADDITIVE_COLOR_POSITIVE)
+                    xy=(xLeftOffset + plotWidth +6, additiveY+TEXT_Y_DISPLACEMENT),
+                    font=additiveScaleFont, fill=self.ADDITIVE_COLOR_POSITIVE)
 
             im_drawer.line(
-                xy=((xLeftOffset+plotWidth,additiveY),
-                    (xLeftOffset+plotWidth,yZero)),
+                xy=((xLeftOffset+plotWidth, additiveY),
+                    (xLeftOffset+plotWidth, yZero)),
                 fill=self.ADDITIVE_COLOR_POSITIVE, width=1*zoom)
 
         im_drawer.line(
@@ -2643,7 +2671,7 @@ class DisplayMappingResults(object):
                 chrFontZoom = 2
             else:
                 chrFontZoom = 1
-            chrLabelFont=ImageFont.truetype(font=VERDANA_FILE,size=24*chrFontZoom)
+            chrLabelFont=ImageFont.truetype(font=VERDANA_FILE, size=24*chrFontZoom)
 
             for i, _chr in enumerate(self.genotype):
                 if (i % 2 == 0):
@@ -2665,16 +2693,16 @@ class DisplayMappingResults(object):
                 TEXT_Y_DISPLACEMENT = 0
                 im_drawer.text(xy=(chrStartPix, yTopOffset + TEXT_Y_DISPLACEMENT),
                                text=_chr.name, font=chrLabelFont, fill=BLACK)
-                COORDS = "%d,%d,%d,%d" %(chrStartPix, yTopOffset, chrEndPix,yTopOffset +20)
+                COORDS = "%d,%d,%d,%d" %(chrStartPix, yTopOffset, chrEndPix, yTopOffset +20)
 
                 #add by NL 09-03-2010
-                HREF = "javascript:chrView(%d,%s);" % (i,self.ChrLengthMbList)
+                HREF = "javascript:chrView(%d,%s);" % (i, self.ChrLengthMbList)
                 #HREF = "javascript:changeView(%d,%s);" % (i,self.ChrLengthMbList)
                 Areas = HtmlGenWrapper.create_area_tag(
                     shape='rect',
                     coords=COORDS,
                     href=HREF)
-                gifmap.areas.append(Areas)
+                gifmap.append(Areas)
                 startPosX +=  (self.ChrLengthDistList[i]+self.GraphInterval)*plotXScale
 
         return plotXScale
@@ -2760,7 +2788,7 @@ class DisplayMappingResults(object):
 
                 this_row = [] #container for the cells of each row
                 selectCheck = HtmlGenWrapper.create_input_tag(
-                    type="checkbox",
+                    type_="checkbox",
                     name="selectCheck",
                     value=theGO["GeneSymbol"],
                     Class="checkbox trait_checkbox")  # checkbox for each row
@@ -2774,9 +2802,17 @@ class DisplayMappingResults(object):
                     geneIdString = 'http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=%s' % theGO["GeneID"]
 
                     if theGO["snpCount"]:
-                        snpString = HT.Href(url="http://genenetwork.org/webqtl/main.py?FormID=snpBrowser&chr=%s&start=%s&end=%s&geneName=%s&s1=%d&s2=%d" % (theGO["Chromosome"],
-                                theGO["TxStart"], theGO["TxEnd"], theGO["GeneSymbol"], self.diffCol[0], self.diffCol[1]),
-                                text=theGO["snpCount"], target="_blank", Class="normalsize")
+                        snpString = HT.Link(
+                            (f"http://genenetwork.org/webqtl/main.py?FormID=snpBrowser&"
+                             f"chr={theGO['Chromosome']}&"
+                             f"start={theGO['TxStart']}&"
+                             f"end={theGO['TxEnd']}&"
+                             f"geneName={theGO['GeneSymbol']}&"
+                             f"s1={self.diffCol[0]}&s2=%d"),
+                            str(theGO["snpCount"]) # The text to display
+                        )
+                        snpString.set_blank_target()
+                        snpString.set_attribute("class", "normalsize")
                     else:
                         snpString = 0
 
@@ -2817,7 +2853,7 @@ class DisplayMappingResults(object):
                     else:
                         chr_as_int = int(theGO["Chromosome"]) - 1
                     if refGene:
-                        literatureCorrelationString = str(self.getLiteratureCorrelation(self.cursor,refGene,theGO['GeneID']) or "N/A")
+                        literatureCorrelationString = str(self.getLiteratureCorrelation(self.cursor, refGene, theGO['GeneID']) or "N/A")
 
                         this_row = [selectCheck.__str__(),
                                     str(tableIterationsCnt),
@@ -2879,13 +2915,10 @@ class DisplayMappingResults(object):
             for gIndex, theGO in enumerate(geneCol):
                 this_row = []  # container for the cells of each row
                 selectCheck = str(HtmlGenWrapper.create_input_tag(
-                    type="checkbox",
+                    type_="checkbox",
                     name="selectCheck",
                     Class="checkbox trait_checkbox"))  # checkbox for each row
 
-                #ZS: May want to get this working again later
-                #webqtlSearch = HT.Href(os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE)+"?cmd=sch&gene=%s&alias=1&species=rat" % theGO["GeneSymbol"], ">>", target="_blank").__str__()
-
                 if theGO["GeneID"] != "":
                     geneSymbolNCBI = str(HtmlGenWrapper.create_link_tag(
                         "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids={}".format(theGO["GeneID"]),
@@ -2955,8 +2988,8 @@ class DisplayMappingResults(object):
         lCorr = None
         try:
             query = 'SELECT Value FROM LCorrRamin3 WHERE GeneId1 = %s and GeneId2 = %s'
-            for x,y in [(geneId1,geneId2),(geneId2,geneId1)]:
-                cursor.execute(query,(x,y))
+            for x, y in [(geneId1, geneId2), (geneId2, geneId1)]:
+                cursor.execute(query, (x, y))
                 lCorr =  cursor.fetchone()
                 if lCorr:
                     lCorr = lCorr[0]
diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py
index b858b573..68a8d5ba 100644
--- a/wqflask/wqflask/marker_regression/gemma_mapping.py
+++ b/wqflask/wqflask/marker_regression/gemma_mapping.py
@@ -218,9 +218,9 @@ def parse_loco_output(this_dataset, gwa_output_filename):
                             marker['chr'] = int(line.split("\t")[0][3:])
                         else:
                             marker['chr'] = int(line.split("\t")[0])
-                        if marker['chr'] > previous_chr:
+                        if marker['chr'] > int(previous_chr):
                             previous_chr = marker['chr']
-                        elif marker['chr'] < previous_chr:
+                        elif marker['chr'] < int(previous_chr):
                             break
                     else:
                         marker['chr'] = line.split("\t")[0]
diff --git a/wqflask/wqflask/marker_regression/plink_mapping.py b/wqflask/wqflask/marker_regression/plink_mapping.py
index 2f327faf..fd91b6ca 100644
--- a/wqflask/wqflask/marker_regression/plink_mapping.py
+++ b/wqflask/wqflask/marker_regression/plink_mapping.py
@@ -54,7 +54,7 @@ def gen_pheno_txt_file_plink(this_trait, dataset, vals, pheno_filename = ''):
     for i, sample in enumerate(ped_sample_list):
         try:
             value = vals[i]
-            value = str(value).replace('value=','')
+            value = str(value).replace('value=', '')
             value = value.strip()
         except:
             value = -9999
@@ -78,13 +78,13 @@ def gen_pheno_txt_file_plink(this_trait, dataset, vals, pheno_filename = ''):
 
 # get strain name from ped file in order
 def get_samples_from_ped_file(dataset):
-    ped_file= open("{}{}.ped".format(flat_files('mapping'), dataset.group.name),"r")
+    ped_file= open("{}{}.ped".format(flat_files('mapping'), dataset.group.name), "r")
     line = ped_file.readline()
     sample_list=[]
 
     while line:
-        lineList = string.split(string.strip(line), '\t')
-        lineList = map(string.strip, lineList)
+        lineList = line.strip().split('\t')
+        lineList = [item.strip() for item in lineList]
 
         sample_name = lineList[0]
         sample_list.append(sample_name)
@@ -111,7 +111,7 @@ def parse_plink_output(output_filename, species):
         line_list = build_line_list(line=line)
 
         # only keep the records whose chromosome name is in db
-        if species.chromosomes.chromosomes.has_key(int(line_list[0])) and line_list[-1] and line_list[-1].strip()!='NA':
+        if int(line_list[0]) in species.chromosomes.chromosomes and line_list[-1] and line_list[-1].strip()!='NA':
 
             chr_name = species.chromosomes.chromosomes[int(line_list[0])]
             snp = line_list[1]
@@ -121,7 +121,7 @@ def parse_plink_output(output_filename, species):
                 if p_value < threshold_p_value:
                     p_value_dict[snp] = float(p_value)
 
-            if plink_results.has_key(chr_name):
+            if chr_name in plink_results:
                 value_list = plink_results[chr_name]
 
                 # pvalue range is [0,1]
@@ -155,8 +155,8 @@ def parse_plink_output(output_filename, species):
 # output: lineList list
 #######################################################
 def build_line_list(line=None):
-    line_list = string.split(string.strip(line),' ')# irregular number of whitespaces between columns
-    line_list = [item for item in line_list if item <>'']
-    line_list = map(string.strip, line_list)
+    line_list = line.strip().split(' ')# irregular number of whitespaces between columns
+    line_list = [item for item in line_list if item !='']
+    line_list = [item.strip() for item in line_list]
 
-    return line_list
\ No newline at end of file
+    return line_list
diff --git a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
index 6b4c05ea..78b1f7b0 100644
--- a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
+++ b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
@@ -252,4 +252,4 @@ def natural_sort(marker_list):
     """
     convert = lambda text: int(text) if text.isdigit() else text.lower()
     alphanum_key = lambda key: [ convert(c) for c in re.split('([0-9]+)', str(marker_list[key]['chr'])) ]
-    return sorted(range(len(marker_list)), key = alphanum_key)
\ No newline at end of file
+    return sorted(list(range(len(marker_list))), key = alphanum_key)
\ No newline at end of file
diff --git a/wqflask/wqflask/marker_regression/rqtl_mapping.py b/wqflask/wqflask/marker_regression/rqtl_mapping.py
index c5590a85..0a5758af 100644
--- a/wqflask/wqflask/marker_regression/rqtl_mapping.py
+++ b/wqflask/wqflask/marker_regression/rqtl_mapping.py
@@ -42,7 +42,7 @@ def run_rqtl_geno(vals, samples, dataset, mapping_scale, method, model, permChec
     png           = ro.r["png"]                     # Map the png function
     dev_off       = ro.r["dev.off"]                 # Map the device off function
 
-    print(r_library("qtl"))                         # Load R/qtl
+    print((r_library("qtl")))                         # Load R/qtl
 
     logger.info("QTL library loaded");
 
diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py
index 8a44b3fd..fa61272f 100644
--- a/wqflask/wqflask/marker_regression/run_mapping.py
+++ b/wqflask/wqflask/marker_regression/run_mapping.py
@@ -1,5 +1,3 @@
-from __future__ import absolute_import, print_function, division
-
 from base.trait import GeneralTrait
 from base import data_set  #import create_dataset
 
@@ -18,7 +16,7 @@ import uuid
 import rpy2.robjects as ro
 import numpy as np
 
-import cPickle as pickle
+import pickle as pickle
 import itertools
 
 import simplejson as json
@@ -140,7 +138,7 @@ class RunMapping(object):
             mapping_results_filename = self.dataset.group.name + "_" + ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6))
             self.mapping_results_path = "{}{}.csv".format(webqtlConfig.GENERATED_IMAGE_DIR, mapping_results_filename)
 
-        if start_vars['manhattan_plot'] == "True":
+        if start_vars['manhattan_plot'] == "true":
             self.manhattan_plot = True
         else:
             self.manhattan_plot = False
@@ -347,7 +345,7 @@ class RunMapping(object):
                   if marker['chr1'] > 0 or marker['chr1'] == "X" or marker['chr1'] == "X/Y":
                       if marker['chr1'] > highest_chr or marker['chr1'] == "X" or marker['chr1'] == "X/Y":
                           highest_chr = marker['chr1']
-                      if 'lod_score' in marker.keys():
+                      if 'lod_score' in list(marker.keys()):
                           self.qtl_results.append(marker)
 
               self.trimmed_markers = results
@@ -411,8 +409,8 @@ class RunMapping(object):
 
                   self.results_for_browser.append(browser_marker)
                   self.annotations_for_browser.append(annot_marker)
-                  if marker['chr'] > 0 or marker['chr'] == "X" or marker['chr'] == "X/Y":
-                      if marker['chr'] > highest_chr or marker['chr'] == "X" or marker['chr'] == "X/Y":
+                  if str(marker['chr']) > '0' or str(marker['chr']) == "X" or str(marker['chr']) == "X/Y":
+                      if str(marker['chr']) > str(highest_chr) or str(marker['chr']) == "X" or str(marker['chr']) == "X/Y":
                           highest_chr = marker['chr']
                       if ('lod_score' in marker.keys()) or ('lrs_value' in marker.keys()):
                           if 'Mb' in marker.keys():
@@ -547,9 +545,9 @@ def export_mapping_results(dataset, trait, markers, results_path, mapping_scale,
             output_file.write("Mb," + score_type)
         if 'cM' in markers[0]:
             output_file.write("Cm," + score_type)
-        if "additive" in markers[0].keys():
+        if "additive" in list(markers[0].keys()):
             output_file.write(",Additive")
-        if "dominance" in markers[0].keys():
+        if "dominance" in list(markers[0].keys()):
             output_file.write(",Dominance")
         output_file.write("\n")
         for i, marker in enumerate(markers):
@@ -562,17 +560,17 @@ def export_mapping_results(dataset, trait, markers, results_path, mapping_scale,
                 output_file.write(str(marker['lod_score']))
             else:
                 output_file.write(str(marker['lrs_value']))
-            if "additive" in marker.keys():
+            if "additive" in list(marker.keys()):
                 output_file.write("," + str(marker['additive']))
-            if "dominance" in marker.keys():
+            if "dominance" in list(marker.keys()):
                 output_file.write("," + str(marker['dominance']))
             if i < (len(markers) - 1):
                 output_file.write("\n")
 
 def trim_markers_for_figure(markers):
-    if 'p_wald' in markers[0].keys():
+    if 'p_wald' in list(markers[0].keys()):
         score_type = 'p_wald'
-    elif 'lod_score' in markers[0].keys():
+    elif 'lod_score' in list(markers[0].keys()):
         score_type = 'lod_score'
     else:
         score_type = 'lrs_value'
@@ -630,7 +628,7 @@ def trim_markers_for_figure(markers):
     return filtered_markers
 
 def trim_markers_for_table(markers):
-    if 'lod_score' in markers[0].keys():
+    if 'lod_score' in list(markers[0].keys()):
         sorted_markers = sorted(markers, key=lambda k: k['lod_score'], reverse=True)
     else:
         sorted_markers = sorted(markers, key=lambda k: k['lrs_value'], reverse=True)
@@ -714,10 +712,10 @@ def get_genofile_samplelist(dataset):
 def get_perm_strata(this_trait, sample_list, categorical_vars, used_samples):
     perm_strata_strings = []
     for sample in used_samples:
-        if sample in sample_list.sample_attribute_values.keys():
+        if sample in list(sample_list.sample_attribute_values.keys()):
             combined_string = ""
             for var in categorical_vars:
-                if var in sample_list.sample_attribute_values[sample].keys():
+                if var in list(sample_list.sample_attribute_values[sample].keys()):
                     combined_string += str(sample_list.sample_attribute_values[sample][var])
                 else:
                     combined_string += "NA"
@@ -726,8 +724,8 @@ def get_perm_strata(this_trait, sample_list, categorical_vars, used_samples):
 
         perm_strata_strings.append(combined_string)
 
-    d = dict([(y,x+1) for x,y in enumerate(sorted(set(perm_strata_strings)))])
+    d = dict([(y, x+1) for x, y in enumerate(sorted(set(perm_strata_strings)))])
     list_to_numbers = [d[x] for x in perm_strata_strings]
     perm_strata = list_to_numbers
 
-    return perm_strata
\ No newline at end of file
+    return perm_strata
diff --git a/wqflask/wqflask/model.py b/wqflask/wqflask/model.py
index 38117a8e..772f74e4 100644
--- a/wqflask/wqflask/model.py
+++ b/wqflask/wqflask/model.py
@@ -1,5 +1,3 @@
-from __future__ import print_function, division, absolute_import
-
 import uuid
 import datetime
 
@@ -18,7 +16,7 @@ from wqflask.database import Base, init_db
 
 class User(Base):
     __tablename__ = "user"
-    id = Column(Unicode(36), primary_key=True, default=lambda: unicode(uuid.uuid4()))
+    id = Column(Unicode(36), primary_key=True, default=lambda: str(uuid.uuid4()))
     email_address = Column(Unicode(50), unique=True, nullable=False)
 
     # Todo: Turn on strict mode for Mysql
@@ -120,7 +118,7 @@ class User(Base):
 
 class Login(Base):
     __tablename__ = "login"
-    id = Column(Unicode(36), primary_key=True, default=lambda: unicode(uuid.uuid4()))
+    id = Column(Unicode(36), primary_key=True, default=lambda: str(uuid.uuid4()))
     user = Column(Unicode(36), ForeignKey('user.id'))
     timestamp = Column(DateTime(), default=lambda: datetime.datetime.utcnow())
     ip_address = Column(Unicode(39))
@@ -138,7 +136,7 @@ class Login(Base):
 
 class UserCollection(Base):
     __tablename__ = "user_collection"
-    id = Column(Unicode(36), primary_key=True, default=lambda: unicode(uuid.uuid4()))
+    id = Column(Unicode(36), primary_key=True, default=lambda: str(uuid.uuid4()))
     user = Column(Unicode(36), ForeignKey('user.id'))
 
     # I'd prefer this to not have a length, but for the index below it needs one
@@ -168,4 +166,4 @@ def display_collapsible(number):
 
 def user_uuid():
     """Unique cookie for a user"""
-    user_uuid = request.cookies.get('user_uuid')
\ No newline at end of file
+    user_uuid = request.cookies.get('user_uuid')
diff --git a/wqflask/wqflask/network_graph/network_graph.py b/wqflask/wqflask/network_graph/network_graph.py
index f61c40b4..723a749f 100644
--- a/wqflask/wqflask/network_graph/network_graph.py
+++ b/wqflask/wqflask/network_graph/network_graph.py
@@ -1,4 +1,4 @@
-## Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
+# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
 #
 # This program is free software: you can redistribute it and/or modify it
 # under the terms of the GNU Affero General Public License
@@ -18,50 +18,21 @@
 #
 # This module is used by GeneNetwork project (www.genenetwork.org)
 
-from __future__ import absolute_import, print_function, division
-
-import sys
-
-import string
-import cPickle
-import os
-import time
-import pp
-import math
-import collections
-import resource
-
 import scipy
-
 import simplejson as json
 
-from rpy2.robjects.packages import importr
-import rpy2.robjects as robjects
-
-from pprint import pformat as pf
-
-from utility.THCell import THCell
-from utility.TDCell import TDCell
 from base.trait import create_trait
 from base import data_set
-from utility import webqtlUtil, helper_functions, corr_result_helpers
+from utility import helper_functions
+from utility import corr_result_helpers
 from utility.tools import GN2_BRANCH_URL
-from db import webqtlDatabaseFunction
-import utility.webqtlUtil #this is for parallel computing only.
-from wqflask.correlation import correlation_functions
-from utility.benchmark import Bench
-
-from MySQLdb import escape_string as escape
-
-from pprint import pformat as pf
-
-from flask import Flask, g
 
 
 class NetworkGraph(object):
 
     def __init__(self, start_vars):
-        trait_db_list = [trait.strip() for trait in start_vars['trait_list'].split(',')]
+        trait_db_list = [trait.strip()
+                         for trait in start_vars['trait_list'].split(',')]
 
         helper_functions.get_trait_db_obs(self, trait_db_list)
 
@@ -89,7 +60,8 @@ class NetworkGraph(object):
                     this_trait_vals.append('')
             self.sample_data.append(this_trait_vals)
 
