Worked on search page code; got to the part that actually does the search

Renamed RISet and cross to "group" throughout webqtlDataset.py and search_results.py

6 files changed, 821 insertions, 841 deletions

diff --git a/wqflask/base/webqtlDataset.py b/wqflask/base/webqtlDataset.py
index 4f98e90c..933077fd 100755
--- a/wqflask/base/webqtlDataset.py
+++ b/wqflask/base/webqtlDataset.py
@@ -34,6 +34,7 @@ class webqtlDataset:
     """
     Dataset class defines a dataset in webqtl, can be either Microarray,
     Published phenotype, genotype, or user input dataset(temp)
+
     """
 
     def __init__(self, dbName, cursor=None):
@@ -42,7 +43,7 @@ class webqtlDataset:
         self.id = 0
         self.name = ''
         self.type = ''
-        self.riset = ''
+        self.group = ''
         self.cursor = cursor
 
         #temporary storage
@@ -81,14 +82,15 @@ class webqtlDataset:
         self.name = dbName
         if self.cursor and self.id == 0:
             self.retrieveName()
-
-    def __str__(self):
-        return self.name
-
-    __repr__ = __str__
+            
+    
+    # Delete this eventually
+    @property
+    def riset():
+        Weve_Renamed_This_As_Group
 
 
-    def getRISet(self):
+    def get_group(self):
         assert self.cursor
         if self.type == 'Publish':
             query = '''
@@ -124,12 +126,12 @@ class webqtlDataset:
         else:
             return ""
         self.cursor.execute(query)
-        RISet, RIID = self.cursor.fetchone()
-        if RISet == 'BXD300':
-            RISet = "BXD"
-        self.riset = RISet
-        self.risetid = RIID
-        return RISet
+        group, RIID = self.cursor.fetchone()
+        if group == 'BXD300':
+            group = "BXD"
+        self.group = group
+        self.group_id = RIID
+        return group
 
 
     def retrieveName(self):
diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py
index 1b846771..2269b9e7 100644
--- a/wqflask/wqflask/search_results.py
+++ b/wqflask/wqflask/search_results.py
@@ -36,17 +36,9 @@ from wqflask import parser
 from utility import webqtlUtil
 from dbFunction import webqtlDatabaseFunction
 
-#import logging
-#logging.basicConfig(filename=app.config['LOGFILE'], level=logging.INFO)
-#
-#_log = logging.getLogger("search")
-#_ch = logging.StreamHandler()
-#_log.addHandler(_ch)
-
 from utility import formatting
 
 import sys
-#_log.info("sys.path  is: %s" % (sys.path))
 
 
 #from base.JinjaPage import JinjaEnv, JinjaPage
@@ -64,116 +56,112 @@ class SearchResultPage(templatePage):
         import logging_tree
         logging_tree.printout()
         self.fd = fd
-        if not self.openMysql():
-            print("ge0")
-            #return
-
-        print("Start...")
-        print("Type of fd:", type(fd))
-        print("Value of fd:", pf(fd))
-        database = [fd['database']]
-        print("End...")
-
-        # change back to self.database
-        if not self.database or self.database == 'spacer':
-            #Error, No database selected
+        templatePage.__init__(self, fd)
+        assert self.openMysql(), "Couldn't open MySQL"
+
+        print("fd is:", pf(fd))
+        self.dataset = fd['dataset']
+
+        # change back to self.dataset
+        if not self.dataset or self.dataset == 'spacer':
+            #Error, No dataset selected
             heading = "Search Result"
-            detail = ['''No database was selected for this search, please
-                go back and SELECT at least one database.''']
-            print("ge0.6")
-            self.error(heading=heading,detail=detail,error="No Database Selected")
-            #return
+            detail = ['''No dataset was selected for this search, please
+                go back and SELECT at least one dataset.''']
+            self.error(heading=heading,detail=detail,error="No dataset Selected")
+            return
 