-        self.lowest_overlap = 8 #ZS: Variable set to the lowest overlapping samples in order to notify user, or 8, whichever is lower (since 8 is when we want to display warning)
+        # ZS: Variable set to the lowest overlapping samples in order to notify user, or 8, whichever is lower (since 8 is when we want to display warning)
+        self.lowest_overlap = 8
 
         self.nodes_list = []
         self.edges_list = []
@@ -101,9 +73,9 @@ class NetworkGraph(object):
             this_sample_data = this_trait.data
 
             corr_result_row = []
-            is_spearman = False #ZS: To determine if it's above or below the diagonal
+            is_spearman = False  # ZS: To determine if it's above or below the diagonal
 
-            max_corr = 0 #ZS: Used to determine whether node should be hidden when correlation coefficient slider is used
+            max_corr = 0  # ZS: Used to determine whether node should be hidden when correlation coefficient slider is used
 
             for target in self.trait_list:
                 target_trait = target[0]
@@ -122,20 +94,23 @@ class NetworkGraph(object):
                         this_trait_vals.append(sample_value)
                         target_vals.append(target_sample_value)
 
-                this_trait_vals, target_vals, num_overlap = corr_result_helpers.normalize_values(this_trait_vals, target_vals)
+                this_trait_vals, target_vals, num_overlap = corr_result_helpers.normalize_values(
+                    this_trait_vals, target_vals)
 
                 if num_overlap < self.lowest_overlap:
                     self.lowest_overlap = num_overlap
                 if num_overlap == 0:
                     continue
                 else:
-                    pearson_r, pearson_p = scipy.stats.pearsonr(this_trait_vals, target_vals)
+                    pearson_r, pearson_p = scipy.stats.pearsonr(
+                        this_trait_vals, target_vals)
                     if is_spearman == False:
                         sample_r, sample_p = pearson_r, pearson_p
                         if sample_r == 1:
                             continue
                     else:
-                        sample_r, sample_p = scipy.stats.spearmanr(this_trait_vals, target_vals)
+                        sample_r, sample_p = scipy.stats.spearmanr(
+                            this_trait_vals, target_vals)
 
                     if -1 <= sample_r < -0.7:
                         color = "#0000ff"
@@ -153,44 +128,44 @@ class NetworkGraph(object):
                         color = "#ffa500"
                         width = 2
                     elif 0.7 <= sample_r <= 1:
-                        color = "#ff0000"  
-                        width = 3 
+                        color = "#ff0000"
+                        width = 3
                     else:
                         color = "#000000"
-                        width = 0                      
+                        width = 0
 
                     if abs(sample_r) > max_corr:
                         max_corr = abs(sample_r)
 
-                    edge_data = {'id' : str(this_trait.name) + '_to_' + str(target_trait.name),
-                                 'source' : str(this_trait.name) + ":" + str(this_trait.dataset.name),
-                                 'target' : str(target_trait.name) + ":" + str(target_trait.dataset.name),
-                                 'correlation' : round(sample_r, 3),
-                                 'abs_corr' : abs(round(sample_r, 3)),
-                                 'p_value' : round(sample_p, 3),
-                                 'overlap' : num_overlap,
-                                 'color' : color,
-                                 'width' : width }
+                    edge_data = {'id': str(this_trait.name) + '_to_' + str(target_trait.name),
+                                 'source': str(this_trait.name) + ":" + str(this_trait.dataset.name),
+                                 'target': str(target_trait.name) + ":" + str(target_trait.dataset.name),
+                                 'correlation': round(sample_r, 3),
+                                 'abs_corr': abs(round(sample_r, 3)),
+                                 'p_value': round(sample_p, 3),
+                                 'overlap': num_overlap,
+                                 'color': color,
+                                 'width': width}
 
-                    edge_dict = { 'data' : edge_data }
+                    edge_dict = {'data': edge_data}
 
                     self.edges_list.append(edge_dict)
 
             if trait_db[1].type == "ProbeSet":
-                node_dict = { 'data' : {'id' : str(this_trait.name) + ":" + str(this_trait.dataset.name), 
-                                        'label' : this_trait.symbol,
-                                        'symbol' : this_trait.symbol,
-                                        'geneid' : this_trait.geneid,
-                                        'omim' : this_trait.omim,
-                                        'max_corr' : max_corr } }
+                node_dict = {'data': {'id': str(this_trait.name) + ":" + str(this_trait.dataset.name),
+                                      'label': this_trait.symbol,
+                                      'symbol': this_trait.symbol,
+                                      'geneid': this_trait.geneid,
+                                      'omim': this_trait.omim,
+                                      'max_corr': max_corr}}
             elif trait_db[1].type == "Publish":
-                node_dict = { 'data' : {'id' : str(this_trait.name) + ":" + str(this_trait.dataset.name), 
-                                        'label' : this_trait.name,
-                                        'max_corr' : max_corr } }
+                node_dict = {'data': {'id': str(this_trait.name) + ":" + str(this_trait.dataset.name),
+                                      'label': this_trait.name,
+                                      'max_corr': max_corr}}
             else:
-                node_dict = { 'data' : {'id' : str(this_trait.name) + ":" + str(this_trait.dataset.name), 
-                                        'label' : this_trait.name,
-                                        'max_corr' : max_corr } }
+                node_dict = {'data': {'id': str(this_trait.name) + ":" + str(this_trait.dataset.name),
+                                      'label': this_trait.name,
+                                      'max_corr': max_corr}}
             self.nodes_list.append(node_dict)
 
         self.elements = json.dumps(self.nodes_list + self.edges_list)
@@ -200,13 +175,13 @@ class NetworkGraph(object):
         for sample in self.all_sample_list:
             groups.append(1)
 
-        self.js_data = dict(traits = [trait.name for trait in self.traits],
-                            groups = groups,
-                            cols = range(len(self.traits)),
-                            rows = range(len(self.traits)),
-                            samples = self.all_sample_list,
-                            sample_data = self.sample_data,
-                            elements = self.elements,)
+        self.js_data = dict(traits=[trait.name for trait in self.traits],
+                            groups=groups,
+                            cols=list(range(len(self.traits))),
+                            rows=list(range(len(self.traits))),
+                            samples=self.all_sample_list,
+                            sample_data=self.sample_data,
+                            elements=self.elements,)
 
     def get_trait_db_obs(self, trait_db_list):
         self.trait_list = []
@@ -216,6 +191,6 @@ class NetworkGraph(object):
             trait_name, dataset_name = trait_db.split(":")
             dataset_ob = data_set.create_dataset(dataset_name)
             trait_ob = create_trait(dataset=dataset_ob,
-                                   name=trait_name,
-                                   cellid=None)
-            self.trait_list.append((trait_ob, dataset_ob))
\ No newline at end of file
+                                    name=trait_name,
+                                    cellid=None)
+            self.trait_list.append((trait_ob, dataset_ob))
diff --git a/wqflask/wqflask/news.py b/wqflask/wqflask/news.py
index 8bc6b889..0675ec4b 100644
--- a/wqflask/wqflask/news.py
+++ b/wqflask/wqflask/news.py
@@ -1,7 +1,3 @@
-from __future__ import absolute_import, print_function, division
-import sys
-reload(sys)
-sys.setdefaultencoding('utf8')
 from flask import g
 
 class News(object):
diff --git a/wqflask/wqflask/parser.py b/wqflask/wqflask/parser.py
index 1ca5ecff..76fae54b 100644
--- a/wqflask/wqflask/parser.py
+++ b/wqflask/wqflask/parser.py
@@ -17,8 +17,6 @@ be acceptable.]
 
 """
 
-from __future__ import print_function, division
-
 import re
 
 from pprint import pformat as pf
@@ -78,22 +76,6 @@ def parse(pstring):
     logger.debug("* items are:", pf(items) + "\n")
     return(items)
 
-    #def encregexp(self,str):
-    #    if not str:
-    #        return []
-    #    else:
-    #        wildcardkeyword = str.strip()
-    #        wildcardkeyword = string.replace(wildcardkeyword,',',' ')
-    #        wildcardkeyword = string.replace(wildcardkeyword,';',' ')
-    #        wildcardkeyword = wildcardkeyword.split()
-    #    NNN = len(wildcardkeyword)
-    #    for i in range(NNN):
-    #        keyword = wildcardkeyword[i]
-    #        keyword = string.replace(keyword,"*",".*")
-    #        keyword = string.replace(keyword,"?",".")
-    #        wildcardkeyword[i] = keyword#'[[:<:]]'+ keyword+'[[:>:]]'
-    #    return wildcardkeyword
-
 