-        print("ge1")
         ###########################################
         #   Names and IDs of RISet / F2 set
         ###########################################
-        if self.database == ['_allPublish']:
+        if self.dataset == "All Phenotypes":
             self.cursor.execute("""
                 select PublishFreeze.Name, InbredSet.Name, InbredSet.Id from PublishFreeze,
                 InbredSet where PublishFreeze.Name not like 'BXD300%' and InbredSet.Id =
                 PublishFreeze.InbredSetId""")
             results = self.cursor.fetchall()
-            self.database = map(lambda x: webqtlDataset(x[0], self.cursor), results)
-            self.databaseCrosses = map(lambda x: x[1], results)
-            self.databaseCrossIds = map(lambda x: x[2], results)
-            self.singleCross = False
+            self.dataset = map(lambda x: webqtlDataset(x[0], self.cursor), results)
+            self.datasetGroups = map(lambda x: x[1], results)
+            self.datasetGroupIds = map(lambda x: x[2], results)
+            self.single_group = False
         else:
-            self.database = map(lambda x: webqtlDataset(x, self.cursor), self.database)
+            print("self.dataset is:", pf(self.dataset))
+            self.dataset = webqtlDataset(self.dataset, self.cursor)
+            print("self.dataset is now:", pf(self.dataset))
+            #self.dataset = map(lambda x: webqtlDataset(x, self.cursor), self.dataset)
             #currently, webqtl won't allow multiple crosses
             #for other than multiple publish db search
-            #so we can use the first database as example
-            if self.database[0].type=="Publish":
-                pass
-            elif self.database[0].type in ("Geno", "ProbeSet"):
+            #so we can use the first dataset as example
+            #if self.dataset.type=="Publish":
+            #    pass
+            if self.dataset.type in ("Geno", "ProbeSet"):
 
                 #userExist = None
-
-                for individualDB in self.database:
-                    # Can't use paramater substitution for table names apparently
-                    db_type = self.database[0].type + "Freeze"
-                    print("db_type [%s]: %s" % (type(db_type), db_type))
-
-                    query = '''SELECT Id, Name, FullName, confidentiality,
-                                        AuthorisedUsers FROM %s WHERE Name = %%s''' % (db_type)
-
-                    self.cursor.execute(query, (individualDB,))
-
-                    (indId,
-                     indName,
-                     indFullName,
-                     confidential,
-                     AuthorisedUsers) = self.cursor.fetchall()[0]
-
-                    if confidential:
-                        access_to_confidential_dataset = 0
-
-                        #for the dataset that confidentiality is 1
-                        #1. 'admin' and 'root' can see all of the dataset
-                        #2. 'user' can see the dataset that AuthorisedUsers contains his id(stored in the Id field of User table)
-                        if webqtlConfig.USERDICT[self.privilege] > webqtlConfig.USERDICT['user']:
-                            access_to_confidential_dataset = 1
-                        else:
-                            AuthorisedUsersList=AuthorisedUsers.split(',')
-                            if AuthorisedUsersList.__contains__(self.userName):
-                                access_to_confidential_dataset = 1
-
-                        if not access_to_confidential_dataset:
-                            #Error, No database selected
-                            heading = "Search Result"
-                            detail = ["The %s database you selected is not open to the public at this time, please go back and SELECT other database." % indFullName]
-                            self.error(heading=heading,detail=detail,error="Confidential Database")
-                            return
-            else:
-                heading = "Search Result"
-                detail = ['''The database has not been established yet, please
-                    go back and SELECT at least one database.''']
-                self.error(heading=heading,detail=detail,error="No Database Selected")
-                return
-
-            print("ge2")
-            self.database[0].getRISet()
-            self.databaseCrosses = [self.database[0].riset]
-            self.databaseCrossIds = [self.database[0].risetid]
-            self.singleCross = True
-            #XZ, August 24,2010: Since self.singleCross = True, it's safe to assign one species Id.
-            self.speciesId = webqtlDatabaseFunction.retrieveSpeciesId(self.cursor, self.database[0].riset)
+                # Can't use paramater substitution for table names apparently
+                db_type = self.dataset.type + "Freeze"
+                print("db_type [%s]: %s" % (type(db_type), db_type))
+
+                query = '''SELECT Id, Name, FullName, confidentiality,
+                                    AuthorisedUsers FROM %s WHERE Name = %%s''' % (db_type)
+
+                self.cursor.execute(query, self.dataset.name)
+
+                (indId,
+                 indName,
+                 indFullName,
+                 confidential,
+                 AuthorisedUsers) = self.cursor.fetchall()[0]
+
+                if confidential:
+                    # Allow confidential data later
+                    NoConfindetialDataForYouTodaySorry
+                    #access_to_confidential_dataset = 0
+                    #
+                    ##for the dataset that confidentiality is 1
+                    ##1. 'admin' and 'root' can see all of the dataset
+                    ##2. 'user' can see the dataset that AuthorisedUsers contains his id(stored in the Id field of User table)
+                    #if webqtlConfig.USERDICT[self.privilege] > webqtlConfig.USERDICT['user']:
+                    #    access_to_confidential_dataset = 1
+                    #else:
+                    #    AuthorisedUsersList=AuthorisedUsers.split(',')
+                    #    if AuthorisedUsersList.__contains__(self.userName):
+                    #        access_to_confidential_dataset = 1
+                    #
+                    #if not access_to_confidential_dataset:
+                    #    #Error, No dataset selected
+                    #    heading = "Search Result"
+                    #    detail = ["The %s dataset you selected is not open to the public at this time, please go back and SELECT other dataset." % indFullName]
+                    #    self.error(heading=heading,detail=detail,error="Confidential dataset")
+                    #    return
+            #else:
+            #    heading = "Search Result"
+            #    detail = ['''The dataset has not been established yet, please
+            #        go back and SELECT at least one dataset.''']
+            #    self.error(heading=heading,detail=detail,error="No dataset Selected")
+            #    return
+
+            self.dataset.get_group()
+            self.single_group = True
+            #XZ, August 24,2010: Since self.single_group = True, it's safe to assign one species Id.
+            self.species_id = webqtlDatabaseFunction.retrieveSpeciesId(self.cursor,
+                                                                       self.dataset.group)
 
         ###########################################
-        #    make sure search from same type of databases
+        #    make sure search from same type of datasets
         ###########################################
-        #dbTypes = map(lambda X: X.type, self.database)
-        dbTypes = [table.type for table in self.database]
-        self.dbType = dbTypes[0]
-        for item in dbTypes:
-            if item != self.dbType:
-                heading = "Search Result"
-                detail = ["Search can only be performed among the same type of databases"]
-                self.error(heading=heading,detail=detail,error="Error")
-                return
-
-        print("ge3")
-        if self.dbType == "Publish":
+        #dbTypes = map(lambda X: X.type, self.dataset)
+        #db_types = [table.type for table in self.dataset]
+        #self.db_type = db_types[0]
+        #for item in dbTypes:
+        #    if item != self.dbType:
+        #        heading = "Search Result"
+        #        detail = ["Search can only be performed among the same type of datasets"]
+        #        self.error(heading=heading,detail=detail,error="Error")
+        #        return
+
+
+        #self.db_type = self.dataset.type
+        if self.dataset.type == "Publish":
             self.searchField = ['Phenotype.Post_publication_description',
                                 'Phenotype.Pre_publication_description',
                                 'Phenotype.Pre_publication_abbreviation',
@@ -185,7 +173,7 @@ class SearchResultPage(templatePage):
                                 'Publication.Authors',
                                 'PublishXRef.Id']
 
-        elif self.dbType == "ProbeSet":
+        elif self.dataset.type == "ProbeSet":
             self.searchField = ['Name',
                                 'Description',
                                 'Probe_Target_Description',
@@ -194,11 +182,12 @@ class SearchResultPage(templatePage):
                                 'GenbankId',
                                 'UniGeneId',
                                 'RefSeq_TranscriptId']
-        elif self.dbType == "Geno":
+        elif self.dataset.type == "Geno":
             self.searchField = ['Name','Chr']
 
-        print("ge4")
+
         self.do_search()
+        self.gen_search_result()
 
         ###########################################
         #       Search Options
@@ -272,11 +261,11 @@ class SearchResultPage(templatePage):
         #    return
         #self.nresults = self.executeQuery()
         #
-        #if len(self.database) > 1:
-        #    dbUrl =  "Multiple phenotype databases"
+        #if len(self.dataset) > 1:
+        #    dbUrl =  "Multiple phenotype datasets"
         #    dbUrlLink = " were"
         #else:
-        #    dbUrl =  self.database[0].genHTML()
+        #    dbUrl =  self.dataset[0].genHTML()
         #    dbUrlLink = " was"
 
         #SearchText = HT.Blockquote('GeneNetwork searched the ', dbUrl, ' for all records ')
@@ -355,17 +344,13 @@ class SearchResultPage(templatePage):
 
         #TD_LR.append(HT.Paragraph('Search Results', Class="title"), SearchText)
 
-        self.start_search()
-        self.genSearchResultTable()
         #self.dict['body'] = str(TD_LR)
         #self.dict['js1'] = ''
         #self.dict['js2'] = 'onLoad="pageOffset()"'
         #self.dict['layer'] = self.generateWarningLayer()
 
-    def start_search(self):
-        pass
 
-    def genSearchResultTable(self):
+    def gen_search_result(self):
 
         #pageTable = HT.TableLite(cellSpacing=2,cellPadding=0,width="100%",border=0)
 