 if __name__ == '__main__':
     parse("foo=[3 2 1]")
diff --git a/wqflask/wqflask/pbkdf2.py b/wqflask/wqflask/pbkdf2.py
index f7f61a09..aea5b06c 100644
--- a/wqflask/wqflask/pbkdf2.py
+++ b/wqflask/wqflask/pbkdf2.py
@@ -1,140 +1,20 @@
-# -*- coding: utf-8 -*-
-"""
-    pbkdf2
-    ~~~~~~
-
-    This module implements pbkdf2 for Python.  It also has some basic
-    tests that ensure that it works.  The implementation is straightforward
-    and uses stdlib only stuff and can be easily be copy/pasted into
-    your favourite application.
-
-    Use this as replacement for bcrypt that does not need a c implementation
-    of a modified blowfish crypto algo.
-
-    Example usage:
-
-    >>> pbkdf2_hex('what i want to hash', 'the random salt')
-    'fa7cc8a2b0a932f8e6ea42f9787e9d36e592e0c222ada6a9'
-
-    How to use this:
-
-    1.  Use a constant time string compare function to compare the stored hash
-        with the one you're generating::
-
-            def safe_str_cmp(a, b):
-                if len(a) != len(b):
-                    return False
-                rv = 0
-                for x, y in izip(a, b):
-                    rv |= ord(x) ^ ord(y)
-                return rv == 0
-
-    2.  Use `os.urandom` to generate a proper salt of at least 8 byte.
-        Use a unique salt per hashed password.
-
-    3.  Store ``algorithm$salt:costfactor$hash`` in the database so that
-        you can upgrade later easily to a different algorithm if you need
-        one.  For instance ``PBKDF2-256$thesalt:10000$deadbeef...``.
-
-
-    :copyright: (c) Copyright 2011 by Armin Ronacher.
-    :license: BSD, see LICENSE for more details.
-"""
-import hmac
 import hashlib
-from struct import Struct
-from operator import xor
-from itertools import izip, starmap
 
+from werkzeug.security import safe_str_cmp as ssc
 
-_pack_int = Struct('>I').pack
 
-
-def pbkdf2_hex(data, salt, iterations=1000, keylen=24, hashfunc=None):
-    """Like :func:`pbkdf2_bin` but returns a hex encoded string."""
-    return pbkdf2_bin(data, salt, iterations, keylen, hashfunc).encode('hex')
-
-
-def pbkdf2_bin(data, salt, iterations=1000, keylen=24, hashfunc=None):
-    """Returns a binary digest for the PBKDF2 hash algorithm of `data`
-    with the given `salt`.  It iterates `iterations` time and produces a
-    key of `keylen` bytes.  By default SHA-1 is used as hash function,
-    a different hashlib `hashfunc` can be provided.
+# Replace this because it just wraps around Python3's internal
+# functions. Added this during migration.
+def pbkdf2_hex(data, salt, iterations=1000, keylen=24, hashfunc="sha1"):
+    """Wrapper function of python's hashlib.pbkdf2_hmac.
     """
-    hashfunc = hashfunc or hashlib.sha1
-    mac = hmac.new(data, None, hashfunc)
-    def _pseudorandom(x, mac=mac):
-        h = mac.copy()
-        h.update(x)
-        return map(ord, h.digest())
-    buf = []
-    for block in xrange(1, -(-keylen // mac.digest_size) + 1):
-        rv = u = _pseudorandom(salt + _pack_int(block))
-        for i in xrange(iterations - 1):
-            u = _pseudorandom(''.join(map(chr, u)))
-            rv = list(starmap(xor, izip(rv, u)))
-        buf.extend(rv)
-    return ''.join(map(chr, buf))[:keylen]
+    dk = hashlib.pbkdf2_hmac(hashfunc,
+                             bytes(data, "utf-8"),  # password
+                             bytes(salt, "utf-8"),  # salt
+                             iterations,
+                             keylen)
+    return dk.hex()
 
 
 def safe_str_cmp(a, b):
-    if len(a) != len(b):
-        return False
-    rv = 0
-    for x, y in izip(a, b):
-        rv |= ord(x) ^ ord(y)
-    return rv == 0
-
-
-
-def test():
-    failed = []
-    def check(data, salt, iterations, keylen, expected):
-        rv = pbkdf2_hex(data, salt, iterations, keylen)
-        if rv != expected:
-            print 'Test failed:'
-            print '  Expected:   %s' % expected
-            print '  Got:        %s' % rv
-            print '  Parameters:'
-            print '    data=%s' % data
-            print '    salt=%s' % salt
-            print '    iterations=%d' % iterations
-            print
-            failed.append(1)
-
-    # From RFC 6070
-    check('password', 'salt', 1, 20,
-          '0c60c80f961f0e71f3a9b524af6012062fe037a6')
-    check('password', 'salt', 2, 20,
-          'ea6c014dc72d6f8ccd1ed92ace1d41f0d8de8957')
-    check('password', 'salt', 4096, 20,
-          '4b007901b765489abead49d926f721d065a429c1')
-    check('passwordPASSWORDpassword', 'saltSALTsaltSALTsaltSALTsaltSALTsalt',
-          4096, 25, '3d2eec4fe41c849b80c8d83662c0e44a8b291a964cf2f07038')
-    check('pass\x00word', 'sa\x00lt', 4096, 16,
-          '56fa6aa75548099dcc37d7f03425e0c3')
-    # This one is from the RFC but it just takes for ages
-    ##check('password', 'salt', 16777216, 20,
-    ##      'eefe3d61cd4da4e4e9945b3d6ba2158c2634e984')
-
-    # From Crypt-PBKDF2
-    check('password', 'ATHENA.MIT.EDUraeburn', 1, 16,
-          'cdedb5281bb2f801565a1122b2563515')
-    check('password', 'ATHENA.MIT.EDUraeburn', 1, 32,
-          'cdedb5281bb2f801565a1122b25635150ad1f7a04bb9f3a333ecc0e2e1f70837')
-    check('password', 'ATHENA.MIT.EDUraeburn', 2, 16,
-          '01dbee7f4a9e243e988b62c73cda935d')
-    check('password', 'ATHENA.MIT.EDUraeburn', 2, 32,
-          '01dbee7f4a9e243e988b62c73cda935da05378b93244ec8f48a99e61ad799d86')
-    check('password', 'ATHENA.MIT.EDUraeburn', 1200, 32,
-          '5c08eb61fdf71e4e4ec3cf6ba1f5512ba7e52ddbc5e5142f708a31e2e62b1e13')
-    check('X' * 64, 'pass phrase equals block size', 1200, 32,
-          '139c30c0966bc32ba55fdbf212530ac9c5ec59f1a452f5cc9ad940fea0598ed1')
-    check('X' * 65, 'pass phrase exceeds block size', 1200, 32,
-          '9ccad6d468770cd51b10e6a68721be611a8b4d282601db3b36be9246915ec82a')
-
-    raise SystemExit(bool(failed))
-
-
-if __name__ == '__main__':
-    test()
+    return ssc(a, b)
diff --git a/wqflask/wqflask/resource_manager.py b/wqflask/wqflask/resource_manager.py
index 14ff2183..85cbb2fd 100644
--- a/wqflask/wqflask/resource_manager.py
+++ b/wqflask/wqflask/resource_manager.py
@@ -1,5 +1,3 @@
-from __future__ import print_function, division, absolute_import
-
 import json
 
 from flask import (Flask, g, render_template, url_for, request, make_response,
@@ -125,10 +123,10 @@ def add_group_to_resource():
 
 def get_group_names(group_masks):
     group_masks_with_names = {}
-    for group_id, group_mask in group_masks.iteritems():
+    for group_id, group_mask in list(group_masks.items()):
         this_mask = group_mask
         group_name = get_group_info(group_id)['name']
         this_mask['name'] = group_name
         group_masks_with_names[group_id] = this_mask
     
-    return group_masks_with_names
\ No newline at end of file
+    return group_masks_with_names
diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py
index f63a84d1..ce836ce2 100644
--- a/wqflask/wqflask/search_results.py
+++ b/wqflask/wqflask/search_results.py
@@ -1,5 +1,3 @@
-from __future__ import absolute_import, print_function, division
-
 import re
 import uuid
 from math import *
@@ -53,7 +51,7 @@ views.py).
         search = self.search_terms
         self.original_search_string = self.search_terms
         # check for dodgy search terms
-        rx = re.compile(r'.*\W(href|http|sql|select|update)\W.*',re.IGNORECASE)
+        rx = re.compile(r'.*\W(href|http|sql|select|update)\W.*', re.IGNORECASE)
         if rx.match(search):
             logger.info("Regex failed search")
             self.search_term_exists = False
@@ -123,7 +121,7 @@ views.py).
                 trait_dict['hmac'] = hmac.data_hmac('{}:{}'.format(this_trait.name, this_trait.dataset.name))
                 if this_trait.dataset.type == "ProbeSet":
                     trait_dict['symbol'] = this_trait.symbol
-                    trait_dict['description'] = this_trait.description_display.decode('utf-8', 'replace')
+                    trait_dict['description'] = this_trait.description_display
                     trait_dict['location'] = this_trait.location_repr
                     trait_dict['mean'] = "N/A"
                     trait_dict['additive'] = "N/A"
@@ -151,6 +149,10 @@ views.py).
                     trait_dict['additive'] = "N/A"
                     if this_trait.additive != "":
                         trait_dict['additive'] = '%.3f' % this_trait.additive
+                # Convert any bytes in dict to a normal utf-8 string
+                for key in trait_dict.keys():
+                    if isinstance(trait_dict[key], bytes):
+                        trait_dict[key] = trait_dict[key].decode('utf-8')
                 trait_list.append(trait_dict)
 
         self.trait_list = json.dumps(trait_list)
@@ -272,7 +274,7 @@ def get_GO_symbols(a_search):
 def insert_newlines(string, every=64):
     """ This is because it is seemingly impossible to change the width of the description column, so I'm just manually adding line breaks """
     lines = []
-    for i in xrange(0, len(string), every):
+    for i in range(0, len(string), every):
         lines.append(string[i:i+every])
     return '\n'.join(lines)
 
diff --git a/wqflask/wqflask/send_mail.py b/wqflask/wqflask/send_mail.py
index bf5d0dd8..86e8a558 100644
--- a/wqflask/wqflask/send_mail.py
+++ b/wqflask/wqflask/send_mail.py
@@ -1,5 +1,3 @@
-from __future__ import absolute_import, division, print_function
-
 import datetime
 import time
 
diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py
index 356db7bc..37c1d6d5 100644
--- a/wqflask/wqflask/show_trait/SampleList.py
+++ b/wqflask/wqflask/show_trait/SampleList.py
@@ -1,35 +1,27 @@
-from __future__ import absolute_import, print_function, division
-
+import re
 import itertools
 
-import numpy as np
-from flask import Flask, g
+from flask import g
+from base import webqtlCaseData
 from pprint import pformat as pf
-from scipy import stats
 
-from base import webqtlCaseData
-from base.trait import GeneralTrait
-from utility import logger
-from utility import webqtlUtil
 from utility import Plot
 from utility import Bunch
 
-logger = logger.getLogger(__name__ )
-
 class SampleList(object):
     def __init__(self,
                  dataset,
                  sample_names,
                  this_trait,
-                 sample_group_type = "primary",
-                 header = "Samples"):
+                 sample_group_type="primary",
+                 header="Samples"):
 
         self.dataset = dataset
         self.this_trait = this_trait
         self.sample_group_type = sample_group_type    # primary or other
         self.header = header
 
-        self.sample_list = [] # The actual list
+        self.sample_list = []  # The actual list
         self.sample_attribute_values = {}
 
         self.get_attributes()
@@ -40,39 +32,55 @@ class SampleList(object):
         for counter, sample_name in enumerate(sample_names, 1):
             sample_name = sample_name.replace("_2nd_", "")
 
-            if type(self.this_trait) is list: # ZS: self.this_trait will be a list if it is a Temp trait
-                if counter <= len(self.this_trait) and str(self.this_trait[counter-1]).upper() != 'X':
-                    sample = webqtlCaseData.webqtlCaseData(name=sample_name, value=float(self.this_trait[counter-1]))
+            # ZS: self.this_trait will be a list if it is a Temp trait
+            if isinstance(self.this_trait, list):
+                if (counter <= len(self.this_trait) and
+                        str(self.this_trait[counter-1]).upper() != 'X'):
+                    sample = webqtlCaseData.webqtlCaseData(
+                        name=sample_name,
+                        value=float(self.this_trait[counter-1]))
                 else:
                     sample = webqtlCaseData.webqtlCaseData(name=sample_name)
             else:
-                # ZS - If there's no value for the sample/strain, create the sample object (so samples with no value are still displayed in the table)
+                # ZS - If there's no value for the sample/strain,
+                # create the sample object (so samples with no value
+                # are still displayed in the table)
                 try:
                     sample = self.this_trait.data[sample_name]
                 except KeyError:
                     sample = webqtlCaseData.webqtlCaseData(name=sample_name)
 
             sample.extra_info = {}
-            if self.dataset.group.name == 'AXBXA' and sample_name in ('AXB18/19/20','AXB13/14','BXA8/17'):
+            if (self.dataset.group.name == 'AXBXA' and
+                    sample_name in ('AXB18/19/20', 'AXB13/14', 'BXA8/17')):
                 sample.extra_info['url'] = "/mouseCross.html#AXB/BXA"
                 sample.extra_info['css_class'] = "fs12"
 
             sample.this_id = str(counter)
 
-            # ZS: For extra attribute columns; currently only used by several datasets
+            # ZS: For extra attribute columns; currently only used by
+            # several datasets
             if self.sample_attribute_values:
-                sample.extra_attributes = self.sample_attribute_values.get(sample_name, {})
+                sample.extra_attributes = self.sample_attribute_values.get(
+                    sample_name, {})
 
             self.sample_list.append(sample)
 
         self.se_exists = any(sample.variance for sample in self.sample_list)
+        self.num_cases_exists = any(sample.num_cases for sample in self.sample_list)
+
+        first_attr_col = self.get_first_attr_col()
+        for sample in self.sample_list:
+            sample.first_attr_col = first_attr_col
+
         self.do_outliers()
 
     def __repr__(self):
         return "<SampleList> --> %s" % (pf(self.__dict__))
 
     def do_outliers(self):
-        values = [sample.value for sample in self.sample_list if sample.value != None]
+        values = [sample.value for sample in self.sample_list
+                  if sample.value is not None]
         upper_bound, lower_bound = Plot.find_outliers(values)
 
         for sample in self.sample_list:
@@ -100,9 +108,9 @@ class SampleList(object):
             key, name = attr
             self.attributes[key] = Bunch()
             self.attributes[key].name = name
-            self.attributes[key].distinct_values = [item.Value for item in values]
-            self.attributes[key].distinct_values.sort(key=natural_sort_key)
-
+            self.attributes[key].distinct_values = [
+                item.Value for item in values]
+            natural_sort(self.attributes[key].distinct_values)
             all_numbers = True
             for value in self.attributes[key].distinct_values:
                 try:
@@ -135,7 +143,8 @@ class SampleList(object):
                     attribute_value = item.Value
 
                     # ZS: If it's an int, turn it into one for sorting
-                    # (for example, 101 would be lower than 80 if they're strings instead of ints)
+                    # (for example, 101 would be lower than 80 if
+                    # they're strings instead of ints)
                     try:
                         attribute_value = int(attribute_value)
                     except ValueError:
@@ -144,11 +153,21 @@ class SampleList(object):
                     attribute_values[self.attributes[item.Id].name] = attribute_value
                 self.sample_attribute_values[sample_name] = attribute_values
 
-def natural_sort_key(x):
-    """Get expected results when using as a key for sort - ints or strings are sorted properly"""
-
-    try:
-        x = int(x)
-    except ValueError:
-        pass
-    return x
+    def get_first_attr_col(self):
+        first_attr_col = 4
+        if self.se_exists:
+            first_attr_col += 2
+        if self.num_cases_exists:
+            first_attr_col += 1
+
+        return first_attr_col
+
+def natural_sort(list, key=lambda s: s):
+    """
+    Sort the list into natural alphanumeric order.
+    """
+    def get_alphanum_key_func(key):
+        def convert(text): return int(text) if text.isdigit() else text
+        return lambda s: [convert(c) for c in re.split('([0-9]+)', key(s))]
+    sort_key = get_alphanum_key_func(key)
+    list.sort(key=sort_key)
\ No newline at end of file
diff --git a/wqflask/wqflask/show_trait/export_trait_data.py b/wqflask/wqflask/show_trait/export_trait_data.py
index 253c887b..379b746c 100644
--- a/wqflask/wqflask/show_trait/export_trait_data.py
+++ b/wqflask/wqflask/show_trait/export_trait_data.py
@@ -1,9 +1,7 @@
-from __future__ import print_function, division
-
 import simplejson as json
 
 from pprint import pformat as pf
-
+from functools import cmp_to_key
 from base.trait import create_trait
 from base import data_set
 
@@ -16,10 +14,16 @@ def export_sample_table(targs):
 
     final_sample_data = meta_data
 
+    column_headers = ["Name", "Value"]
+    if any(sample["se"] for sample in sample_data['primary_samples']):
+        column_headers.append("SE")
+    if any(sample["num_cases"] for sample in sample_data['primary_samples']):
+        column_headers.append("N")
+
+    final_sample_data.append(column_headers)
     for sample_group in ['primary_samples', 'other_samples']:
         for row in sample_data[sample_group]:
             sorted_row = dict_to_sorted_list(row)
-            print("sorted_row is:", pf(sorted_row))
             final_sample_data.append(sorted_row)
 
     return trait_name, final_sample_data
@@ -37,18 +41,26 @@ def get_export_metadata(trait_id, dataset_name):
         metadata.append(["Phenotype URL: " + "http://genenetwork.org/show_trait?trait_id=" + trait_id + "&dataset=" + dataset_name])
         metadata.append(["Group: " + dataset.group.name])
         metadata.append(["Phenotype: " + this_trait.description_display.replace(",", "\",\"")])
-        metadata.append(["Authors: " + this_trait.authors])
-        metadata.append(["Title: " + this_trait.title])
-        metadata.append(["Journal: " + this_trait.journal])
+        metadata.append(["Authors: " + (this_trait.authors if this_trait.authors else "N/A")])
+        metadata.append(["Title: " + (this_trait.title if this_trait.title else "N/A")])
+        metadata.append(["Journal: " + (this_trait.journal if this_trait.journal else "N/A")])
         metadata.append(["Dataset Link: http://gn1.genenetwork.org/webqtl/main.py?FormID=sharinginfo&InfoPageName=" + dataset.name])
-        metadata.append([])
+    else:
+        metadata.append(["Record ID: " + trait_id])
+        metadata.append(["Trait URL: " + "http://genenetwork.org/show_trait?trait_id=" + trait_id + "&dataset=" + dataset_name])
+        if this_trait.symbol:
+            metadata.append(["Symbol: " + this_trait.symbol])
+        metadata.append(["Dataset: " + dataset.name])
+        metadata.append(["Group: " + dataset.group.name])
+
+    metadata.append([])
 
     return metadata
 
 
 def dict_to_sorted_list(dictionary):
-    sorted_list = [item for item in dictionary.iteritems()]
-    sorted_list = sorted(sorted_list, cmp=cmp_samples)
+    sorted_list = [item for item in list(dictionary.items())]
+    sorted_list = sorted(sorted_list, key=cmp_to_key(cmp_samples))
     sorted_values = [item[1] for item in sorted_list]
     return sorted_values
 
@@ -71,4 +83,4 @@ def cmp_samples(a, b):
         else:
             return 1
     else:
-        return -1
\ No newline at end of file
+        return -1
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 30b03e66..edf9638c 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -1,9 +1,7 @@
-from __future__ import absolute_import, print_function, division
-
 import string
 import os
 import datetime
-import cPickle
+import pickle
 import uuid
 import requests
 import json as json
@@ -230,8 +228,8 @@ class ShowTrait(object):
         hddn = OrderedDict()
 
         if self.dataset.group.allsamples:
-            hddn['allsamples'] = string.join(self.dataset.group.allsamples, ' ')
-        hddn['primary_samples'] = string.join(self.primary_sample_names, ',')
+            hddn['allsamples'] = ''.join(self.dataset.group.allsamples)
+        hddn['primary_samples'] = ''.join(self.primary_sample_names)
         hddn['trait_id'] = self.trait_id
         hddn['trait_display_name'] = self.this_trait.display_name
         hddn['dataset'] = self.dataset.name
@@ -260,7 +258,7 @@ class ShowTrait(object):
         hddn['export_data'] = ""
         hddn['export_format'] = "excel"
         if len(self.scales_in_geno) < 2:
-            hddn['mapping_scale'] = self.scales_in_geno[self.scales_in_geno.keys()[0]][0][0]
+            hddn['mapping_scale'] = self.scales_in_geno[list(self.scales_in_geno.keys())[0]][0][0]
 
         # We'll need access to this_trait and hddn in the Jinja2 Template, so we put it inside self
         self.hddn = hddn
@@ -373,7 +371,7 @@ class ShowTrait(object):
             this_group = self.dataset.group.name
 
         # We're checking a string here!
-        assert isinstance(this_group, basestring), "We need a string type thing here"
+        assert isinstance(this_group, str), "We need a string type thing here"
         if this_group[:3] == 'BXD' and this_group != "BXD-Harvested":
             this_group = 'BXD'
 
@@ -409,9 +407,10 @@ class ShowTrait(object):
         if not self.temp_trait:
             other_sample_names = []
 
-            for sample in self.this_trait.data:
-                if self.this_trait.data[sample].name2 != self.this_trait.data[sample].name:
-                    if (self.this_trait.data[sample].name2 in primary_sample_names) and (self.this_trait.data[sample].name not in primary_sample_names):
+            for sample in list(self.this_trait.data.keys()):
+                if (self.this_trait.data[sample].name2 != self.this_trait.data[sample].name):
+                    if ((self.this_trait.data[sample].name2 in primary_sample_names) and
+                        (self.this_trait.data[sample].name not in primary_sample_names)):
                         primary_sample_names.append(self.this_trait.data[sample].name)
                         primary_sample_names.remove(self.this_trait.data[sample].name2)
 
@@ -568,7 +567,7 @@ def get_table_widths(sample_groups, has_num_cases=False):
 def has_num_cases(this_trait):
     has_n = False
     if this_trait.dataset.type != "ProbeSet" and this_trait.dataset.type != "Geno":
-        for name, sample in this_trait.data.iteritems():
+        for name, sample in list(this_trait.data.items()):
             if sample.num_cases:
                 has_n = True
                 break
@@ -625,7 +624,7 @@ def get_categorical_variables(this_trait, sample_list):
     if len(sample_list.attributes) > 0:
         for attribute in sample_list.attributes:
             attribute_vals = []
-            for sample_name in this_trait.data.keys():
+            for sample_name in list(this_trait.data.keys()):
                 if sample_list.attributes[attribute].name in this_trait.data[sample_name].extra_attributes:
                     attribute_vals.append(this_trait.data[sample_name].extra_attributes[sample_list.attributes[attribute].name])
                 else:
@@ -640,7 +639,7 @@ def get_categorical_variables(this_trait, sample_list):
 
 def get_genotype_scales(genofiles):
     geno_scales = {}
-    if type(genofiles) is list:
+    if isinstance(genofiles, list):
         for the_file in genofiles:
             file_location = the_file['location']
             geno_scales[file_location] = get_scales_from_genofile(file_location)
diff --git a/wqflask/wqflask/snp_browser/snp_browser.py b/wqflask/wqflask/snp_browser/snp_browser.py
index 1d28d76a..6c3fcf53 100644
--- a/wqflask/wqflask/snp_browser/snp_browser.py
+++ b/wqflask/wqflask/snp_browser/snp_browser.py
@@ -1,5 +1,3 @@
-from __future__ import absolute_import, print_function, division
-
 from flask import Flask, g, url_for
 
 import string
@@ -458,8 +456,8 @@ class SnpBrowser(object):
 
                 function_list = []
                 if function_details:
-                    function_list = string.split(string.strip(function_details), ",")
-                    function_list = map(string.strip, function_list)
+                    function_list = function_details.strip().split(",")
+                    function_list = [item.strip() for item in function_list]
                     function_list[0] = function_list[0].title()
                     function_details = ", ".join(item for item in function_list)
                     function_details = function_details.replace("_", " ")
@@ -477,7 +475,7 @@ class SnpBrowser(object):
 
                 the_bases = []
                 for j, item in enumerate(allele_value_list):
-                    if item and isinstance(item, basestring):
+                    if item and isinstance(item, str):
                         this_base = [str(item), base_color_dict[item]]
                     else:
                         this_base = ""
@@ -612,7 +610,7 @@ class SnpBrowser(object):
             this_allele_list = []
 
             for item in self.allele_list:
-                if item and isinstance(item, basestring) and (item.lower() not in this_allele_list) and (item != "-"):
+                if item and isinstance(item, str) and (item.lower() not in this_allele_list) and (item != "-"):
                     this_allele_list.append(item.lower())
 
             total_allele_count = len(this_allele_list)
@@ -724,12 +722,12 @@ def get_effect_details_by_category(effect_name = None, effect_value = None):
     new_codon_group_list = ['Start Gained']
     codon_effect_group_list = ['Start Lost', 'Stop Gained', 'Stop Lost', 'Nonsynonymous', 'Synonymous']
 
-    effect_detail_list = string.split(string.strip(effect_value), '|')
-    effect_detail_list = map(string.strip, effect_detail_list)
+    effect_detail_list = effect_value.strip().split('|')
+    effect_detail_list = [item.strip() for item in effect_detail_list]
 
     for index, item in enumerate(effect_detail_list):
-        item_list = string.split(string.strip(item), ',')
-        item_list = map(string.strip, item_list)
+        item_list = item.strip().split(',')
+        item_list = [item.strip() for item in item_list]
 
         gene_id = item_list[0]
         gene_name = item_list[1]
@@ -748,13 +746,13 @@ def get_effect_details_by_category(effect_name = None, effect_value = None):
             if effect_name in new_codon_group_list:
                 new_codon = item_list[6]
                 tmp_list = [biotype, new_codon]
-                function_detail_list.append(string.join(tmp_list, ", "))
+                function_detail_list.append(", ".join(tmp_list))
             elif effect_name in codon_effect_group_list:
                 old_new_AA = item_list[6]
                 old_new_codon = item_list[7]
                 codon_num = item_list[8]
                 tmp_list = [biotype, old_new_AA, old_new_codon, codon_num]
-                function_detail_list.append(string.join(tmp_list, ", "))
+                function_detail_list.append(", ".join(tmp_list))
             else:
                 function_detail_list.append(biotype)
 
@@ -854,7 +852,7 @@ def get_gene_id_name_dict(species_id, gene_name_list):
     if len(gene_name_list) == 0:
         return ""
     gene_name_str_list = ["'" + gene_name + "'" for gene_name in gene_name_list]
-    gene_name_str = string.join(gene_name_str_list, ",")
+    gene_name_str = ",".join(gene_name_str_list)
 
     query = """
                 SELECT
diff --git a/wqflask/wqflask/static/new/css/main.css b/wqflask/wqflask/static/new/css/main.css
index 097cd997..d5fb8a61 100644
--- a/wqflask/wqflask/static/new/css/main.css
+++ b/wqflask/wqflask/static/new/css/main.css
@@ -33,4 +33,8 @@
     .collapsing {
         overflow: hidden!important;
     }
+}
+
+.checkbox {
+    min-height: 20px;
 }
\ No newline at end of file
diff --git a/wqflask/wqflask/static/new/css/show_trait.css b/wqflask/wqflask/static/new/css/show_trait.css
index 7a7f5455..d8964f5d 100644
--- a/wqflask/wqflask/static/new/css/show_trait.css
+++ b/wqflask/wqflask/static/new/css/show_trait.css
@@ -1,17 +1,17 @@
 tr .outlier {
-    background-color: #ffff99;
+  background-color: #ffff99;
 }
 
 table.dataTable tbody tr.selected {
-    background-color: #ffee99;
+  background-color: #ffee99;
 }
 
 #bar_chart_container {
-    overflow-x:scroll;
+  overflow-x:scroll;
 }
 
 div.sample_group {
-    overflow: auto; # needed because it contains float dataTable wrapper
+  overflow: auto; # needed because it contains float dataTable wrapper
 }
 
 .js-plotly-plot .plotly .modebar {
@@ -35,8 +35,13 @@ table.dataTable thead th, table.dataTable tfoot {
   padding: 4px 18px 4px 10px;
 }
 
+/* Header for a column with a numeric value that should be right-aligned */
+table.dataTable thead th div.numeric_header {
+  text-align: right;
+}
+
 table.dataTable tbody td {
-  padding: 4px 15px 2px 10px;
+  padding: 2px 15px 0px 10px;
 }
 
 table.dataTable.cell-border tbody th, table.dataTable.cell-border tbody td {
@@ -54,8 +59,204 @@ table.dataTable.cell-border tbody tr td:first-child {
 
 .trait_value_input {
   text-align: right;
+}
 
 .glyphicon {
   position: relative;
   top: 2px;
+}
+
+.showtrait-main-div {
+  min-width: 700px;
+}
+
+table.dataTable tbody td.column_name-Checkbox {
+  padding: 1px 0px 0px 9px; /* The left padding here is because text-align:center does not seem to be working properly. No idea why this is. */
+  text-align: center;
+  vertical-align: middle;
+}
+
+table.dataTable tbody td.column_name-Index {
+  padding: 2px 4px 0px 2px;
+  text-align: right;
+}
+
+/* the column with +/- in it that appears in the table when there's an SE column */
+table.dataTable tbody td.column_name-PlusMinus {
+  padding-left: 2px;
+  padding-right: 2px;
+  text-align: center;
+}
+
+table.dataTable tbody td.column_name-Value, table.dataTable tbody td.column_name-SE, table.dataTable tbody td.column_name-num_cases {
+  text-align: right;
+}
+
+div.btn-toolbar {
+  margin-bottom:15px;
+}
+
+/* div containing the form options for each segment of the trait page - correlations, statistics, mapping, etc */
+div.section-form-div {
+  padding: 20px;
+}
+
+table.left-float {
+  float: left;
+}
+
+div.scatterplot-btn-div {
+  margin-bottom:40px;
+}
+
+div.correlation-main {
+  min-width: 1200px;
+}
+
+div.correlation-options {
+  min-width: 700px;
+}
+
+.min-expr-field {
+  width: 70px;
+}
+
+div.p-range-slider {
+  width: 200px;
+  margin-left: 15px;
+}
+
+span.p-range-lower {
+  margin-top: 5px;
+  font: 400 12px Arial;
+  color: #888; 
+  display: inline-block;
+}
+
+span.p-range-upper {
+  font: 400 12px Arial;
+  color: #888;
+  display: inline-block;
+  margin: 5px 0px 0px 170px;
+}
+
+input.corr-location {
+  width: 50px;
+  display: inline;
+}
+
+div.block-by-index-div {
+  margin-bottom: 10px;
+}
+
+div.block-by-attribute-div {
+  margin-top:10px;
+  margin-bottom:10px;
+}
+
+div.normalize-div {
+  margin-top:10px;
+}
+
+div.mapping-main {
+  min-width: 1200px;
+}
+div.mapping-options {
+  min-width: 500px;
+}
+
+div.covar-options {
+  padding-top: 7px;
+}
+
+.control-label {
+  text-align: right;
+}
+
+.chr-select, .maf-select, .scale-select, .reaper-ver-select {
+  width: 80px;
+}
+
+span.covar-text {
+  font-size: 13px;
+  font-weight: 400;
+}
+
+div.select-covar-div {
+  margin-bottom: 10px;
+}
+
+.select-covar-button {
+  width: 80px;
+  padding-right: 10px;
+}
+
+.selected-covariates {
+  overflow-y: scroll;
+  resize: none;
+  width: 200px;
+}
+
+.cofactor-input {
+  width: 160px;
+  display: inline-block;
+}
+
+.no-control-radio {
+  margin-left: 10px;
+}
+
+.map-method-text {
+  margin-top: 20px;
+}
+
+.rqtl-description {
+  padding-top: 40px;
+  display: none;
+}
+
+div.sample-table-container {
+  padding-bottom: 10px;
+}
+
+div.sample-table-search-container {
+  display: inline;
+  height: 40px;
+}
+
+input.sample-table-search {
+  width: 200px;
+  display: inline;
+  float: left;
+  vertical-align: top;
+}
+
+div.sample-table-export-container {
+  padding-left: 10px;
+  display: inline;
+}
+
+div.export-code-container {
+  padding-top: 20px;
+  width: 600px;
+  display: none;
+}
+
+.export-code-field {
+  padding-top: 0px;
+  padding-bottom: 0px;
+  height: 150px;
+}
+
+table.sample-table {
+  float: left;
+  width:100%;
+}
+
+input.trait-value-input {
+  text-align: right;
+}
+
+div.inline-div {
+  display: inline;
 }
\ No newline at end of file
diff --git a/wqflask/wqflask/static/new/javascript/get_covariates_from_collection.js b/wqflask/wqflask/static/new/javascript/get_covariates_from_collection.js
index a8a3041d..3e414034 100644
--- a/wqflask/wqflask/static/new/javascript/get_covariates_from_collection.js
+++ b/wqflask/wqflask/static/new/javascript/get_covariates_from_collection.js
@@ -104,7 +104,7 @@ submit_click = function() {
   //covariates_display_string = covariates_display_string.substring(0, covariates_display_string.length - 2)
 
   $("input[name=covariates]").val(covariates_string)
-  $(".selected_covariates").val(covariates_display_string)
+  $(".selected-covariates").val(covariates_display_string)
 
   return $.colorbox.close();
 };
@@ -114,7 +114,7 @@ trait_click = function() {
   trait = $(this).parent().find('.trait').text();
   dataset = $(this).parent().find('.dataset').data("dataset");
   $("input[name=covariates]").val(trait + ":" + dataset)
-  $(".selected_covariates").text(trait)
+  $(".selected-covariates").text(trait)
   return $.colorbox.close();
 };
 
diff --git a/wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js b/wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js
index 49822cd2..5a4f151c 100644
--- a/wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js
+++ b/wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js
@@ -75,7 +75,7 @@ build_columns = function() {
     );
   }
 
-  if (js_data.has_num_cases === "true") {
+  if (js_data.has_num_cases === true) {
     column_list.push(
       {
         'title': "<div style='text-align: right;'>N</div>",
@@ -101,7 +101,8 @@ build_columns = function() {
         'type': "natural",
         'data': null,
         'render': function(data, type, row, meta) {
-          attr_name = Object.keys(data.extra_attributes).sort((a, b) => (a > b) ? 1 : -1)[meta.col - data.first_attr_col]
+          attr_name = Object.keys(data.extra_attributes).sort()[meta.col - data.first_attr_col]
+
           if (attr_name != null && attr_name != undefined){
               return data.extra_attributes[attr_name]
           } else {
@@ -111,7 +112,6 @@ build_columns = function() {
       }
     )
   }
-
   return column_list
 }
 
@@ -132,23 +132,22 @@ var primary_table = $('#samples_primary').DataTable( {
       $('td', row).eq(3).addClass("column_name-Value")
       if (js_data.se_exists) {
         $('td', row).eq(5).addClass("column_name-SE")
-        if (js_data.has_num_cases === "true") {
+        if (js_data.has_num_cases === true) {
           $('td', row).eq(6).addClass("column_name-num_cases")
         } else {
-          if (js_data.has_num_cases === "true") {
+          if (js_data.has_num_cases === true) {
             $('td', row).eq(4).addClass("column_name-num_cases")
           }
         }
       } else {
-        if (js_data.has_num_cases === "true") {
+        if (js_data.has_num_cases === true) {
           $('td', row).eq(4).addClass("column_name-num_cases")
         }
       }
 
-      sorted_key_list = Object.keys(js_data.attributes).sort()
-      for (i=0; i < sorted_key_list.length; i++) {
-        $('td', row).eq(attribute_start_pos + i + 1).addClass("column_name-" + js_data.attributes[sorted_key_list[i]].name)
-        $('td', row).eq(attribute_start_pos + i + 1).attr("style", "text-align: " + js_data.attributes[sorted_key_list[i]].alignment + "; padding-top: 2px; padding-bottom: 0px;")
+      for (i=0; i < attr_keys.length; i++) {
+        $('td', row).eq(attribute_start_pos + i).addClass("column_name-" + js_data.attributes[attr_keys[i]].name)
+        $('td', row).eq(attribute_start_pos + i).attr("style", "text-align: " + js_data.attributes[attr_keys[i]].alignment + "; padding-top: 2px; padding-bottom: 0px;")
       }
     },
     'data': js_data['sample_lists'][0],
@@ -190,23 +189,22 @@ if (js_data.sample_lists.length > 1){
         $('td', row).eq(3).addClass("column_name-Value")
         if (js_data.se_exists) {
           $('td', row).eq(5).addClass("column_name-SE")
-          if (js_data.has_num_cases === "true") {
+          if (js_data.has_num_cases === true) {
             $('td', row).eq(6).addClass("column_name-num_cases")
           } else {
-            if (js_data.has_num_cases === "true") {
+            if (js_data.has_num_cases === true) {
               $('td', row).eq(4).addClass("column_name-num_cases")
             }
           }
         } else {
-          if (js_data.has_num_cases === "true") {
+          if (js_data.has_num_cases === true) {
             $('td', row).eq(4).addClass("column_name-num_cases")
           }
         }
 
-        sorted_key_list = Object.keys(js_data.attributes).sort()
-        for (i=0; i < sorted_key_list.length; i++) {
-          $('td', row).eq(attribute_start_pos + i + 1).addClass("column_name-" + js_data.attributes[sorted_key_list[i]].name)
-          $('td', row).eq(attribute_start_pos + i + 1).attr("style", "text-align: " + js_data.attributes[sorted_key_list[i]].alignment + "; padding-top: 2px; padding-bottom: 0px;")
+        for (i=0; i < attr_keys.length; i++) {
+          $('td', row).eq(attribute_start_pos + i + 1).addClass("column_name-" + js_data.attributes[attr_keys[i]].name)
+          $('td', row).eq(attribute_start_pos + i + 1).attr("style", "text-align: " + js_data.attributes[attr_keys[i]].alignment + "; padding-top: 2px; padding-bottom: 0px;")
         }
       },
       'data': js_data['sample_lists'][1],
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index eaad0a4c..a34811f8 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -107,14 +107,14 @@ d3.select("#select_covariates").on("click", (function(_this) {
 })(this));
 $("#remove_covariates").click(function () {
     $("input[name=covariates]").val("")
-    $(".selected_covariates").val("")
+    $(".selected-covariates").val("")
 });
 $(".select_covariates").click(function () {
   open_covariate_selection();
 });
 $(".remove_covariates").click(function () {
   $("input[name=covariates]").val("")
-  $(".selected_covariates").val("")
+  $(".selected-covariates").val("")
 });
 d3.select("#clear_compare_trait").on("click", (function(_this) {
   return function() {
@@ -601,7 +601,7 @@ block_by_attribute_value = function() {
       var row;
       if ($.trim($(element).text()) === exclude_by_value) {
         row = $(element).parent('tr');
-        return $(row).find(".trait_value_input").val("x");
+        return $(row).find(".trait-value-input").val("x");
       }
     };
   })(this));
@@ -641,13 +641,14 @@ block_by_index = function() {
   for (_k = 0, _len1 = index_list.length; _k < _len1; _k++) {
     index = index_list[_k];
     val_nodes[index - 1].childNodes[0].value = "x";
+
   }
 };
 
 hide_no_value = function() {
   return $('.value_se').each((function(_this) {
     return function(_index, element) {
-      if ($(element).find('.trait_value_input').val() === 'x') {
+      if ($(element).find('.trait-value-input').val() === 'x') {
         return $(element).hide();
       }
     };
@@ -658,7 +659,7 @@ $('#hide_no_value').click(hide_no_value);
 block_outliers = function() {
   return $('.outlier').each((function(_this) {
     return function(_index, element) {
-      return $(element).find('.trait_value_input').val('x');
+      return $(element).find('.trait-value-input').val('x');
     };
   })(this));
 };
@@ -667,7 +668,6 @@ $('#block_outliers').click(block_outliers);
 reset_samples_table = function() {
   $('input[name="transform"]').val("");
   $('span[name="transform_text"]').text("")
-
   tables = ['samples_primary', 'samples_other'];
   for (_i = 0, _len = tables.length; _i < _len; _i++) {
     table = tables[_i];
@@ -871,7 +871,7 @@ $('#normalize').hover(function(){
 $('#normalize').click(normalize_data)
 
 switch_qnorm_data = function() {
-  return $('.trait_value_input').each((function(_this) {
+  return $('.trait-value-input').each((function(_this) {
     return function(_index, element) {
       transform_val = $(element).data('transform')
       if (transform_val != "") {
@@ -885,26 +885,65 @@ $('#qnorm').click(switch_qnorm_data);
 get_sample_table_data = function(table_name) {
   var samples;
   samples = [];
-  $('#' + table_name).find('.value_se').each((function(_this) {
-    return function(_index, element) {
-      var attribute_info, key, row_data, _ref;
-      row_data = {};
-      row_data.name = $.trim($(element).find('.column_name-Sample').text());
-      row_data.value = $(element).find('.edit_sample_value:eq(0)').val();
-      if ($(element).find('.edit_sample_se').length > 0) {
-        row_data.se = $(element).find('.edit_sample_se').val();
+
+  var se_exists = false;
+  var n_exists = false;
+
+  if ($('#' + table_name).length){
+    table_api = $('#' + table).DataTable();
+    sample_vals = [];
+
+    name_nodes = table_api.column(2).nodes().to$();
+    val_nodes = table_api.column(3).nodes().to$();
+    if (js_data.se_exists){
+      var_nodes = table_api.column(5).nodes().to$();
+      if (js_data.has_num_cases) {
+        n_nodes = table_api.column(6).nodes().to$();
       }
-      if ($(element).find('.edit_sample_num_cases').length > 0) {
-        row_data.num_cases = $(element).find('.edit_sample_num_cases').val();
+    } else {
+      if (js_data.has_num_cases){
+        n_nodes = table_api.column(4).nodes().to$();
       }
-      attr_keys = Object.keys(js_data.attributes).sort()
-      for (i=0; i < attr_keys.length; i++) {
-        attribute_info = js_data.attributes[attr_keys[i]];
-        row_data[attribute_info.name] = $.trim($(element).find('.column_name-' + attribute_info.name.replace(" ", "_").replace("/", "\\/")).text());
+    }
+
+    for (_j = 0; _j < val_nodes.length; _j++){
+      sample_val = val_nodes[_j].childNodes[0].value
+      sample_name = $.trim(name_nodes[_j].childNodes[0].textContent)
+      if (is_number(sample_val) && sample_val !== "") {
+        sample_val = parseFloat(sample_val);
+        if (typeof var_nodes == 'undefined'){
+          sample_var = null;
+        } else {
+          sample_var = var_nodes[_j].childNodes[0].value;
+          if (is_number(sample_var)) {
+            sample_var = parseFloat(sample_var);
+            se_exists = true;
+          } else {
+            sample_var = null;
+          }
+        }
+        if (typeof n_nodes == 'undefined'){
+          sample_n = null;
+        } else {
+          sample_n = n_nodes[_j].childNodes[0].value;
+          if (is_number(sample_n)) {
+            n_exists = true;
+            sample_n = parseInt(sample_n);
+          } else {
+            sample_n = null;
+          }
+        }
+        row_dict = {
+          name: sample_name,
+          value: sample_val,
+          se: sample_var,
+          num_cases: sample_n
+        }
+        samples.push(row_dict)
       }
-      return samples.push(row_data);
-    };
-  })(this));
+    }
+  }
+
   return samples;
 };
 export_sample_table_data = function() {
diff --git a/wqflask/wqflask/submit_bnw.py b/wqflask/wqflask/submit_bnw.py
index 59e60dfd..a0e84c8c 100644
--- a/wqflask/wqflask/submit_bnw.py
+++ b/wqflask/wqflask/submit_bnw.py
@@ -1,5 +1,3 @@
-from __future__ import absolute_import, print_function, division
-
 from base.trait import GeneralTrait
 from base import data_set
 from utility import helper_functions
@@ -8,4 +6,4 @@ import utility.logger
 logger = utility.logger.getLogger(__name__ )
 
 def get_bnw_input(start_vars):
-    logger.debug("BNW VARS:", start_vars)
\ No newline at end of file
+    logger.debug("BNW VARS:", start_vars)
diff --git a/wqflask/wqflask/templates/admin/manage_resource.html b/wqflask/wqflask/templates/admin/manage_resource.html
index 0b12eaae..33a37594 100644
--- a/wqflask/wqflask/templates/admin/manage_resource.html
+++ b/wqflask/wqflask/templates/admin/manage_resource.html
@@ -65,7 +65,7 @@
                         </tr>
                     </thead>
                     <tbody>
-                        {% for key, value in group_masks.iteritems() %}
+                        {% for key, value in group_masks.items() %}
                         <tr>
                             <td>{{ value.name }}</td>
                             <td>{{ value.data }}</td>
diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html
index b44538cf..0f4e5ef5 100644
--- a/wqflask/wqflask/templates/base.html
+++ b/wqflask/wqflask/templates/base.html
@@ -9,6 +9,9 @@
 
     <meta name="description" content="">
     <meta name="author" content="">
+    <script type="text/javascript">
+     var pageLoadStart = Date.now();
+    </script>
     <link rel="icon" type="image/png" sizes="64x64" href="/static/new/images/CITGLogo.png">
     <link rel="apple-touch-icon" type="image/png" sizes="64x64" href="/static/new/images/CITGLogo.png">
     <link REL="stylesheet" TYPE="text/css" href="/static/packages/bootstrap/css/bootstrap.css" />
@@ -203,6 +206,7 @@
             {% if version: %}
             <p><small>GeneNetwork {{ version }}</small></p>
             {% endif %}
+            <p> It took the server {{ g.request_time() }} seconds to process this page.</p>
 
         </div>
         <div class="col-xs-2">
@@ -256,6 +260,12 @@
     {% block js %}
     {% endblock %}
 
-
+    <script type="text/javascript">
+     $(window).load(function() {
+         let timeToLoad = document.createElement("p");
+         timeToLoad.innerHTML = "It took your browser " + ((Date.now() - pageLoadStart)/1000) + " second(s) to render this page";
+         document.querySelector("footer .row .col-xs-6").appendChild(timeToLoad);
+     });
+    </script>
 </body>
 </html>
diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html
index fb218e29..134f15be 100644
--- a/wqflask/wqflask/templates/correlation_page.html
+++ b/wqflask/wqflask/templates/correlation_page.html
@@ -170,7 +170,8 @@
                         {% endif %}
                         <td data-export="{{ trait.description_display }}">{% if trait.description_display|length > 70 %}{{ trait.description_display[:70] }}...{% else %}{{ trait.description_display }}{% endif %}</td>
                         {% if trait.authors %}
-                        <td data-export="{{ trait.authors }}">{% if trait.authors.split(',') > 6 %}{{ trait.authors.split(',')[:6]|join(', ') }}, et al.{% else %}{{ trait.authors }}{% endif %}</td>
+                        {% set authors_list = trait.authors.split(',') %}
+                        <td data-export="{{ trait.authors }}">{% if authors_list|length > 6 %}{{ authors_list[:6]|join(', ') }}, et al.{% else %}{{ trait.authors }}{% endif %}</td>
                         {% else %}
                         <td data-export="N/A">N/A</td>
                         {% endif %}
diff --git a/wqflask/wqflask/templates/loading.html b/wqflask/wqflask/templates/loading.html
index 15ab4080..9b335dfe 100644
--- a/wqflask/wqflask/templates/loading.html
+++ b/wqflask/wqflask/templates/loading.html
@@ -1,7 +1,7 @@
 <title>Loading {{ start_vars.tool_used }} Results</title>
 <link REL="stylesheet" TYPE="text/css" href="/static/packages/bootstrap/css/bootstrap.css" />
 <form method="post" action="" name="loading_form" id="loading_form" class="form-horizontal">
-  {% for key, value in start_vars.iteritems() %}
+  {% for key, value in start_vars.items() %}
   <input type="hidden" name="{{ key }}" value="{{ value }}">
   {% endfor %}
   <div class="container">
@@ -44,4 +44,4 @@
 
 $("#loading_form").attr("action", "{{ start_vars.form_url }}");
 setTimeout(function(){ $("#loading_form").submit()}, 350);
-</script>
\ No newline at end of file
+</script>
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index 5ed7a90b..7b74a3f6 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -37,7 +37,7 @@
         <input type="hidden" name="covariates" value="">
         <input type="hidden" name="transform" value="">
 
-        <div class="container" style="min-width: 700px;">
+        <div class="container showtrait-main-div">
             <div class="panel-group" id="accordion">
                 <div class="panel panel-default">
                     <div class="panel-heading" data-toggle="collapse" data-parent="#accordion" data-target="#collapseOne" aria-expanded="true">
diff --git a/wqflask/wqflask/templates/show_trait_calculate_correlations.html b/wqflask/wqflask/templates/show_trait_calculate_correlations.html
index 9420c9c6..bc1d4091 100644
--- a/wqflask/wqflask/templates/show_trait_calculate_correlations.html
+++ b/wqflask/wqflask/templates/show_trait_calculate_correlations.html
@@ -1,149 +1,150 @@
-<div>
-  <div class="col-xs-6" style="min-width: 800px;">
-    <div style="padding: 20px" class="form-horizontal">
-        
-        <div class="form-group">
-            <label for="corr_type" class="col-xs-2 control-label">Method</label>
-            <div class="col-xs-3 controls">
-                <select name="corr_type" class="form-control">
-                    <option value="sample">Sample r</option>
-                    <option value="lit">Literature r</option>
-                    <option value="tissue">Tissue r</option>
-                </select>
-            </div>