@@ -399,8 +384,8 @@ class SearchResultPage(templatePage):
             #tbl = HT.TableLite(cellSpacing=2,cellPadding=0,width="90%",border=0)
             #seq = self.pageNumber*self.NPerPage+1  //Edited out because we show all results in one page now - Zach 2/22/11
             seq = 1
-            RISet = self.databaseCrosses[i]
-            self.thisFormName = thisFormName = 'showDatabase'+RISet
+            group = self.databaseCrosses[i]
+            self.thisFormName = thisFormName = 'showDatabase'+group
             #selectall = HT.Href(url="#", onClick="checkAll(document.getElementsByName('%s')[0]);" % thisFormName)
             #selectall_img = HT.Image("/images/select_all2_final.jpg", name="selectall", alt="Select All", title="Select All", style="border:none;")
             #selectall.append(selectall_img)
@@ -423,7 +408,7 @@ class SearchResultPage(templatePage):
 
             tblobj = {}
             mainfmName = thisFormName
-            species = webqtlDatabaseFunction.retrieveSpecies(cursor=self.cursor, RISet=RISet)
+            species = webqtlDatabaseFunction.retrieveSpecies(cursor=self.cursor, RISet=group)
 
             if thisTrait.db.type=="Geno":
                 tblobj['header'] = self.getTableHeaderForGeno(worksheet=worksheet, newrow=newrow, headingStyle=headingStyle)
@@ -480,7 +465,7 @@ class SearchResultPage(templatePage):
 