-        </div>
-        
-        <div class="form-group">
-            <label for="corr_dataset" class="col-xs-2 control-label">Database</label>
-            <div class="col-xs-10 controls">
-                <select name="corr_dataset" class="form-control">
-                    {% for tissue in corr_tools.dataset_menu %}
-                        {% if tissue.tissue %}
-                            <optgroup label="{{ tissue.tissue }} ------">
-                        {% endif %}
-                        {% for dataset in tissue.datasets %}
-                            <option value="{{ dataset[1] }}" 
-                            {% if corr_tools.dataset_menu_selected == dataset[1] %}     
-                                selected           
-                            {% endif %}>          
-                              {{ dataset[0] }}
-                            </option>
-                        {% endfor %}
-                        {% if tissue.tissue %}
-                            </optgroup>
-                        {% endif %}
-                    {% endfor %}
-                </select>
-            </div>
-        </div>
-        
-        <div class="form-group">
-            <label for="corr_return_results" class="col-xs-2 control-label">Return</label>
-            <div class="col-xs-4 controls">
-                <select name="corr_return_results" class="form-control">
-                    {% for return_result in corr_tools.return_results_menu %}
-                        <option value="{{ return_result }}" 
-                        {% if corr_tools.return_results_menu_selected == return_result %}
-                            selected
-                        {% endif %}>
-                        Top {{ return_result }}
-                        </option>
-                    {% endfor %}
-                </select>
-            </div>
-        </div>
-        
-        <div class="form-group">
-            <label for="corr_samples_group" class="col-xs-2 control-label">Samples</label>
-            <div class="col-xs-4 controls">
-                <select name="corr_samples_group" class="form-control">
-                    {% for group, pretty_group in sample_group_types.items() %}
-                        <option value="{{ group }}">{{ pretty_group }}</option>
-                    {% endfor %}
-                </select>
-            </div>
-        </div>
-            
-        <div id="corr_sample_method" class="form-group">
-            <label for="corr_sample_method" class="col-xs-2 control-label">Type</label>
-            <div class="col-xs-4 controls">
-                <select name="corr_sample_method" class="form-control">
-                    <option value="pearson">Pearson</option>
-                    <option value="spearman">Spearman Rank</option>
-                    <option value="bicor">Biweight Midcorrelation</option>
-                </select>
-            </div>
-        </div>
-        {% if dataset.type != "Publish" %}
-        <div class="form-group">
-            <label class="col-xs-2 control-label">Min Expr</label>
-            <div class="col-xs-4 controls">
-                <input name="min_expr" value="" type="text" class="form-control" style="width: 70px;">
-            </div>
-        </div>
-        <div class="form-group">
-            <label class="col-xs-2 control-label">Location</label>
-            <div class="col-xs-5 controls">
-                <span>
-                Chr: <input name="loc_chr" value="" type="text" class="form-control" style="width: 50px; display: inline;">&nbsp;&nbsp;&nbsp;
-                Mb: <input name="min_loc_mb" value="" type="text" class="form-control" style="width: 50px; display: inline;"> &nbsp;to&nbsp; <input name="max_loc_mb" value="" type="text" class="form-control" style="width: 50px; display: inline;">
-                </span>
-                <br>
-            </div>
-        </div>
-        {% endif %}
-        <div class="form-group">
-            <label class="col-xs-2 control-label">Range</label>
-            <div class="col-xs-5 controls">
-                <input name="p_range_lower" value="" type="hidden">
-                <input name="p_range_upper" value="" type="hidden">
-                <span style="display: inline;">
-                <div id="p_range_slider" style="width: 200px;"></div>
-                <span style="font: 400 12px Arial; color: #888; display: inline; margin: 25px 0; width: 20px;" id="p_range_lower"></span>
-                <span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span>
-                <span style="font: 400 12px Arial; color: #888; display: inline; margin: 15px 0; width: 20px;" id="p_range_upper"></span>
-                </span>
-            </div>
-        </div>
-        
-        <div class="form-group">
-            <label for="corr_sample_method" class="col-xs-2 control-label"></label>
-            <div class="col-xs-3 controls">
-                <input type="button" class="btn corr_compute submit_special btn-success" data-url="/corr_compute" title="Compute Correlation" value="Compute">
-            </div>
-        </div>
+<div class="row correlation-main">
+    <div class="col-xs-3 correlation-options">
+      <div class="form-horizontal section-form-div">
+
+          <div class="form-group">
+              <label for="corr_type" class="col-xs-2 control-label">Method</label>
+              <div class="col-xs-3 controls">
+                  <select name="corr_type" class="form-control">
+                      <option value="sample">Sample r</option>
+                      <option value="lit">Literature r</option>
+                      <option value="tissue">Tissue r</option>
+                  </select>
+              </div>
+          </div>
+
+          <div class="form-group">
+              <label for="corr_dataset" class="col-xs-2 control-label">Database</label>
+              <div class="col-xs-10 controls">
+                  <select name="corr_dataset" class="form-control">
+                      {% for tissue in corr_tools.dataset_menu %}
+                          {% if tissue.tissue %}
+                              <optgroup label="{{ tissue.tissue }} ------">
+                          {% endif %}
+                          {% for dataset in tissue.datasets %}
+                              <option value="{{ dataset[1] }}"
+                              {% if corr_tools.dataset_menu_selected == dataset[1] %}
+                                  selected
+                              {% endif %}>
+                                {{ dataset[0] }}
+                              </option>
+                          {% endfor %}
+                          {% if tissue.tissue %}
+                              </optgroup>
+                          {% endif %}
+                      {% endfor %}
+                  </select>
+              </div>
+          </div>
+
+          <div class="form-group">
+              <label for="corr_return_results" class="col-xs-2 control-label">Return</label>
+              <div class="col-xs-4 controls">
+                  <select name="corr_return_results" class="form-control">
+                      {% for return_result in corr_tools.return_results_menu %}
+                          <option value="{{ return_result }}"
+                          {% if corr_tools.return_results_menu_selected == return_result %}
+                              selected
+                          {% endif %}>
+                          Top {{ return_result }}
+                          </option>
+                      {% endfor %}
+                  </select>
+              </div>
+          </div>
+
+          <div class="form-group">
+              <label for="corr_samples_group" class="col-xs-2 control-label">Samples</label>
+              <div class="col-xs-4 controls">
+                  <select name="corr_samples_group" class="form-control">
+                      {% for group, pretty_group in sample_group_types.items() %}
+                          <option value="{{ group }}">{{ pretty_group }}</option>
+                      {% endfor %}
+                  </select>
+              </div>
+          </div>
+
+          <div id="corr_sample_method" class="form-group">
+              <label for="corr_sample_method" class="col-xs-2 control-label">Type</label>
+              <div class="col-xs-4 controls">
+                  <select name="corr_sample_method" class="form-control">
+                      <option value="pearson">Pearson</option>
+                      <option value="spearman">Spearman Rank</option>
+                      <option value="bicor">Biweight Midcorrelation</option>
+                  </select>
+              </div>
+          </div>
+          {% if dataset.type != "Publish" %}
+          <div class="form-group">
+              <label class="col-xs-2 control-label">Min Expr</label>
+              <div class="col-xs-4 controls">
+                  <input name="min_expr" value="" type="text" class="form-control min-expr-field">
+              </div>
+          </div>
+          <div class="form-group">
+              <label class="col-xs-2 control-label">Location</label>
+              <div class="col-xs-6 controls">
+                  <span>
+                  Chr: <input name="loc_chr" value="" type="text" class="form-control corr-location">&nbsp;&nbsp;&nbsp;
+                  Mb: <input name="min_loc_mb" value="" type="text" class="form-control corr-location"> &nbsp;to&nbsp; <input name="max_loc_mb" value="" type="text" class="form-control corr-location">
+                  </span>
+                  <br>
+              </div>
+          </div>
+          {% endif %}
+          <div class="form-group">
+              <label class="col-xs-2 control-label">Range</label>
+              <div class="col-xs-5 controls">
+                  <input name="p_range_lower" value="" type="hidden">
+                  <input name="p_range_upper" value="" type="hidden">
+                  <span class="inline-div">
+                  <div id="p_range_slider" class="p-range-slider"></div>
+                  <span id="p_range_lower" class="p-range-lower"></span>
+                  <span id="p_range_upper" class="p-range-upper"></span>
+                  </span>
+              </div>
+          </div>
+
+          <div class="form-group">
+              <label for="corr_sample_method" class="col-xs-2 control-label"></label>
+              <div class="col-xs-3 controls">
+                  <input type="button" class="btn corr_compute submit_special btn-success" data-url="/corr_compute" title="Compute Correlation" value="Compute">
+              </div>
+          </div>
+      </div>
     </div>
-  </div>
-  <div>
-    <span id="sample_r_desc" class="correlation_desc fs12">
-        The <a href="http://genenetwork.org/correlationAnnotation.html#genetic_r">Sample Correlation</a>
-        is computed
-        between trait data and any
-        other traits in the sample database selected above. Use
-        <a href="http://www.genenetwork.org/glossary.html#Correlations">Spearman
-        Rank</a>
-        when the sample size is small (&lt;20) or when there are influential outliers.
-    </span>
-    <span id="lit_r_desc" style="display: none;" class="correlation_desc fs12">
-        The <a href="http://genenetwork.org/correlationAnnotation.html#literatureCorr">Literature Correlation</a>
-        (Lit r) between
-        this gene and all other genes is computed<br>
-        using the <a href="https://grits.eecs.utk.edu/sgo/sgo.html">
-        Semantic Gene Organizer</a>
-        and human, rat, and mouse data from PubMed.
-        Values are ranked by Lit r, but Sample r and Tissue r are also displayed.<br>
-        <a href="http://genenetwork.org/glossary.html#Literature">More on using Lit r</a>
-    </span>
-    <span id="tissue_r_desc" style="display: none;" class="correlation_desc fs12">
-        The <a href="http://genenetwork.org/webqtl/main.py?FormID=tissueCorrelation">Tissue Correlation</a>
-        (Tissue r)
-        estimates the similarity of expression of two genes
-        or transcripts across different cells, tissues, or organs
-        (<a href="http://genenetwork.org/correlationAnnotation.html#tissueCorr">glossary</a>).
-        Tissue correlations
-        are generated by analyzing expression in multiple samples usually taken from single cases.<br>
-        <strong>Pearson</strong> and <strong>Spearman Rank</strong> correlations have been
-        computed for all pairs of genes using data from mouse samples.<br>
-    </span>
-  </div>
-</div>
\ No newline at end of file
+    <div class="col-xs-4">
+      <div class="section-form-div">
+        <span id="sample_r_desc" class="correlation_desc">
+            The <a href="http://genenetwork.org/correlationAnnotation.html#genetic_r">Sample Correlation</a>
+            is computed
+            between trait data and any
+            other traits in the sample database selected above. Use
+            <a href="http://www.genenetwork.org/glossary.html#Correlations">Spearman
+            Rank</a>
+            when the sample size is small (&lt;20) or when there are influential outliers.
+        </span>
+        <span id="lit_r_desc" style="display: none;" class="correlation_desc">
+            The <a href="http://genenetwork.org/correlationAnnotation.html#literatureCorr">Literature Correlation</a>
+            (Lit r) between
+            this gene and all other genes is computed<br>
+            using the <a href="https://grits.eecs.utk.edu/sgo/sgo.html">
+            Semantic Gene Organizer</a>
+            and human, rat, and mouse data from PubMed.
+            Values are ranked by Lit r, but Sample r and Tissue r are also displayed.<br>
+            <a href="http://genenetwork.org/glossary.html#Literature">More on using Lit r</a>
+        </span>
+        <span id="tissue_r_desc" style="display: none;" class="correlation_desc">
+            The <a href="http://genenetwork.org/webqtl/main.py?FormID=tissueCorrelation">Tissue Correlation</a>
+            (Tissue r)
+            estimates the similarity of expression of two genes
+            or transcripts across different cells, tissues, or organs
+            (<a href="http://genenetwork.org/correlationAnnotation.html#tissueCorr">glossary</a>).
+            Tissue correlations
+            are generated by analyzing expression in multiple samples usually taken from single cases.<br>
+            <strong>Pearson</strong> and <strong>Spearman Rank</strong> correlations have been
+            computed for all pairs of genes using data from mouse samples.<br>
+        </span>
+      </div>
+    </div>
+  </div>
\ No newline at end of file
diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html
index 4aced50c..d2999eef 100644
--- a/wqflask/wqflask/templates/show_trait_details.html
+++ b/wqflask/wqflask/templates/show_trait_details.html
@@ -1,20 +1,20 @@
-<table class="table" style="max-width: 1400px;">
+<table class="table">
     <tr>
-        <td width="150px"><b>Group</b></td>
+        <td><b>Group</b></td>
         <td>{{ this_trait.dataset.group.species[0]|upper }}{{ this_trait.dataset.group.species[1:] }}: {{ this_trait.dataset.group.name }} group</td>
     </tr>
     {% if this_trait.dataset.type == 'Publish' %}
     <tr>
         <td><b>Phenotype</b></td>
-        <td><div style="width:40%;">{{ this_trait.description_fmt }}</div></td>
+        <td><div>{{ this_trait.description_fmt }}</div></td>
     </tr>
     <tr>
         <td><b>Authors</b></td>
-        <td><div style="width:40%;">{{ this_trait.authors }}</div></td>
+        <td><div>{{ this_trait.authors }}</div></td>
     </tr>
     <tr>
         <td><b>Title</b></td>
-        <td><div style="width:40%;">{{ this_trait.title }}</div></td>
+        <td><div>{{ this_trait.title }}</div></td>
     </tr>
     <tr>
         <td><b>Journal</b></td>
@@ -213,7 +213,7 @@
     {% endif %}
 </table>
 
-<div style="margin-bottom:15px;" class="btn-toolbar">
+<div class="btn-toolbar">
     <div class="btn-group">
         <button type="button" id="add_to_collection" class="btn btn-success" title="Add to Collection">Add</button>
         {% if this_trait.dataset.type == 'ProbeSet' or this_trait.dataset.type == 'Geno' %}
diff --git a/wqflask/wqflask/templates/show_trait_edit_data.html b/wqflask/wqflask/templates/show_trait_edit_data.html
index a8ed91b1..2e730248 100644
--- a/wqflask/wqflask/templates/show_trait_edit_data.html
+++ b/wqflask/wqflask/templates/show_trait_edit_data.html
@@ -1,10 +1,10 @@
 <div>
     {% for sample_type in sample_groups %}
-      <div style="padding-bottom: 10px;">
-        <div style="display: inline; height: 40px;">
-          <input type="text" id="{{ sample_type.sample_group_type }}_searchbox" class="form-control" style="width: 200px; display: inline; float: left; vertical-align: top;" placeholder="Search This Table For ...">
+      <div class="sample-table-container">
+        <div class="sample-table-search-container">
+          <input type="text" id="{{ sample_type.sample_group_type }}_searchbox" class="form-control sample-table-search" placeholder="Search This Table For ...">
         </div>
-        <div style="padding-left: 10px; display: inline;">
+        <div class="sample-table-export-container">
           <button class="btn btn-default export">Export <span class="glyphicon glyphicon-download-alt"></span></button>
           <select class="select optional span2 export_format">
             <option value="excel">Excel</option>
@@ -12,33 +12,33 @@
           </select>
           <input type="button" class="btn btn-success reset" value="Reset">
         </div>
-      </div>
-      <div id="export_code" style="width: 600px; display: none;">
-        <pre style="padding-top: 0px; padding-bottom: 0px; height: 150px;">
-          <code>
-# read into R
-trait <- read.csv("{{ this_trait.display_name}}.csv", header = TRUE, comment.char = "#")
+        <div id="export_code" class="export-code-container">
+          <pre class="export-code_field">
+            <code>
+  # read into R
+  trait <- read.csv("{{ this_trait.display_name}}.csv", header = TRUE, comment.char = "#")
 
-# read into python
-import pandas as pd
-trait = pd.read_csv("{{ this_trait.display_name}}.csv", header = 0, comment = "#")
-          </code>
-        </pre>
+  # read into python
+  import pandas as pd
+  trait = pd.read_csv("{{ this_trait.display_name}}.csv", header = 0, comment = "#")
+            </code>
+          </pre>
+        </div>
       </div>
-        {% set outer_loop = loop %}
-        <div class="sample_group" style="width:{{ trait_table_width }};">
-          <div style="position: relative;">
-            <div style="display: inline;"><h3 style="float: left;">{{ sample_type.header }}<span name="transform_text"></span></h3>
-          </div>
-          <div id="table_container">
-          <table class="table-hover table-striped cell-border" id="samples_{{ sample_type.sample_group_type }}" style="float: left; width:100%;">
-              <tbody>
-                <td colspan="100%" align="center"><br><b><font size="15">Loading...</font></b><br></td>
-              </tbody>
-          </table>
-          </div>
+      {% set outer_loop = loop %}
+      <div class="sample_group" style="width:{{ trait_table_width }};">
+        <div style="position: relative;">
+          <div class="inline-div"><h3 style="float: left;">{{ sample_type.header }}<span name="transform_text"></span></h3></div>
         </div>
-        <br>
+        <div id="table_container">
+        <table class="table-hover table-striped cell-border sample-table" id="samples_{{ sample_type.sample_group_type }}">
+            <tbody>
+              <td colspan="100%" align="center"><br><b><font size="15">Loading...</font></b><br></td>
+            </tbody>
+        </table>
+        </div>
+      </div>
+      <br>
     {% endfor %}
     <input type="hidden" name="Default_Name">
 </div>
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index 94388b2f..eca436c6 100755
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -1,38 +1,35 @@
-<div>
+<div class="row mapping-main">
     {% if dataset.group.mapping_names|length > 0 %}
-    <div class="col-xs-3" style="min-width: 400px;">
+    <div class="col-xs-2 mapping-options">
         <div class="tabbable"> <!-- Only required for left/right tabs -->
 
             <ul class="nav nav-pills">
                 {% for mapping_method in dataset.group.mapping_names %}
                 {% if mapping_method == "GEMMA" %}
-                <li class="gemma_tab mapping_tab {% if dataset.group.mapping_id == '1' or dataset.group.mapping_id == '2' %}active{% endif %}">
+                <li class="gemma-tab mapping-tab {% if dataset.group.mapping_id == '1' or dataset.group.mapping_id == '2' %}active{% endif %}">
                     <a href="#gemma" data-toggle="tab">GEMMA</a>
                 </li>
                 {% elif mapping_method == "R/qtl" %}
-                <li class="rqtl_geno_tab mapping_tab {% if dataset.group.mapping_id == '3' %}active{% endif %}">
+                <li class="rqtl-geno-tab mapping-tab {% if dataset.group.mapping_id == '3' %}active{% endif %}">
                     <a href="#rqtl_geno" data-toggle="tab">R/qtl</a>
                 </li>
                 {% elif mapping_method == "QTLReaper" %}
-                <li class="reaper_tab mapping_tab">
+                <li class="reaper-tab mapping-tab">
                     <a href="#interval_mapping" data-toggle="tab">Haley-Knott Regression</a>
                 </li>
                 {% endif %}
                 {% endfor %}
-                <!--<li>
-                    <a href="#pair_scan" data-toggle="tab">Pair Scan</a>
-                </li>-->
             </ul>
 
             <div class="tab-content">
                 {% for mapping_method in dataset.group.mapping_names %}
                 {% if mapping_method == "GEMMA" %}
                 <div class="tab-pane {% if dataset.group.mapping_id == '1' or dataset.group.mapping_id == '2' %}active{% endif %}" id="gemma">
-                    <div style="padding-top: 20px;" class="form-horizontal">
+                    <div class="form-horizontal section-form-div">
                         <div class="mapping_method_fields form-group">
-                            <label for="chr_select" style="text-align: right;" class="col-xs-3 control-label">Chromosome</label>
-                            <div style="margin-left:20px;" class="col-xs-2 controls">
-                                <select id="chr_gemma" class="form-control" style="width: 80px;">
+                            <label for="chr_select" class="col-xs-3 control-label">Chromosome</label>
+                            <div class="col-xs-2 controls">
+                                <select id="chr_gemma" class="form-control chr-select">
                                     {% for item in chr_list %}
                                     <option value="{{ item[1] }}">{{ item[0] }}</option>
                                     {% endfor %}
@@ -41,8 +38,8 @@
                         </div>
                         {% if genofiles and genofiles|length>0 %}
                         <div class="mapping_method_fields form-group">
-                            <label for="genofiles" style="text-align: right;" class="col-xs-3 control-label">Genotypes</label>
-                            <div style="margin-left:20px;" class="col-xs-4 controls">
+                            <label for="genofiles" class="col-xs-3 control-label">Genotypes</label>
+                            <div class="col-xs-8 controls">
                                 <select id="genofile_gemma" class="form-control">
                                     {% for item in genofiles %}
                                     <option value="{{item['location']}}:{{item['title']}}">{{item['title']}}</option>
@@ -52,14 +49,14 @@
                         </div>
                         {% endif %}
                         <div class="mapping_method_fields form-group">
-                            <label for="maf_gemma" style="text-align: right;" class="col-xs-3 control-label">MAF >=</label>
-                            <div style="margin-left:20px;" class="col-xs-4 controls">
-                                <input name="maf_gemma" value="{{ maf }}" type="text" class="form-control" style="width: 80px;">
+                            <label for="maf_gemma" class="col-xs-3 control-label">MAF >=</label>
+                            <div class="col-xs-4 controls">
+                                <input name="maf_gemma" value="{{ maf }}" type="text" class="form-control maf-select">