 
             #traitForm = HT.Form(cgi= os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), enctype='multipart/form-data', name=thisFormName, submit=HT.Input(type='hidden'))
-            hddn = {'FormID':'showDatabase','ProbeSetID':'_','database':'_','CellID':'_','RISet':RISet}
+            hddn = {'FormID':'showDatabase','ProbeSetID':'_','database':'_','CellID':'_','group':group}
             hddn['incparentsf1']='ON'
         #    for key in hddn.keys():
         #        traitForm.append(HT.Input(name=key, value=hddn[key], type='hidden'))
diff --git a/wqflask/wqflask/templates/index_page.html b/wqflask/wqflask/templates/index_page.html
index db0b2d9e..695129a9 100644
--- a/wqflask/wqflask/templates/index_page.html
+++ b/wqflask/wqflask/templates/index_page.html
@@ -1,320 +1,423 @@
-{% extends "base.html" %}
-{% block title %}GeneNetwork{% endblock %}
-{% block content %} 
-  <!-- Start of body -->
-    <tr>
-      <td bgcolor="#EEEEEE" class="solidBorder">
-        <table width="100%" cellspacing="0" cellpadding="5">
-          <tr>
-            <td valign="top" width="40%" align="left" height="10" bgcolor="#EEEEEE">
-              <p style="font-size:18px;font-family:verdana;color:black"><b>Select and
-              Search</b></p>
-
-              <form method="get" action="/search" class="form-search" name="SEARCHFORM">
-                <table width="100%">
-                  <!--  SPECIES  SELECTION -->
-
-                  <tr>
-                    <td align="right" height="35" style=
-                    "font-size:14px;font-family:verdana;color:black" width="16%">
-                    <b>Species:</b></td>
-
-                    <td width="3%"></td>
-
-                    <td nowrap width="85%" align="left">
-                      <div id="menu0">
-                        <select name="species" size="1" id="species" onchange=
-                        "fillOptions('species');">
-                          </select>
-                      </div>
-                    </td>
-                  </tr><!--  GROUP  SELECTION -->
-
-                  <tr>
-                    <td align="right" height="35" style=
-                    "font-size:14px;font-family:verdana;color:black"><b>Group:</b></td>
-
-                    <td width="3%"></td>
-
-                    <td nowrap width="85%" align="left">
-                      <div id="menu1">
-                        <select name="cross" size="1" id="cross" onchange="fillOptions('cross');">
-                          </select> <input type="button" class="btn" value="Info" onclick=
-                          "javascript:crossinfo();">
-                      </div>
-                    </td>
-                  </tr><!--  TYPE  SELECTION -->
-
-                  <tr>
-                    <td align="right" height="35" style=
-                    "font-size:14px;font-family:verdana;color:black"><b>Type:</b></td>
-
-                    <td width="3%"></td>
-
-                    <td nowrap width="85%" align="left">
-                      <div id="menu2">
-                        <select name="tissue" size="1" id="tissue" onchange=
-                        "fillOptions('tissue');">
-                          </select>
-                      </div>
-                    </td>
-                  </tr><!--  DATABASE  SELECTION -->
-
-                  <tr>
-                    <td align="right" height="35" style=
-                    "font-size:14px;font-family:verdana;color:black"><b>Database:</b></td>
-
-                    <td width="3%"></td>
-
-                    <td nowrap width="85%" align="left">
-                      <div id="menu3">
-                        <select name="database" size="1" id="database">
-                          </select> <input type="submit" class="btn" value="Info" name=
-                          "info_database">
-                      </div>
-                    </td>
-                  </tr><!--  USER HELP   -->
-
-                  <tr>
-                    <td align="right" height="20" width="10%"></td>
-
-                    <td width="3%"></td>
-
-                    <td align="left" width="85%">
-                      <p class="fs12">&nbsp;&nbsp;&nbsp;&nbsp;Databases marked with <b>**</b>
-                      suffix are not public yet.<br>
-                      &nbsp;&nbsp;&nbsp;&nbsp;Access requires <a href="/account.html" target=
-                      "_blank" class="fs14"><small>user login</small></a>.</p>
-                    </td>
-                  </tr><!--  GET ANY  SEARCH -->
-
-                  <tr>
-                    <td align="right" height="35" nowrap="on" style=
-                    "font-size:14px;font-family:verdana;color:black" width="10%">
-                    <b>Search:</b></td>
-
-                    <td width="3%"></td>
-
-                    <td nowrap width="85%" align="left"><input class="input-medium search-query"
-                    id="tfor" name="search_terms" style=
-                    "width:420px; background-color:white; font-family:verdana; font-size:14px"
-                    type="text" maxlength="500"></td>
-                  </tr><!--  GET ANY HELP   -->
-
-                  <tr>
-                    <td align="right" height="20" width="10%"></td>
-
-                    <td width="3%"></td>
-
-                    <td width="85%" align="left">
-                      <p class="fs12">&nbsp;&nbsp;&nbsp;&nbsp;Enter terms, genes, ID numbers in the
-                      <b>Search</b> field.<br>
-                      &nbsp;&nbsp;&nbsp;&nbsp;Use <b>*</b> or <b>?</b> wildcards (Cyp*a?,
-                      synap*).<br>
-                      &nbsp;&nbsp;&nbsp;&nbsp;Use <b>quotes</b> for terms such as <i>"tyrosine
-                      kinase"</i>.</p>
-                    </td>
-                  </tr><!--  SEARCH, MAKE DEFAULT, ADVANCED SEARCH -->
-
-                  <tr align="center">
-                    <td width="3%"></td>
-
-                    <td width="3%"></td>
-
-                    <td align="left" height="40" colspan="3"><input id="btsearch" type="submit"
-                    class="btn btn-primary" value="Search">&nbsp;&nbsp;&nbsp;&nbsp; <input type=
-                    "button" class="btn" value="Make Default" onclick=
-                    "setDefault(this.form);">&nbsp;&nbsp;&nbsp;&nbsp; <input type="button" class=
-                    "btn" value="Advanced Search" onclick=
-                    "javascript:window.open('/index3.html', '_self');"></td>
-                  </tr>
-                </table><input type="hidden" name="FormID" value="searchResult"> <input type=
-                "hidden" name="RISet" value="BXD"> <script src="/javascript/selectDatasetMenu.js"
-                type="text/javascript">
-</script>
-              </form><!--  QUICK HELP  -->
-
-              <p>&nbsp;______________________________________________________</p>
-
-              <p style="font-size:13px;font-family:verdana;color:black"><b>&nbsp; Quick HELP
-              Examples and</b> <a href="http://www.genenetwork.org/index4.html" target="_blank"
-              class="fs14"><b>User's Guide</b></a></p>&nbsp;&nbsp;You can also use advanced
-              commands. Copy these simple examples<br>
-              &nbsp;&nbsp;into the <b>Get Any</b> or <b>Combined</b> search fields:
-
-              <ul style="font-size:12px;font-family:verdana;color:black">
-                <li><b><i>POSITION=(chr1 25 30)</i></b> finds genes, markers, or transcripts on
-                chromosome 1 between 25 and 30 Mb.</li>
-
-                <li><b><i>MEAN=(15 16) LRS=(23 46)</i></b> in the <b>Combined</b> field finds
-                highly expressed genes (15 to 16 log2 units) AND with peak <a href=
-                "http://www.genenetwork.org/glossary.html#L" target="_blank" class=
-                "fs14"><small>LRS</small></a> linkage between 23 and 46.</li>
-
-                <li><b><i>RIF=mitochondrial</i></b> searches RNA databases for <a href=
-                "http://www.ncbi.nlm.nih.gov/projects/GeneRIF/GeneRIFhelp.html" target="_blank"
-                class="fs14"><small>GeneRIF</small></a> links.</li>
-
-                <li><b><i>WIKI=nicotine</i></b> searches <a href=
-                "http://www.genenetwork.org/webqtl/main.py?FormID=geneWiki" target="_blank" class=
-                "fs14"><small>GeneWiki</small></a> for genes that you or other users have annotated
-                with the word <i>nicotine</i>.</li>
-
-                <li><b><i>GO:0045202</i></b> searches for synapse-associated genes listed in the
-                <a href="http://www.godatabase.org/cgi-bin/amigo/go.cgi" target="_blank" class=
-                "fs14"><small>Gene Ontology</small></a>.</li>
-
-                <li><b><i>GO:0045202 LRS=(9 99 Chr4 122 155) cisLRS=(9 999 10)</i></b><br>
-                in <b>Combined</b> finds synapse-associated genes with <a href=
-                "http://www.genenetwork.org/glossary.html#E" target="_blank" class=
-                "fs14"><small>cis eQTL</small></a> on Chr 4 from 122 and 155 Mb with LRS scores
-                between 9 and 999.</li>
-
-                <li><b><i>RIF=diabetes LRS=(9 999 Chr2 100 105) transLRS=(9 999 10)</i></b><br>
-                in <b>Combined</b> finds diabetes-associated transcripts with peak <a href=
-                "http://www.genenetwork.org/glossary.html#E" target="_blank" class=
-                "fs14"><small>trans eQTLs</small></a> on Chr 2 between 100 and 105 Mb with LRS
-                scores between 9 and 999.</li>
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <meta charset="utf-8">
+    <title>GeneNetwork</title>
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <meta name="description" content="">
+    <meta name="author" content="">
+    <link REL="stylesheet" TYPE="text/css" href="/static/packages/bootstrap/css/bootstrap.min.css" />
+    <link REL="stylesheet" TYPE="text/css" href="/static/packages/bootstrap/css/bootstrap-responsive.min.css" />
+    <link REL="stylesheet" TYPE="text/css" href="/static/packages/bootstrap/css/docs.css" />
+
+    <!-- HTML5 shim, for IE6-8 support of HTML5 elements -->
+    <!--[if lt IE 9]>
+      <script src="http://html5shim.googlecode.com/svn/trunk/html5.js"></script>
+    <![endif]-->
+
+
+</head>
+
+<body data-spy="scroll" data-target=".bs-docs-sidebar">
+    <!-- Navbar
+    ================================================== -->
+    <div class="navbar navbar-inverse navbar-fixed-top">
+      <div class="navbar-inner">
+        <div class="container">
+          <button type="button" class="btn btn-navbar" data-toggle="collapse" data-target=".nav-collapse">
+            <span class="icon-bar"></span>
+            <span class="icon-bar"></span>
+            <span class="icon-bar"></span>
+          </button>
+          <a class="brand" href="/">GeneNetwork</a>
+          <div class="nav-collapse collapse">
+            <ul class="nav">
+              <li class="active">
+                <a href="/">Home</a>
+              </li>
+              <li class="dropdown">
+                <a id="drop1" href="#" role="button" class="dropdown-toggle" data-toggle="dropdown">
+                    Search <b class="caret"></b>
+                </a>
+                    <ul class="dropdown-menu" role="menu" aria-labelledby="drop1">
+                        <li><a tabindex="-1" href="/webqtl/main.py?FormID=tissueCorrelation">Tissue Corrleation</a></li>
+                        <li><a tabindex="-1" href="/webqtl/main.py?FormID=snpBrowser">SNP Browser</a></li>
+                        <li class="divider"></li>
+                        <li><a tabindex="-1" href="/webqtl/main.py?FormID=geneWiki">Gene Wiki</a></li>
+                    </ul>
+              </li>
+              <li class="">
+                <a href="#">Help</a>
+              </li>
+              <li class="">
+                <a href="/whats_new">News</a>
+              </li>
+              <li class="">
+                <a href="./reference.html">References</a>
+              </li>
+              <li class="">
+                <a href="./policies">Policies</a>
+              </li>
+              <li class="">
+                <a href="./links">Links</a>
+              </li>
+            </ul>
+          </div>
+        </div>
+      </div>
+    </div>
+
+    <header class="jumbotron subhead" id="overview">
+        <div class="container">
+            <h1>GeneNetwork</h1>
+            <p class="lead">Open source bioinformatics for systems genetics<br />
+            Brought to you by the University of Tennessee</p>
+        </div>
+    </header>
+
+
+    <div class="container">
+        <div class="row">
+            <div class="span3 bs-docs-sidebar">
+              <ul class="nav nav-list bs-docs-sidenav">
+                <li><a href="#search"><i class="icon-chevron-right"></i> Search</a></li>
+                <li><a href="#getting-started"><i class="icon-chevron-right"></i> Getting started</a></li>
+                <li><a href="#advanced"><i class="icon-chevron-right"></i> Advanced commands</a></li>
+                <li><a href="#tour-info"><i class="icon-chevron-right"></i> Tour and more info</a></li>
+                <li><a href="#websites"><i class="icon-chevron-right"></i> Affiliates and mirrors</a></li>
               </ul>
-            </td><!-- END OF FIND SELECTOR PULL-DOWN PANEL (LEFT SIDE)  -->
-            <!-- START OF TOP RIGHT PANEL  -->
+            </div>
 