                             </div>
                         </div>
                         <div class="mapping_method_fields form-group">
-                            <label style="text-align: right;" class="col-xs-3 control-label">Use LOCO</label>
-                            <div style="margin-left:20px;" class="col-xs-6 controls">
+                            <label class="col-xs-3 control-label">Use LOCO</label>
+                            <div class="col-xs-6 controls">
                                 <label class="radio-inline">
                                     <input type="radio" name="use_loco" value="True" checked="">
                                     Yes
@@ -71,25 +68,22 @@
                             </div>
                         </div>
                         <div class="mapping_method_fields form-group">
-                            <div class="col-xs-3" style="text-align: right;">
-                            <label class="control-label">Covariates</label>
-                            <font size="2">Select covariate(s) from a collection</font>
-                            </div>
-                            <div style="margin-left:20px;" class="col-xs-7">
+                            <label class="col-xs-3 control-label">Covariates<br><span class="covar-text">Select covariate(s) from a collection</span></label>
+                            <div class="col-xs-8 covar-options">
                               {% if g.user_session.num_collections < 1 %}
                               No collections available. Please add traits to a collection to use them as covariates.
                               {% else %}
-                              <div style="margin-bottom: 10px;">
-                                <button type="button" id="select_covariates" class="btn btn-default" style="width: 80px; padding-right: 10px;">Select</button>
-                                <button type="button" id="remove_covariates" class="btn btn-default" style="width: 80px;">Remove</button>
+                              <div class="select-covar-div">
+                                <button type="button" id="select_covariates" class="btn btn-default select-covar-button">Select</button>
+                                <button type="button" id="remove_covariates" class="btn btn-default select-covar-button">Remove</button>
                               </div>
-                              <textarea rows="3" cols="50" readonly placeholder="No covariates selected" style="overflow-y: scroll; resize: none; width: 200px;" class="selected_covariates"></textarea>
+                              <textarea rows="3" cols="50" readonly placeholder="No covariates selected" class="selected-covariates"></textarea>
                               {% endif %}
                             </div>
                         </div>
                         <div class="mapping_method_fields form-group">
                           <label class="col-xs-3 control-label"></label>
-                          <div style="margin-left:20px;" class="col-xs-6">
+                          <div class="col-xs-6">
                             <button id="gemma_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Marker Regression" value="Compute">Compute</button>
                           </div>
                         </div>
@@ -97,20 +91,20 @@
                 </div>
                 {% elif mapping_method == "QTLReaper" %}
                 <div class="tab-pane" id="interval_mapping">
-                    <div style="margin-top: 20px" class="form-horizontal">
+                    <div class="form-horizontal section-form-div">
                         <div class="mapping_method_fields form-group">
-                            <label for="reaper_version" style="text-align: right;" class="col-xs-3 control-label">Version<sup><a href="https://github.com/chfi/rust-qtlreaper" target="_blank" title="'New' is the new qtlreaper implementation written in RUST by Christian Fischer. 'Original' corresponds to the original version written in C.">?</a></sup></label>
-                            <div style="margin-left:20px;" class="col-xs-3 controls">
-                                <select name="reaper_version" class="form-control" style="width: 80px;">
+                            <label for="reaper_version" class="col-xs-3 control-label">Version<sup><a href="https://github.com/chfi/rust-qtlreaper" target="_blank" title="'New' is the new qtlreaper implementation written in RUST by Christian Fischer. 'Original' corresponds to the original version written in C.">?</a></sup></label>
+                            <div class="col-xs-3 controls">
+                                <select name="reaper_version" class="form-control reaper-ver-select">
                                     <option value="new">New</option>
                                     <option value="original">Original</option>
                                 </select>
                             </div>
                         </div>
                         <div class="mapping_method_fields form-group">
-                            <label for="chr_select" style="text-align: right;" class="col-xs-3 control-label">Chromosome</label>
-                            <div style="margin-left:20px;" class="col-xs-2 controls">
-                                    <select id="chr_reaper" class="form-control" style="width: 80px;">
+                            <label for="chr_select" class="col-xs-3 control-label">Chromosome</label>
+                            <div class="col-xs-2 controls">
+                                    <select id="chr_reaper" class="form-control chr-select">
                                     {% for item in chr_list %}
                                     <option value="{{ item[1] }}">{{ item[0] }}</option>
                                     {% endfor %}
@@ -119,9 +113,9 @@
                         </div>
                         {% if genofiles and genofiles|length>0 %}
                         <div class="mapping_method_fields form-group">
-                            <label for="scale_select" style="text-align: right;" class="col-xs-3 control-label">Map Scale</label>
-                            <div style="margin-left:20px;" class="col-xs-2 controls">
-                                <select id="scale_reaper" class="form-control" style="width: 80px;">
+                            <label for="scale_select" class="col-xs-3 control-label">Map Scale</label>
+                            <div class="col-xs-2 controls">
+                                <select id="scale_reaper" class="form-control scale-select">
                                     {% for item in scales_in_geno[genofiles[0]['location']] %}
                                     <option value="{{ item[0] }}">{{ item[1] }}</option>
                                     {% endfor %}
@@ -129,8 +123,8 @@
                             </div>
                         </div>
                         <div class="mapping_method_fields form-group">
-                            <label style="text-align: right;" for="genofiles" class="col-xs-3 control-label">Genotypes</label>
-                            <div style="margin-left:20px;" class="col-xs-4 controls">
+                            <label for="genofiles" class="col-xs-3 control-label">Genotypes</label>
+                            <div class="col-xs-4 controls">
                                 <select id="genofile_reaper" class="form-control">
                                     {% for item in genofiles %}
                                     <option value="{{item['location']}}:{{item['title']}}">{{item['title']}}</option>
@@ -140,9 +134,9 @@
                         </div>
                         {% else %}
                         <div class="mapping_method_fields form-group">
-                            <label for="scale_select" style="text-align: right;" class="col-xs-3 control-label">Map Scale</label>
-                            <div style="margin-left:20px;" class="col-xs-2 controls">
-                                <select id="scale_reaper" class="form-control" style="width: 80px;">
+                            <label for="scale_select" class="col-xs-3 control-label">Map Scale</label>
+                            <div class="col-xs-2 controls">
+                                <select id="scale_reaper" class="form-control scale-select">
                                     {% for item in scales_in_geno[dataset.group.name + ".geno"] %}
                                     <option value="{{ item[0] }}">{{ item[1] }}</option>
                                     {% endfor %}
@@ -151,79 +145,48 @@
                         </div>
                         {% endif %}
                         <div class="mapping_method_fields form-group">
-                            <label style="text-align: right;" for="mapping_permutations" class="col-xs-3 control-label">Permutations</label>
-                            <div style="margin-left:20px;" class="col-xs-4 controls">
+                            <label for="mapping_permutations" class="col-xs-3 control-label">Permutations</label>
+                            <div class="col-xs-4 controls">
                                 <input name="num_perm_reaper" value="2000" type="text" class="form-control">
                             </div>
                         </div>
                         <div class="mapping_method_fields form-group">
-                            <label style="text-align: right;" for="mapping_bootstraps" class="col-xs-3 control-label">Bootstraps</label>
-                            <div style="margin-left:20px;" class="col-xs-4 controls">
-                                <input name="num_bootstrap" value="2000" type="text" class="form-control">
-                            </div>
-                        </div>
-                        <div class="mapping_method_fields form-group">
-                            <label style="text-align: right;" for="control_for" class="col-xs-3 control-label">Control&nbsp;for<br>Cofactors</label>
-                            <div style="margin-left:20px;" class="col-xs-6 controls">
-                                {% if dataset.type == 'ProbeSet' and this_trait.locus_chr != "" %}
-                                <input name="control_reaper" value="{{ nearest_marker }}" type="text" style="width: 160px; display: inline-block;" class="form-control" />
-                                {% else %}
-                                <input name="control_reaper" value="" type="text" style="display: inline-block; padding-right: 10px;" class="form-control" />
-                                {% endif %}
-                                <input type="radio" name="do_control_reaper" value="true"> Yes&nbsp;&nbsp;<input type="radio" name="do_control_reaper" value="false" checked="" style="margin-left: 10px;"> No</span>
-                                <!--
-                                <label class="radio-inline">
-                                    <input type="radio" name="do_control_reaper" value="true">
-                                    Yes
-                                </label>
-                                <label class="radio-inline">
-                                    <input type="radio" name="do_control_reaper" value="false" checked="">
-                                    No
-                                </label>
-                            -->
-                            </div>
-                        </div>
-
-<!--
-                        <div class="mapping_method_fields form-group">
-                            <label for="mapping_bootstraps" class="col-xs-3 control-label" title="Bootstrapping Resamples">Bootstrap Test (n=2000)</label>
+                            <label for="mapping_bootstraps" class="col-xs-3 control-label">Bootstraps</label>
                             <div class="col-xs-4 controls">
-                                <label>
-                                    <input type="checkbox" name="bootCheck" id="bootCheck"> Bootstrap Test (n=2000)
-                                </label>
+                                <input name="num_bootstrap" value="2000" type="text" class="form-control">
                             </div>
                         </div>
-
                         <div class="mapping_method_fields form-group">
-                            <label style="text-align:left;" class="col-xs-12 control-label">Display Additive Effect</label>
-                            <div class="col-xs-12 controls" id="display_additive_effect">
+                            <label for="control_for" class="col-xs-3 control-label">Control&nbsp;for<br>Cofactors</label>
+                            <div class="col-xs-6 controls">
+                                <input name="control_reaper" value="{% if dataset.type == 'ProbeSet' and this_trait.locus_chr != '' %}{{ nearest_marker }}{% endif %}" type="text" class="form-control cofactor-input" />
+                                <br>
                                 <label class="radio-inline">
-                                    <input type="radio" name="display_additive" id="display_additive" value="yes" checked="">
-                                    Yes
+                                  <input type="radio" name="do_control_reaper" value="true" checked="">
+                                  Yes
                                 </label>
                                 <label class="radio-inline">
-                                    <input type="radio" name="display_additive" id="display_additive" value="no">
-                                    No
+                                  <input type="radio" name="do_control_reaper" value="false">
+                                  No
                                 </label>
                             </div>
                         </div>
--->
                         <div class="mapping_method_fields form-group">
-                            <label style="text-align: right;" class="col-xs-3 control-label">Interval Map</label>
-                            <div style="margin-left:20px;" class="col-xs-6 controls">
+                            <label class="col-xs-3 control-label">Interval Map</label>
+                            <div class="col-xs-6 controls">
                                 <label class="radio-inline">
-                                    <input type="radio" name="manhattan_plot_reaper" value="False" checked="">
+                                    <input type="radio" name="manhattan_plot_reaper" value="false" checked="">
                                     Yes
                                 </label>
                                 <label class="radio-inline">
-                                    <input type="radio" name="manhattan_plot_reaper" value="True">
+                                    <input type="radio" name="manhattan_plot_reaper" value="true">
                                     No
                                </label>
                             </div>
                         </div>
                         <div class="mapping_method_fields form-group">
                             <label class="col-xs-3 control-label"></label>
-                            <div style="margin-left:20px;" class="col-xs-6">
+                            <div class="col-xs-6">
                               <button id="interval_mapping_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Interval Mapping" value="Compute">Compute</button>
                             </div>
                         </div>
@@ -231,11 +194,11 @@
                 </div>
                 {% elif mapping_method == "R/qtl" %}
                 <div class="tab-pane {% if dataset.group.mapping_id == '3' %}active{% endif %}" id="rqtl_geno">
-                    <div style="margin-top: 20px" class="form-horizontal">
+                    <div class="form-horizontal section-form-div">
                         <div class="mapping_method_fields form-group">
-                            <label for="chr_select" style="text-align: right;" class="col-xs-3 control-label">Chromosome</label>
-                            <div style="margin-left:20px;" class="col-xs-2 controls">
-                                    <select id="chr_rqtl_geno" class="form-control" style="width: 80px;">
+                            <label for="chr_select" class="col-xs-3 control-label">Chromosome</label>
+                            <div class="col-xs-2 controls">
+                                    <select id="chr_rqtl_geno" class="form-control chr-select">
                                     {% for item in chr_list %}
                                     <option value="{{ item[1] }}">{{ item[0] }}</option>
                                     {% endfor %}
@@ -244,9 +207,9 @@
                         </div>
                         {% if genofiles and genofiles|length > 0 %}
                         <div class="mapping_method_fields form-group">
-                            <label for="scale_select" style="text-align: right;" class="col-xs-3 control-label">Map Scale</label>
-                            <div style="margin-left:20px;" class="col-xs-2 controls">
-                                <select id="scale_rqtl_geno" class="form-control" style="width: 80px;">
+                            <label for="scale_select" class="col-xs-3 control-label">Map Scale</label>
+                            <div class="col-xs-2 controls">
+                                <select id="scale_rqtl_geno" class="form-control scale-select">
                                     {% for item in scales_in_geno[genofiles[0]['location']] %}
                                     <option value="{{ item[0] }}">{{ item[1] }}</option>
                                     {% endfor %}
@@ -254,8 +217,8 @@
                             </div>
                         </div>
                         <div class="mapping_method_fields form-group">
-                            <label style="text-align:right;" for="genofiles" class="col-xs-3 control-label">Genotypes</label>
-                            <div style="margin-left:20px;" class="col-xs-4 controls">
+                            <label for="genofiles" class="col-xs-3 control-label">Genotypes</label>
+                            <div class="col-xs-4 controls">
                                 <select id="genofile_rqtl_geno" class="form-control">
                                     {% for item in genofiles %}
                                     <option value="{{item['location']}}:{{item['title']}}">{{item['title']}}</option>
@@ -265,15 +228,15 @@
                         </div>
                         {% endif %}
                         <div class="mapping_method_fields form-group">
-                            <label style="text-align:right;" for="mapping_permutations" class="col-xs-3 control-label">Permutations</label>
-                            <div style="margin-left:20px;" class="col-xs-4 controls">
+                            <label for="mapping_permutations" class="col-xs-3 control-label">Permutations</label>
+                            <div class="col-xs-4 controls">
                                 <input name="num_perm_rqtl_geno" value="200" type="text" class="form-control">
                             </div>
                         </div>
                         {% if sample_groups[0].attributes|length > 0 %}
                         <div class="mapping_method_fields form-group">
-                            <label style="text-align:right;" class="col-xs-3 control-label">Stratified</label>
-                            <div style="margin-left:20px;" class="col-xs-6 controls">
+                            <label class="col-xs-3 control-label">Stratified</label>
+                            <div class="col-xs-6 controls">
                                 <label class="radio-inline">
                                     <input type="radio" name="perm_strata" value="True" checked=""> 
                                     Yes
@@ -286,27 +249,23 @@
                         </div>
                         {% endif %}
                         <div class="mapping_method_fields form-group">
-                            <label style="text-align:right;" for="control_for" class="col-xs-3 control-label">Control&nbsp;for</label>
-                            <div style="margin-left:20px;" class="col-xs-6 controls">
-                                {% if dataset.type == 'ProbeSet' and this_trait.locus_chr != "" %}
-                                <input name="control_rqtl_geno" value="{{ nearest_marker }}" type="text" style="width: 160px;" class="form-control" />
-                                {% else %}
-                                <input name="control_rqtl_geno" value="" type="text" class="form-control" />
-                                {% endif %}
-                                <label class="radio-inline">
-                                    <input type="radio" name="do_control_rqtl" value="true">
-                                    Yes
-                                </label>
-                                <label class="radio-inline">
-                                    <input type="radio" name="do_control_rqtl" value="false" checked="">
-                                    No
-                                </label>
+                            <label for="control_for" class="col-xs-3 control-label">Control&nbsp;for</label>
+                            <div class="col-xs-6 controls">
+                              <input name="control_rqtl_geno" value="{% if dataset.type == 'ProbeSet' and this_trait.locus_chr != '' %}{{ nearest_marker }}{% endif %}" type="text" class="form-control cofactor-input" />
+                              <label class="radio-inline">
+                                  <input type="radio" name="do_control_rqtl" value="true">
+                                  Yes
+                              </label>
+                              <label class="radio-inline">
+                                  <input type="radio" name="do_control_rqtl" value="false" checked="">
+                                  No
+                              </label>
                             </div>
                         </div>
 
                         <div class="mapping_method_fields form-group">
-                            <label style="text-align:right;" for="mapmodel_rqtl_geno" class="col-xs-3 control-label">Model</label>
-                            <div style="margin-left:20px;" class="col-xs-4 controls">
+                            <label for="mapmodel_rqtl_geno" class="col-xs-3 control-label">Model</label>
+                            <div class="col-xs-4 controls">
                               <select id="mapmodel_rqtl_geno" name="mapmodel_rqtl_geno" class="form-control">
                                 <option value="normal">Normal</option>
                                 {% if binary == "true" %}<option value="binary">Binary</option>{% endif %}
@@ -317,8 +276,8 @@
                         </div>
 
                         <div class="mapping_method_fields form-group">
-                            <label style="text-align:right;" for="mapmethod_rqtl_geno" class="col-xs-3 control-label">Method</label>
-                            <div style="margin-left:20px;" class="col-xs-6 controls">
+                            <label for="mapmethod_rqtl_geno" class="col-xs-3 control-label">Method</label>
+                            <div class="col-xs-6 controls">
                               <select id="mapmethod_rqtl_geno" name="mapmethod_rqtl_geno" class="form-control">
                                 <option value="hk" selected>Haley-Knott</option>
                                 <option value="ehk">Extended Haley-Knott</option>
@@ -329,8 +288,8 @@
                             </div>
                         </div>
                         <div id="missing_geno_div" class="mapping_method_fields form-group" style="display: none;">
-                            <label style="text-align:right;" for="missing_genotypes" class="col-xs-3 control-label"></label>
-                            <div style="margin-left:20px;" class="col-xs-6 controls">
+                            <label for="missing_genotypes" class="col-xs-3 control-label"></label>
+                            <div class="col-xs-6 controls">
                               <select id="missing_genotype" name="missing_genotypes" class="form-control">
                                 <option value="mr">Remove Samples w/o Genotypes</option>