-            <td valign="top" width="40%" bgcolor="#FFFFFF">
-              <p style="font-size:15px;font-family:verdana;color:black"><b>Websites Affiliated with
-              GeneNetwork</b></p>
+            <div class="span9">
+                <section id="search">
+                    <div class="page-header">
+                        <h1>Select and search</h1>
+                    </div>
+                    <form method="get" action="/search"  name="SEARCHFORM">
+                        <fieldset>
+                            <!--<legend>Select and Search</legend>-->
+                            <label for="species">Species:</label>
+                                <select name="species" id="species" class="input-xlarge ds_selector">
+                                </select>
 
-              <p style="font-size:12px;font-family:verdana;color:black"></p>
+                            <div class="input-append">
+                                <label for="group">Group: </label>
+                                    <select name="group" id="group" class="input-xlarge ds_selector"></select>
+                                    <!--<i class="icon-question-sign"></i>-->
+                                    <input type="button" class="btn" value="Info" id="group_info" />
+                            </div>
 
-              <ul>
-                <li><a href="http://ucscbrowser.genenetwork.org/" target="_blank">Genome
-                Browser</a> at UTHSC</li>
 
-                <li><a href="http://galaxy.genenetwork.org/" target="_blank">Galaxy</a> at
-                UTHSC</li>
+                            <label for="tissue">Type:</label>
+                                <select name="type" id="type" class="input-xlarge ds_selector"></select>
 
-                <li>GeneNetwork at <a href="http://ec2.genenetwork.org/" target="_blank">Amazon
-                Cloud (EC2)</a></li>
+                            <div class="input-append">
+                                <label for="dataset">Dataset:</label>
+                                    <select name="dataset" id="dataset" class="input-xlarge"></select>
+                                    <input type="button" class="btn" value="Info" id="dataset_info" />
+                            </div>
+                            <!--  USER HELP   -->
 
-                <li>GeneNetwork Source Codes at <a href=
-                "http://sourceforge.net/projects/genenetwork/" target="_blank">SourceForge</a></li>
 
-                <li>GeneNetwork Source Codes at <a href=
-                "https://github.com/genenetwork/genenetwork" target="_blank">GitHub</a></li>
-              </ul>
+                                <!--<p >Databases marked with <b>**</b>-->
+                                <!--      suffix are not public yet.<br>-->
+                                <!--     Access requires <a href="/account.html" target=-->
+                                <!--      "_blank" class="fs14">user login</a>.</p>-->
 
-              <p>____________________________</p>
+                                <!--  GET ANY  SEARCH -->
 
-              <p style="font-size:15px;font-family:verdana;color:black"><b>Getting Started</b>
-              &nbsp;&nbsp;</p>
+                            <label for="tfor">Search:</label>
 
-              <ol style="font-size:12px;font-family:verdana;color:black">
-                <li>Select <b>Species</b> (or select All)</li>
+                            <input class="search-query input-xlarge"
+                                id="tfor" name="search_terms"
+                                type="text" maxlength="500">
 
-                <li>Select <b>Group</b> (a specific sample)</li>
+                            <!--  GET ANY HELP   -->
 
-                <li>Select <b>Type</b> of data:
+                            <p>Enter terms, genes, ID numbers in the
+                                  <b>Search</b> field<br>
+                                  Use <b>*</b> or <b>?</b> wildcards (Cyp*a?,
+                                  synap*)<br>
+                                  Use <b>quotes</b> for terms such as <i>"tyrosine
+                                  kinase"</i></p>
 
-                  <ul>
-                    <li>Phenotype (traits)</li>
+                                <!--  SEARCH, MAKE DEFAULT, ADVANCED SEARCH -->
 
-                    <li>Genotype (markers)</li>
 
-                    <li>Expression (mRNAs)</li>
-                  </ul>
-                </li>
+                               <input id="btsearch" type="submit"
+                                class="btn btn-primary" value="Search">
 
-                <li>Select a <b>Database</b></li>
+                                <input type="button" class="btn" value="Make Default"
+                                       id="make_default">
 
-                <li>Enter search terms in the <b>Get Any</b> or <b>Combined</b> field: words,
-                genes, ID numbers, probes, advanced search commands</li>
+                                <input type="button" class=
+                                    "btn" value="Advanced Search" onclick=
+                                    "javascript:window.open('/index3.html', '_self');">
 
-                <li>Click on the <b>Search</b> button</li>
+                                <input type="hidden" name="FormID" value="searchResult"> <input type=
+                                "hidden" name="RISet" value="BXD">
+                        </fieldset>
+                    </form>
+                </section>
 