                                 <option value="mr-imp">Single Imputation</option>
@@ -338,25 +297,9 @@
                               </select>
                             </div>
                         </div>
-
-                        <!--
-                        <div class="mapping_method_fields form-group">
-                            <label style="text-align:left;" class="col-xs-12 control-label">Pair Scan</label>
-                            <div class="col-xs-12 controls">
-                                <label class="radio-inline">
-                                    <input type="radio" name="pair_scan" value="true">
-                                    Yes
-                                </label>
-                                <label class="radio-inline">
-                                    <input type="radio" name="pair_scan" value="false" checked="">
-                                    No
-                               </label>
-                            </div>
-                        </div>
-                        -->
                         <div class="mapping_method_fields form-group">
-                            <label style="text-align:right;" class="col-xs-3 control-label">Manhattan<br>Plot</label>
-                            <div style="margin-left:20px;" class="col-xs-6 controls">
+                            <label class="col-xs-3 control-label">Manhattan<br>Plot</label>
+                            <div class="col-xs-6 controls">
                                 <label class="radio-inline">
                                     <input type="radio" name="manhattan_plot_rqtl" value="True">
                                     Yes
@@ -368,25 +311,22 @@
                             </div>
                         </div>
                         <div class="mapping_method_fields form-group">
-                            <div class="col-xs-3" style="text-align: right;">
-                            <label class="control-label">Covariates</label>
-                            <font size="2">Select covariate(s) from a collection</font>
-                            </div>
-                            <div style="margin-left:20px;" class="col-xs-7">
-                              {% if g.user_session.num_collections < 1 %}
-                              No collections available. Please add traits to a collection to use them as covariates.
-                              {% else %}
-                              <div style="margin-bottom: 10px;">
-                                <button type="button" class="btn btn-default select_covariates" style="width: 80px; padding-right: 10px;">Select</button>
-                                <button type="button" class="btn btn-default remove_covariates" style="width: 80px;">Remove</button>
-                              </div>
-                              <textarea rows="3" cols="50" readonly placeholder="No covariates selected" style="overflow-y: scroll; resize: none; width: 200px;" class="selected_covariates"></textarea>
-                              {% endif %}
-                            </div>
+                          <label class="col-xs-3 control-label">Covariates<br><span class="covar-text">Select covariate(s) from a collection</span></label>
+                          <div class="col-xs-8 covar-options">
+                            {% if g.user_session.num_collections < 1 %}
+                            No collections available. Please add traits to a collection to use them as covariates.
+                            {% else %}
+                            <div class="select-covar-div">
+                              <button type="button" id="select_covariates" class="btn btn-default select-covar-button">Select</button>
+                              <button type="button" id="remove_covariates" class="btn btn-default select-covar-button">Remove</button>
+                            </div>
+                            <textarea rows="3" cols="50" readonly placeholder="No covariates selected" class="selected-covariates"></textarea>
+                            {% endif %}
+                          </div>
                         </div>
                         <div class="mapping_method_fields form-group">
                             <label class="col-xs-3 control-label"></label>
-                            <div style="margin-left:20px;" class="col-xs-6">
+                            <div class="col-xs-6 controls">
                               <button id="rqtl_geno_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Marker Regression" value="Compute">Compute</button>
                             </div>
                         </div>
@@ -397,23 +337,25 @@
             </div>
         </div>
     </div>
-    <div>
-        <dl>
-             {% for mapping_method in dataset.group.mapping_names %}
-             {% if mapping_method == "GEMMA" %}
-             <dt style="padding-top: 20px;">GEMMA</dt>
-             <dd>Maps traits with correction for kinship among samples using a linear mixed model method, and also allows users to fit multiple covariates such as sex, age, treatment, and genetic markers (<a href="https://www.ncbi.nlm.nih.gov/pubmed/24531419">PMID: 2453419</a>, and <a href="https://github.com/genetics-statistics/GEMMA"> GitHub code</a>). GEMMA incorporates the Leave One Chromosome Out (LOCO) method to ensure that the correction for kinship does not remove useful genetic variance near each marker. Markers can be filtered to include only those with minor allele frequencies (MAF) above a threshold. The default MAF is 0.05.</dd>
-             {% elif mapping_method == "R/qtl" %}
-             <dt style="margin-top: 20px;">R/qtl (version 1.44.9</dt>
-             <dd>The original R/qtl mapping package that supports classic experimental crosses including 4-parent F2 intercrosses (e.g., NIA ITP UM-HET3). R/qtl is ideal for populations that do not have complex kinship or admixture (<a href="https://www.ncbi.nlm.nih.gov/pubmed/12724300">PMID: 12724300</a>). Both R/qtl as implemented here, and R/qtl2 (<a href="https://www.ncbi.nlm.nih.gov/pubmed/30591514">PMID: 30591514</a>) are available as <a href="https://kbroman.org/pages/software.html">R suites</a>.</dd>
-             {% elif mapping_method == "QTLReaper" %}
-             <dt style="margin-top: 20px;">Haley-Knott Regression</dt>
-             <dd>Fast linear mapping method (<a href="https://www.ncbi.nlm.nih.gov/pubmed/16718932">PMID 16718932</a>) works well with F2 intercrosses and backcrosses, but that is not recommended for complex or admixed populations (e.g., GWAS or heterogeneous stock studies) or for advanced intercrosses, recombinant inbred families, or diallel crosses. Interactive plots in GeneNetwork have relied on the fast HK mapping for two decades and we still use this method for mapping omics data sets and computing genome-wide permutation threshold (<a href="https://github.com/pjotrp/QTLReaper">QTL Reaper code</a>).</dd>
-             {% endif %}
-             {% endfor %}
-        </dl>
-        <div class="rqtl_description" style="padding-top: 40px; display: none;">
-        More information on R/qtl mapping models and methods can be found <a href="http://www.rqtl.org/tutorials/rqtltour.pdf">here</a>.
+    <div class="col-xs-6">
+        <div class="section-form-div">
+            <dl>
+                {% for mapping_method in dataset.group.mapping_names %}
+                {% if mapping_method == "GEMMA" %}
+                <dt>GEMMA</dt>
+                <dd>Maps traits with correction for kinship among samples using a linear mixed model method, and also allows users to fit multiple covariates such as sex, age, treatment, and genetic markers (<a href="https://www.ncbi.nlm.nih.gov/pubmed/24531419">PMID: 2453419</a>, and <a href="https://github.com/genetics-statistics/GEMMA"> GitHub code</a>). GEMMA incorporates the Leave One Chromosome Out (LOCO) method to ensure that the correction for kinship does not remove useful genetic variance near each marker. Markers can be filtered to include only those with minor allele frequencies (MAF) above a threshold. The default MAF is 0.05.</dd>
+                {% elif mapping_method == "R/qtl" %}
+                <dt class="map-method-text">R/qtl (version 1.44.9</dt>
+                <dd>The original R/qtl mapping package that supports classic experimental crosses including 4-parent F2 intercrosses (e.g., NIA ITP UM-HET3). R/qtl is ideal for populations that do not have complex kinship or admixture (<a href="https://www.ncbi.nlm.nih.gov/pubmed/12724300">PMID: 12724300</a>). Both R/qtl as implemented here, and R/qtl2 (<a href="https://www.ncbi.nlm.nih.gov/pubmed/30591514">PMID: 30591514</a>) are available as <a href="https://kbroman.org/pages/software.html">R suites</a>.</dd>
+                {% elif mapping_method == "QTLReaper" %}
+                <dt class="map-method-text">Haley-Knott Regression</dt>
+                <dd>Fast linear mapping method (<a href="https://www.ncbi.nlm.nih.gov/pubmed/16718932">PMID 16718932</a>) works well with F2 intercrosses and backcrosses, but that is not recommended for complex or admixed populations (e.g., GWAS or heterogeneous stock studies) or for advanced intercrosses, recombinant inbred families, or diallel crosses. Interactive plots in GeneNetwork have relied on the fast HK mapping for two decades and we still use this method for mapping omics data sets and computing genome-wide permutation threshold (<a href="https://github.com/pjotrp/QTLReaper">QTL Reaper code</a>).</dd>
+                {% endif %}
+                {% endfor %}
+            </dl>
+            <div class="rqtl-description">
+            More information on R/qtl mapping models and methods can be found <a href="http://www.rqtl.org/tutorials/rqtltour.pdf">here</a>.
+            </div>
         </div>
     </div>
     <div id="mapping_result_holder_wrapper" style="display:none;">
diff --git a/wqflask/wqflask/templates/show_trait_statistics.html b/wqflask/wqflask/templates/show_trait_statistics.html
index 7bdb3ef9..4f347d4e 100644
--- a/wqflask/wqflask/templates/show_trait_statistics.html
+++ b/wqflask/wqflask/templates/show_trait_statistics.html
@@ -1,148 +1,137 @@
 <div>
-        <div class="tabbable"> <!-- Only required for left/right tabs -->
-            <ul class="nav nav-pills">
-                <li class="active">
-                    <a href="#stats_tab" data-toggle="tab">Basic Statistics</a>
-                </li>
-                <li>
-                    <a href="#histogram_tab" class="histogram_tab" data-toggle="tab">Histogram</a>
-                </li>
-                {% if num_values < 256 %}
-                <li>
-                    <a href="#bar_chart_tab" class="bar_chart_tab" data-toggle="tab">Bar Chart</a>
-                </li>
-                {% endif %}
-                <li>
-                    <a href="#probability_plot" class="prob_plot_tab" data-toggle="tab">Probability Plot</a>
-                </li>
-                <li>
-                    <a href="#box_plot_tab" class="box_plot_tab" data-toggle="tab">Box Plot</a>
-                </li>
-                <li>
-                    <a href="#violin_plot_tab" class="violin_plot_tab" data-toggle="tab">Violin Plot</a>
-                </li>
-                <li>
-                    <a href="#scatterplot_matrix" data-toggle="tab">Scatterplot Matrix</a>
-                </li>
-            </ul>
-
-            <div class="tab-content">
-                <div class="tab-pane active" id="stats_tab">
-                    <div style="padding: 20px;" class="form-horizontal">
-                            <table id="stats_table" style="width: {{ stats_table_width }}px; float: left;" class="table table-hover table-striped table-bordered"></table>
-                    </div>
-                </div>   
-                <div class="tab-pane" id="histogram_tab">
-                    <div style="padding: 20px" class="form-horizontal">
-                        {% if sample_groups|length != 1 %}
-                        <select class="histogram_samples_group">
-                            {% for group, pretty_group in sample_group_types.items() %}
-                                <option value="{{ group }}">{{ pretty_group }}</option>
-                            {% endfor %}
-                        </select>
-                        <br><br>
-                        {% endif %}
-                        <div id="histogram_container">
-                            <div id="histogram" class="barchart"></div>
-                        </div>
-                    </div>
+    <div class="tabbable"> <!-- Only required for left/right tabs -->
+        <ul class="nav nav-pills">
+            <li class="active">
+                <a href="#stats_tab" data-toggle="tab">Basic Statistics</a>
+            </li>
+            <li>
+                <a href="#histogram_tab" class="histogram_tab" data-toggle="tab">Histogram</a>
+            </li>
+            {% if num_values < 256 %}
+            <li>
+                <a href="#bar_chart_tab" class="bar_chart_tab" data-toggle="tab">Bar Chart</a>
+            </li>
+            {% endif %}
+            <li>
+                <a href="#probability_plot" class="prob_plot_tab" data-toggle="tab">Probability Plot</a>
+            </li>
+            <li>
+                <a href="#box_plot_tab" class="box_plot_tab" data-toggle="tab">Box Plot</a>
+            </li>
+            <li>
+                <a href="#violin_plot_tab" class="violin_plot_tab" data-toggle="tab">Violin Plot</a>
+            </li>
+            <li>
+                <a href="#scatterplot_matrix" data-toggle="tab">Scatterplot Matrix</a>
+            </li>
+        </ul>
+        <div class="tab-content">
+            <div class="tab-pane active" id="stats_tab">
+                <div class="form-horizontal section-form-div">
+                        <table id="stats_table" style="width: {{ stats_table_width }}px;" class="table table-hover table-striped table-bordered left-float"></table>
                 </div>
-                {% if num_values < 256 %}
-                <div class="tab-pane" id="bar_chart_tab">
-                    <div style="padding: 20px" class="form-horizontal">
-                        {% if sample_groups|length != 1 %}
-                        <select class="bar_chart_samples_group">
-                            {% for group, pretty_group in sample_group_types.items() %}
-                                <option value="{{ group }}">{{ pretty_group }}</option>
-                            {% endfor %}
-                        </select>
-                        {% endif %}
-                        {% if sample_groups[0].attributes %}
-                        <div class="input-append">
-                            <select id="color_attribute" size="1">
-                                <option value="None">None</option>
-                                {% for attribute in sample_groups[0].attributes %}
-                                <option value="{{ sample_groups[0].attributes[attribute].name.replace(' ', '_') }}">
-                                    {{ sample_groups[0].attributes[attribute].name }}</option>
-                                {% endfor %}
-                            </select>
-                        </div>
-                        {% endif %}
-                        <div id="update_bar_chart" class="btn-group" style="margin-bottom: 5px;">
-                            <button type="button" class="btn btn-default sort_by_name" value="name">
-                            <i class="icon-resize-horizontal"></i> Sort By Name
-                            </button>
-                            <button type="button" class="btn btn-default sort_by_value" value="value">
-                            <i class="icon-signal"></i> Sort By Value
-                            </button>
-                        </div>
-                        <!--
-                        <div class="btn-group">
-                            <button type="button" class="btn btn-default" id="color_by_trait" style="margin-bottom: 5px;">
-                                <i class="icon-tint"></i> Color by Trait
-                            </button>
-                        </div>
-                        -->
-                        <div id="bar_chart_container">
-                            <div id="bar_chart"></div>
-                        </div>
+            </div>
+            <div class="tab-pane" id="histogram_tab">
+                <div class="form-horizontal section-form-div">
+                    {% if sample_groups|length != 1 %}
+                    Select Group:
+                    <select class="histogram_samples_group">
+                        {% for group, pretty_group in sample_group_types.items() %}
+                            <option value="{{ group }}">{{ pretty_group }}</option>
+                        {% endfor %}
+                    </select>
+                    <br><br>
+                    {% endif %}
+                    <div id="histogram_container">
+                        <div id="histogram" class="barchart"></div>
                     </div>
                 </div>
-                {% endif %}
-                <div class="tab-pane" id="probability_plot">
-                    <div style="padding: 20px" class="form-horizontal">
-                        {% if sample_groups|length != 1 %}
-                        Select Group:
-                        <select class="prob_plot_samples_group">
-                            {% for group, pretty_group in sample_group_types.items() %}
-                                <option value="{{ group }}">{{ pretty_group }}</option>
+            </div>
+            {% if num_values < 256 %}
+            <div class="tab-pane" id="bar_chart_tab">
+                <div class="form-horizontal section-form-div">
+                    {% if sample_groups|length != 1 %}
+                    Select Group:
+                    <select class="bar_chart_samples_group">
+                        {% for group, pretty_group in sample_group_types.items() %}
+                            <option value="{{ group }}">{{ pretty_group }}</option>
+                        {% endfor %}
+                    </select>
+                    {% endif %}
+                    {% if sample_groups[0].attributes %}
+                    <div class="input-append">
+                        <select id="color_attribute" size="1">
+                            <option value="None">None</option>
+                            {% for attribute in sample_groups[0].attributes %}
+                            <option value="{{ sample_groups[0].attributes[attribute].name.replace(' ', '_') }}">
+                                {{ sample_groups[0].attributes[attribute].name }}</option>
                             {% endfor %}
                         </select>
-                        <br>
-                        <br>
-                        {% endif %}
-
-                        <div id="prob_plot_container">
-                            <div id="prob_plot_div"></div>
-                        </div>
-                        <div id="shapiro_wilk_text"></div>
-                        <div>
-                            More about <a href="http://en.wikipedia.org/wiki/Normal_probability_plot">Normal Probability Plots</a> and more
-                            about interpreting these plots from the <a href="http://genenetwork.org/glossary.html#normal_probability">glossary</a>
-                        </div>
-
                     </div>
-
-                </div>
-                <div class="tab-pane" id="box_plot_tab">
-                    <div id="box_plot_container">
-                        <div id="box_plot"></div>
+                    {% endif %}
+                    <div id="update_bar_chart" class="btn-group">
+                        <button type="button" class="btn btn-default sort_by_name" value="name">
+                        <i class="icon-resize-horizontal"></i> Sort By Name
+                        </button>
+                        <button type="button" class="btn btn-default sort_by_value" value="value">
+                        <i class="icon-signal"></i> Sort By Value
+                        </button>
                     </div>
-                </div>
-                <div class="tab-pane" id="violin_plot_tab">
-                    <div id="violin_plot_container">
-                        <div id="violin_plot"></div>
+                    <div id="bar_chart_container">
+                        <div id="bar_chart"></div>
                     </div>
                 </div>
-                <div class="tab-pane" id="scatterplot_matrix">
-                    
-                    <div style="margin-bottom:40px;" class="btn-group">
-                        <button type="button" class="btn btn-default" id="select_compare_trait">
-                            <i class="icon-th-large"></i> Select Traits
-                        </button>
-                        <button type="button" class="btn btn-default" id="clear_compare_trait">
-                            <i class="icon-trash"></i> Clear
-                        </button>
+            </div>
+            {% endif %}
+            <div class="tab-pane" id="probability_plot">
+                <div class="form-horizontal section-form-div">
+                    {% if sample_groups|length != 1 %}
+                    Select Group:
+                    <select class="prob_plot_samples_group">
+                        {% for group, pretty_group in sample_group_types.items() %}
+                            <option value="{{ group }}">{{ pretty_group }}</option>
+                        {% endfor %}
+                    </select>
+                    <br>
+                    <br>
+                    {% endif %}
+
+                    <div id="prob_plot_container">
+                        <div id="prob_plot_div"></div>
                     </div>
-                    <div id="scatterplot_container">
-                        <div id="comparison_scatterplot" class="qtlcharts"></div>
+                    <div id="shapiro_wilk_text"></div>
+                    <div>
+                        More about <a href="http://en.wikipedia.org/wiki/Normal_probability_plot">Normal Probability Plots</a> and more
+                        about interpreting these plots from the <a href="http://genenetwork.org/glossary.html#normal_probability">glossary</a>
                     </div>
                 </div>
             </div>
+            <div class="tab-pane" id="box_plot_tab">
+                <div id="box_plot_container">
+                    <div id="box_plot"></div>
+                </div>
+            </div>
+            <div class="tab-pane" id="violin_plot_tab">
+                <div id="violin_plot_container">
+                    <div id="violin_plot"></div>
+                </div>
+            </div>
+            <div class="tab-pane" id="scatterplot_matrix">
+                <div class="btn-group scatterplot-btn-div">
+                    <button type="button" class="btn btn-default" id="select_compare_trait">
+                        <i class="icon-th-large"></i> Select Traits
+                    </button>
+                    <button type="button" class="btn btn-default" id="clear_compare_trait">
+                        <i class="icon-trash"></i> Clear
+                    </button>
+                </div>
+                <div id="scatterplot_container">
+                    <div id="comparison_scatterplot" class="qtlcharts"></div>
+                </div>
+            </div>
         </div>
-    <!--</div>-->
+    </div>
     <div id="collections_holder_wrapper" style="display:none;">
         <div id="collections_holder"></div>
     </div>
-   
 </div>
diff --git a/wqflask/wqflask/templates/show_trait_transform_and_filter.html b/wqflask/wqflask/templates/show_trait_transform_and_filter.html
index 9fb560a0..0418d972 100644
--- a/wqflask/wqflask/templates/show_trait_transform_and_filter.html
+++ b/wqflask/wqflask/templates/show_trait_transform_and_filter.html
@@ -1,78 +1,74 @@
 <div>
   <div class="form-horizontal">
-          <p>Edit or delete values in the Trait Data boxes, and use the
-              <strong>Reset</strong> option as
-              needed.
-          </p>
-
-          <div id="blockMenuSpan" class="input-append" style="margin-bottom: 10px;">
-              <label for="remove_samples_field">Block samples by index:</label>
-              <input type="text" id="remove_samples_field" placeholder="Example: 3, 5-10, 12">
-              <select id="block_group" size="1">
-                <option value="primary">
-                  {{ sample_group_types['samples_primary'] }}
-                </option>
-                <option value="other">
-                  {{ sample_group_types['samples_other'] }}
-                </option>
-              </select>
-              <input type="button" id="block_by_index" class="btn btn-danger" value="Block">
-          </div>
-          <div id="remove_samples_invalid" class="alert alert-error" style="display:none;">
-                Please check that your input is formatted correctly, e.g. <strong>3, 5-10, 12</strong>
-          </div>
-          {% if sample_groups[0].attributes %}
-          <div class="input-append" style="margin-top:10px; margin-bottom:10px;">
-              <label for="exclude_menu">Block samples by group:</label>
-              <select id="exclude_menu" size=1>
-                {% for attribute in sample_groups[0].attributes %}
-                <option value="{{ sample_groups[0].attributes[attribute].name.replace(' ', '_') }}">
-                    {{ sample_groups[0].attributes[attribute].name }}</option>
-                {% endfor %}
-              </select>
-              <select id="attribute_values" size=1>
-              </select>
-              <input type="button" id="exclude_group" class="btn" value="Block">
-          </div>
-          {% endif %}
-          <div>
-            <input type="button" id="hide_no_value" class="btn btn-default" value="Hide No Value">
-            <input type="button" id="block_outliers" class="btn btn-default" value="Block Outliers">
-            <input type="button" class="btn btn-success reset" value="Reset">
-            <span class="input-append">
-              <input type="button" class="btn btn-default export" value="Export">
-              <select class="select optional span2 export_format">
-                <option value="excel">Excel</option>
-                <option value="csv">CSV</option>
-              </select>
-            </span>
-            <br>
-            <div style="margin-top:10px;">
-            <input type="button" id="normalize" class="btn btn-success" value="Normalize">
-            <select id="norm_method" class="select optional span2">
-              {% if negative_vals_exist == "false" %}
-              <option value="log2">Log2</option>
-              <option value="log10">Log10</option>
-              <option value="sqrt">Square Root</option>
-              {% endif %}
-              <option value="zscore">Z-score</option>
-              <option value="qnorm">Quantile</option>
-              <option value="invert">Invert +/-</option>
-            </select>
-            </div>
-          </div>
+    <p>Edit or delete values in the Trait Data boxes, and use the
+        <strong>Reset</strong> option as
+        needed.
+    </p>
+    <div id="blockMenuSpan" class="input-append block-by-index-div">
+        <label for="remove_samples_field">Block samples by index:</label>
+        <input type="text" id="remove_samples_field" placeholder="Example: 3, 5-10, 12">
+        <select id="block_group" size="1">
+          <option value="primary">
+            {{ sample_group_types['samples_primary'] }}
+          </option>
+          <option value="other">
+            {{ sample_group_types['samples_other'] }}
+          </option>
+        </select>
+        <input type="button" id="block_by_index" class="btn btn-danger" value="Block">
+    </div>
+    <div id="remove_samples_invalid" class="alert alert-error" style="display:none;">
+          Please check that your input is formatted correctly, e.g. <strong>3, 5-10, 12</strong>
+    </div>
+    {% if sample_groups[0].attributes %}
+    <div class="input-append block-by-attribute-div">
+        <label for="exclude_menu">Block samples by group:</label>
+        <select id="exclude_menu" size=1>
+          {% for attribute in sample_groups[0].attributes %}
+          <option value="{{ sample_groups[0].attributes[attribute].name.replace(' ', '_') }}">
+              {{ sample_groups[0].attributes[attribute].name }}</option>
+          {% endfor %}
+        </select>
+        <select id="attribute_values" size=1>
+        </select>
+        <input type="button" id="exclude_group" class="btn" value="Block">
+    </div>
+    {% endif %}
+    <div>
+      <input type="button" id="hide_no_value" class="btn btn-default" value="Hide No Value">
+      <input type="button" id="block_outliers" class="btn btn-default" value="Block Outliers">
+      <input type="button" class="btn btn-success reset" value="Reset">
+      <span class="input-append">
+        <input type="button" class="btn btn-default export" value="Export">
+        <select class="select optional span2 export_format">
+          <option value="excel">Excel</option>
+          <option value="csv">CSV</option>
+        </select>
+      </span>
       <br>
-
-      <div>
-          <p>Outliers highlighted in
-                  <strong style="background-color:orange;">orange</strong>
-                  can be hidden using
-                  the <strong>Hide Outliers</strong> button.
-          </p>
-
-          <p>Samples with no value (x) can be hidden by clicking
-                  <strong>Hide No Value</strong> button.
-          </p>
+      <div class="normalize-div">
+        <input type="button" id="normalize" class="btn btn-success" value="Normalize">
+        <select id="norm_method" class="select optional span2">
+          {% if negative_vals_exist == "false" %}
+          <option value="log2">Log2</option>
+          <option value="log10">Log10</option>
+          <option value="sqrt">Square Root</option>
+          {% endif %}
+          <option value="zscore">Z-score</option>
+          <option value="qnorm">Quantile</option>
+          <option value="invert">Invert +/-</option>
+        </select>
       </div>
+    </div>
+  </div>
+  <br>
+  <div>
+    <p>Outliers highlighted in
+      <strong style="background-color:orange;">orange</strong>
+      can be hidden using
+      the <strong>Hide Outliers</strong> button.
+    </p>
+
+    <p>Samples with no value (x) can be hidden by clicking<strong>Hide No Value</strong> button.</p>
   </div>
 </div>
\ No newline at end of file
diff --git a/wqflask/wqflask/update_search_results.py b/wqflask/wqflask/update_search_results.py
index 68bea9d6..672f95b1 100644
--- a/wqflask/wqflask/update_search_results.py
+++ b/wqflask/wqflask/update_search_results.py
@@ -1,5 +1,3 @@
-from __future__ import absolute_import, print_function, division
-
 import json
 
 from flask import Flask, g
diff --git a/wqflask/wqflask/user_login.py b/wqflask/wqflask/user_login.py
index 077a799b..f25ebc32 100644
--- a/wqflask/wqflask/user_login.py
+++ b/wqflask/wqflask/user_login.py
@@ -1,5 +1,3 @@
-from __future__ import print_function, division, absolute_import
-
 import os
 import hashlib
 import datetime
@@ -39,15 +37,13 @@ def basic_info():
                 ip_address = request.remote_addr,
                 user_agent = request.headers.get('User-Agent'))
 
-def encode_password(pass_gen_fields, unencrypted_password):
-    hashfunc = getattr(hashlib, pass_gen_fields['hashfunc'])
 
-    salt = base64.b64decode(pass_gen_fields['salt'])
+def encode_password(pass_gen_fields, unencrypted_password):
     encrypted_password = pbkdf2.pbkdf2_hex(str(unencrypted_password), 
-                                 pass_gen_fields['salt'], 
-                                 pass_gen_fields['iterations'], 
-                                 pass_gen_fields['keylength'], 
-                                 hashfunc)
+                                           pass_gen_fields['salt'], 
+                                           pass_gen_fields['iterations'], 
+                                           pass_gen_fields['keylength'], 
+                                           pass_gen_fields['hashfunc'])
 
     pass_gen_fields.pop("unencrypted_password", None)
     pass_gen_fields["password"] = encrypted_password
@@ -199,7 +195,7 @@ def login():
             if user_details:
                 submitted_password = params['password']
                 pwfields = user_details['password']
-                if type(pwfields) is str:
+                if isinstance(pwfields, str):
                     pwfields = json.loads(pwfields)
                 encrypted_pass_fields = encode_password(pwfields, submitted_password)
                 password_match = pbkdf2.safe_str_cmp(encrypted_pass_fields['password'], pwfields['password'])
@@ -478,4 +474,4 @@ def register():
 
 @app.errorhandler(401)
 def unauthorized(error):
-    return redirect(url_for('login'))
\ No newline at end of file
+    return redirect(url_for('login'))
diff --git a/wqflask/wqflask/user_manager.py b/wqflask/wqflask/user_manager.py
index a871e91a..7b25b68e 100644
--- a/wqflask/wqflask/user_manager.py
+++ b/wqflask/wqflask/user_manager.py
@@ -1,53 +1,63 @@
-from __future__ import print_function, division, absolute_import
-
 import os
 import hashlib
 import datetime
 import time
-import logging
 import uuid
-import hashlib
 import hmac
 import base64
-import urlparse
-
+import redis  # used for collections
 import simplejson as json
+import requests
 
-#from redis import StrictRedis
-import redis # used for collections
-Redis = redis.StrictRedis()
+from base.data_set import create_datasets_list
 
-from flask import (Flask, g, render_template, url_for, request, make_response,
-                   redirect, flash, abort)
+from flask import g
+from flask import render_template
+from flask import url_for
+from flask import request
+from flask import make_response
+from flask import redirect
+from flask import flash
 
 from wqflask import app
-from pprint import pformat as pf
-
-from wqflask import pbkdf2 # password hashing
+from wqflask import pbkdf2  # password hashing
 from wqflask.database import db_session
 from wqflask import model
 
-from utility import Bunch, Struct, after
+from smtplib import SMTP
+
+from pprint import pformat as pf
 
-import logging
+from utility import Bunch
+from utility import Struct
 from utility.logger import getLogger
-logger = getLogger(__name__)
 
-from base.data_set import create_datasets_list
+from utility.redis_tools import get_user_id
+from utility.redis_tools import get_user_by_unique_column
+from utility.redis_tools import set_user_attribute
+from utility.redis_tools import save_user
+from utility.redis_tools import save_verification_code
+from utility.redis_tools import check_verification_code
+from utility.redis_tools import get_user_collections
+from utility.redis_tools import save_collections
 
-import requests
+from utility.tools import SMTP_CONNECT
+from utility.tools import SMTP_USERNAME
+from utility.tools import SMTP_PASSWORD
 
-from utility.redis_tools import get_user_id, get_user_by_unique_column, set_user_attribute, save_user, save_verification_code, check_verification_code, get_user_collections, save_collections
 
-from smtplib import SMTP
-from utility.tools import SMTP_CONNECT, SMTP_USERNAME, SMTP_PASSWORD, LOG_SQL_ALCHEMY
+logger = getLogger(__name__)
+
+
+Redis = redis.StrictRedis()
 
 THREE_DAYS = 60 * 60 * 24 * 3
-#THREE_DAYS = 45
+
 
 def timestamp():
     return datetime.datetime.utcnow().isoformat()
 
+
 class AnonUser(object):
     """Anonymous user handling"""
     cookie_name = 'anon_user_v1'
@@ -230,29 +240,10 @@ class UserSession(object):
 
         return len(self.user_collections)
 
-###
-# ZS: This is currently not used, but I'm leaving it here commented out because the old "set superuser" code (at the bottom of this file) used it
-###
-#    @property
-#    def user_ob(self):
-#        """Actual sqlalchemy record"""
-#        # Only look it up once if needed, then store it
-#        # raise "OBSOLETE: use ElasticSearch instead"
-#        try:
-#            if LOG_SQL_ALCHEMY:
-#                logging.getLogger('sqlalchemy.pool').setLevel(logging.DEBUG)
-#
-#            # Already did this before
-#            return self.db_object
-#        except AttributeError:
-#            # Doesn't exist so we'll create it
-#            self.db_object = model.User.query.get(self.user_id)
-#            return self.db_object
-
     def add_collection(self, collection_name, traits):
         """Add collection into ElasticSearch"""
 
-        collection_dict = {'id': unicode(uuid.uuid4()),
+        collection_dict = {'id': str(uuid.uuid4()),
                            'name': collection_name,
                            'created_timestamp': datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p'),
                            'changed_timestamp': datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p'),
@@ -867,7 +858,7 @@ def forgot_password_submit():
     email_address = params['email_address']
     next_page = None
     if email_address != "":
-        logger.debug("Wants to send password E-mail to ",email_address)
+        logger.debug("Wants to send password E-mail to ", email_address)
         user_details = get_user_by_unique_column("email_address", email_address)
         if user_details:
             ForgotPasswordEmail(user_details["email_address"])
diff --git a/wqflask/wqflask/user_session.py b/wqflask/wqflask/user_session.py
index 3aa2c151..9f4c5458 100644
--- a/wqflask/wqflask/user_session.py
+++ b/wqflask/wqflask/user_session.py
@@ -1,5 +1,3 @@
-from __future__ import print_function, division, absolute_import
-
 import datetime
 import time
 import uuid
@@ -129,10 +127,10 @@ class UserSession(object):
     @property
     def user_id(self):
         """Shortcut to the user_id"""
-        if 'user_id' not in self.record:
-            self.record['user_id'] = str(uuid.uuid4())
+        if b'user_id' not in self.record:
+            self.record[b'user_id'] = str(uuid.uuid4())
 
-        return self.record['user_id']
+        return self.record[b'user_id']
 
     @property
     def redis_user_id(self):
@@ -184,7 +182,7 @@ class UserSession(object):
     def add_collection(self, collection_name, traits):
         """Add collection into Redis"""
 
-        collection_dict = {'id': unicode(uuid.uuid4()),
+        collection_dict = {'id': str(uuid.uuid4()),
                            'name': collection_name,
                            'created_timestamp': datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p'),
                            'changed_timestamp': datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p'),
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 94ec7137..08673f79 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -2,8 +2,6 @@
 #
 # Main routing table for GN2
 
-from __future__ import absolute_import, division, print_function
-
 import traceback # for error page
 import os        # for error gifs
 import random    # for random error gif
@@ -14,13 +12,13 @@ import csv
 import simplejson as json
 import yaml
 import xlsxwriter
-import StringIO  # Todo: Use cStringIO?
+import io  # Todo: Use cStringIO?
 
 from zipfile import ZipFile, ZIP_DEFLATED
 
 import gc
 import numpy as np
-import cPickle as pickle
+import pickle as pickle
 import uuid
 
 import flask
@@ -54,7 +52,7 @@ from wqflask.docs import Docs, update_text
 from wqflask.db_info import InfoPage
 
 from utility import temp_data
-from utility.tools import SQL_URI,TEMPDIR,USE_REDIS,USE_GN_SERVER,GN_SERVER_URL,GN_VERSION,JS_TWITTER_POST_FETCHER_PATH,JS_GUIX_PATH, CSS_PATH
+from utility.tools import SQL_URI, TEMPDIR, USE_REDIS, USE_GN_SERVER, GN_SERVER_URL, GN_VERSION, JS_TWITTER_POST_FETCHER_PATH, JS_GUIX_PATH, CSS_PATH
 from utility.helper_functions import get_species_groups
 from utility.authentication_tools import check_resource_availability
 from utility.redis_tools import get_redis_conn
@@ -129,10 +127,10 @@ def handle_bad_request(e):
         list = [fn for fn in os.listdir("./wqflask/static/gif/error") if fn.endswith(".gif") ]
         animation = random.choice(list)
 
-    resp = make_response(render_template("error.html",message=err_msg,stack=formatted_lines,error_image=animation,version=GN_VERSION))
+    resp = make_response(render_template("error.html", message=err_msg, stack=formatted_lines, error_image=animation, version=GN_VERSION))
 
     # logger.error("Set cookie %s with %s" % (err_msg, animation))
-    resp.set_cookie(err_msg[:32],animation)
+    resp.set_cookie(err_msg[:32], animation)
     return resp
 
 @app.route("/authentication_needed")
@@ -166,7 +164,7 @@ def tmp_page(img_path):
     logger.info("initial_start_vars:", initial_start_vars)
     imgfile = open(GENERATED_IMAGE_DIR + img_path, 'rb')
     imgdata = imgfile.read()
-    imgB64 = imgdata.encode("base64")
+    imgB64 = base64.b64encode(imgdata)
     bytesarray = array.array('B', imgB64)
     return render_template("show_image.html",
                             img_base64 = bytesarray )
@@ -215,8 +213,6 @@ def search_page():
     result = the_search.__dict__
     valid_search = result['search_term_exists']
 
-    logger.debugf("result", result)
-
     if USE_REDIS and valid_search:
         Redis.set(key, pickle.dumps(result, pickle.HIGHEST_PROTOCOL))
         Redis.expire(key, 60*60)
@@ -264,7 +260,7 @@ def docedit():
 @app.route('/generated/<filename>')
 def generated_file(filename):
     logger.info(request.url)
-    return send_from_directory(GENERATED_IMAGE_DIR,filename)
+    return send_from_directory(GENERATED_IMAGE_DIR, filename)
 
 @app.route("/help")
 def help():
@@ -380,7 +376,7 @@ def export_trait_excel():
 
     logger.info("sample_data - type: %s -- size: %s" % (type(sample_data), len(sample_data)))
 
-    buff = StringIO.StringIO()
+    buff = io.BytesIO()
     workbook = xlsxwriter.Workbook(buff, {'in_memory': True})
     worksheet = workbook.add_worksheet()
     for i, row in enumerate(sample_data):
@@ -404,7 +400,7 @@ def export_trait_csv():
 
     logger.info("sample_data - type: %s -- size: %s" % (type(sample_data), len(sample_data)))
 
-    buff = StringIO.StringIO()
+    buff = io.StringIO()
     writer = csv.writer(buff)
     for row in sample_data:
         writer.writerow(row)
@@ -427,7 +423,7 @@ def export_traits_csv():
         now = datetime.datetime.now()
         time_str = now.strftime('%H:%M_%d%B%Y')
         filename = "export_{}".format(time_str)
-        memory_file = StringIO.StringIO()
+        memory_file = io.StringIO()
         with ZipFile(memory_file, mode='w', compression=ZIP_DEFLATED) as zf:
             for the_file in file_list:
                 zf.writestr(the_file[0], the_file[1])
@@ -470,7 +466,7 @@ def export_perm_data():
         ["#Comment: Results sorted from low to high peak linkage"]
     ]
 
-    buff = StringIO.StringIO()
+    buff = io.StringIO()
     writer = csv.writer(buff)
     writer.writerows(the_rows)
     for item in perm_info['perm_data']:
@@ -543,7 +539,7 @@ def heatmap_page():
 
             result = template_vars.__dict__
 
-            for item in template_vars.__dict__.keys():
+            for item in list(template_vars.__dict__.keys()):
                 logger.info("  ---**--- {}: {}".format(type(template_vars.__dict__[item]), item))
 
             pickled_result = pickle.dumps(result, pickle.HIGHEST_PROTOCOL)
@@ -647,7 +643,7 @@ def loading_page():
     if 'wanted_inputs' in initial_start_vars:
         wanted = initial_start_vars['wanted_inputs'].split(",")
         start_vars = {}
-        for key, value in initial_start_vars.iteritems():
+        for key, value in list(initial_start_vars.items()):
             if key in wanted or key.startswith(('value:')):
                 start_vars[key] = value
 
@@ -747,7 +743,7 @@ def mapping_results_page():
         'transform'
     )
     start_vars = {}
-    for key, value in initial_start_vars.iteritems():
+    for key, value in list(initial_start_vars.items()):
         if key in wanted or key.startswith(('value:')):
             start_vars[key] = value
     #logger.debug("Mapping called with start_vars:", start_vars)
@@ -794,7 +790,7 @@ def mapping_results_page():
                     logger.info("initial_start_vars:", initial_start_vars)
                     imgfile = open(TEMPDIR + img_path, 'rb')
                     imgdata = imgfile.read()
-                    imgB64 = imgdata.encode("base64")
+                    imgB64 = base64.b64encode(imgdata)
                     bytesarray = array.array('B', imgB64)
                     result['pair_scan_array'] = bytesarray
                     rendered_template = render_template("pair_scan_results.html", **result)
@@ -954,8 +950,8 @@ def json_default_handler(obj):
     if hasattr(obj, 'isoformat'):
         return obj.isoformat()
     # Handle integer keys for dictionaries
-    elif isinstance(obj, int):
-        return str(int)
+    elif isinstance(obj, int) or isinstance(obj, uuid.UUID):
+        return str(obj)
     # Handle custom objects
     if hasattr(obj, '__dict__'):
         return obj.__dict__
@@ -963,5 +959,5 @@ def json_default_handler(obj):
     #     logger.info("Not going to serialize Dataset")
     #    return None
     else:
-        raise TypeError, 'Object of type %s with value of %s is not JSON serializable' % (
-            type(obj), repr(obj))
+        raise TypeError('Object of type %s with value of %s is not JSON serializable' % (
+            type(obj), repr(obj)))
diff --git a/wqflask/wqflask/wgcna/wgcna_analysis.py b/wqflask/wqflask/wgcna/wgcna_analysis.py
index 70077703..6bf75216 100644
--- a/wqflask/wqflask/wgcna/wgcna_analysis.py
+++ b/wqflask/wqflask/wgcna/wgcna_analysis.py
@@ -3,21 +3,19 @@ WGCNA analysis for GN2
 
 Author / Maintainer: Danny Arends <Danny.Arends@gmail.com>
 """
+import base64
 import sys
-from numpy import *
-import scipy as sp                            # SciPy
 import rpy2.robjects as ro                    # R Objects
 import rpy2.rinterface as ri
 
+from array import array as arr
+from numpy import *
 from base.webqtlConfig import GENERATED_IMAGE_DIR
-from utility import webqtlUtil                # Random number for the image
-
-import base64
-import array
+from rpy2.robjects.packages import importr
 
+from utility import webqtlUtil                # Random number for the image
 from utility import helper_functions
 
-from rpy2.robjects.packages import importr
 utils = importr("utils")
 
 # Get pointers to some common R functions
@@ -71,8 +69,8 @@ class WGCNA(object):
         self.r_enableWGCNAThreads()
         self.trait_db_list = [trait.strip()
                               for trait in requestform['trait_list'].split(',')]
-        print("Retrieved phenotype data from database",
-              requestform['trait_list'])
+        print(("Retrieved phenotype data from database",
+              requestform['trait_list']))
         helper_functions.get_trait_db_obs(self, self.trait_db_list)
 
         # self.input contains the phenotype values we need to send to R
@@ -127,14 +125,14 @@ class WGCNA(object):
             powers = [int(threshold.strip())
                       for threshold in requestform['SoftThresholds'].rstrip().split(",")]
             rpow = r_unlist(r_c(powers))
-            print("SoftThresholds: {} == {}".format(powers, rpow))
+            print(("SoftThresholds: {} == {}".format(powers, rpow)))
             self.sft = self.r_pickSoftThreshold(
                 rM, powerVector=rpow, verbose=5)
 
-            print("PowerEstimate: {}".format(self.sft[0]))
+            print(("PowerEstimate: {}".format(self.sft[0])))
             self.results['PowerEstimate'] = self.sft[0]
             if self.sft[0][0] is ri.NA_Integer:
-                print "No power is suitable for the analysis, just use 1"
+                print("No power is suitable for the analysis, just use 1")
                 # No power could be estimated
                 self.results['Power'] = 1
             else:
@@ -157,7 +155,7 @@ class WGCNA(object):
         self.results['network'] = network
 
         # How many modules and how many gene per module ?
-        print "WGCNA found {} modules".format(r_table(network[1]))
+        print(("WGCNA found {} modules".format(r_table(network[1]))))
         self.results['nmod'] = r_length(r_table(network[1]))[0]
 
         # The iconic WCGNA plot of the modules in the hanging tree
@@ -172,11 +170,11 @@ class WGCNA(object):
         sys.stdout.flush()
 
     def render_image(self, results):
-        print("pre-loading imgage results:", self.results['imgloc'])
+        print(("pre-loading imgage results:", self.results['imgloc']))
         imgfile = open(self.results['imgloc'], 'rb')
         imgdata = imgfile.read()
-        imgB64 = imgdata.encode("base64")
-        bytesarray = array.array('B', imgB64)
+        imgB64 = base64.b64encode(imgdata)
+        bytesarray = arr('B', imgB64)
         self.results['imgdata'] = bytesarray
 
     def process_results(self, results):