-                <li>Optional: Use the <b>Make Default</b> button to save your preferences</li>
-              </ol>
+                <section id="getting-started">
+                    <div class="page-header">
+                        <h1>Getting started</h1>
+                    </div>
 
-              <p>____________________________</p>
+                <ol style="font-size:12px;font-family:verdana;color:black">
+                  <li>Select <b>Species</b> (or All)</li>
 
-              <p style="font-size:14px;font-family:verdana;color:black"><b>How to Use
-              GeneNetwork</b></p>
+                  <li>Select <b>Group</b> (a specific sample)</li>
 
-              <blockquote>
-                <p style="font-size:12px;font-family:verdana;color:black">Take a 20-40 minute
-                GeneNetwork <a href="http://www.genenetwork.org/tutorial/WebQTLTour/" target=
-                "_blank" class="fs14"><small>Tour</small></a> that includes screen shots and
-                typical steps in the analysis.</p>
-              </blockquote>
+                  <li>Select <b>Type</b> of data:
 
-              <blockquote>
-                <p style="font-size:12px;font-family:verdana;color:black">For information about
-                resources and methods, select the <img src=
-                "http://www.genenetwork.org/images/upload/Info.png" alt="INFO" border="0" valign=
-                "middle"> buttons.</p>
+                    <ul>
+                      <li>Phenotype (traits)</li>
 
-                <p style="font-size:12px;font-family:verdana;color:black">Try the <a href=
-                "http://alexandria.uthsc.edu/" target="_blank" class=
-                "fs14"><small>Workstation</small></a> site to explore data and features that are
-                being implemented.</p>
+                      <li>Genotype (markers)</li>
 
-                <p style="font-size:12px;font-family:verdana;color:black">Review the <a href=
-                "/conditionsofUse.html" target="_blank" class="fs14"><small>Conditions</small></a>
-                and <a href="/statusandContact.html" target="_blank" class=
-                "fs14"><small>Contacts</small></a> pages for information on the status of data sets
-                and advice on their use and citation.</p>
-              </blockquote>
+                      <li>Expression (mRNAs)</li>
+                    </ul>
+                  </li>
 
-              <p style="font-size:14px;font-family:verdana;color:black"><b>Mirror and Development
-              Sites</b></p>
+                  <li>Select a <b>Database</b></li>
 
-              <ul>
-                <li><a href="http://www.genenetwork.org/" target="_blank" style=
-                "font-size:12px;font-family:verdana;color:blue">Main GN site at UTHSC</a> (main
-                site)</li>
+                  <li>Enter terms in the search field: words,
+                  genes, ID numbers, probes, advanced search commands</li>
 
-                <li><a href="http://www.genenetwork.waimr.uwa.edu.au/" target="_blank" style=
-                "font-size:12px;font-family:verdana;color:blue">Australia at the UWA</a></li>
+                  <li>Click the <b>Search</b> button</li>
 
-                <li><a href="http://gn.genetics.ucla.edu/" target="_blank" style=
-                "font-size:12px;font-family:verdana;color:blue">California at UCLA</a></li>
+                  <li>Optional: Use the <b>Make Default</b> button to save your preferences</li>
+                </ol>
 
-                <li><a href="http://genenetwork.helmholtz-hzi.de/" target="_blank" style=
-                "font-size:12px;font-family:verdana;color:blue">Germany at the HZI</a></li>
+                <h3>User Guide</h3>
+                <h5>Read the
+                <a href="http://www.genenetwork.org/index4.html" target="_blank">
+                    user guide</a>.</h5>
 
-                <li><a href="https://genenetwork.hubrecht.eu/" target="_blank" style=
-                "font-size:12px;font-family:verdana;color:blue">Netherlands at the Hubrecht</a>
-                (Development)</li>
+                </section>
 
-                <li><a href="http://genenetwork.memphis.edu/" target="_blank" style=
-                "font-size:12px;font-family:verdana;color:blue">Memphis at the U of M</a></li>
 
-                <li><a href="http://webqtl.bic.nus.edu.sg/" target="_blank" style=
-                "font-size:12px;font-family:verdana;color:blue">Singapore at the NUS</a></li>
+                <section id="advanced">
+                    <div class="page-header">
+                        <h1>Advanced commands</h1>
+                    </div>
 
-                <li><a href="http://genenetwork.epfl.ch/" target="_blank" style=
-                "font-size:12px;font-family:verdana;color:blue">Switzerland at the EPFL</a></li>
-              </ul>
+                    <p>GeneNetwork supports a variety of advanced searches.</p>
 
-              <p style="font-size:14px;font-family:verdana;color:black"><b>History and
-              Archive</b></p>
-
-              <blockquote>
-                <p style="font-size:12px;font-family:verdana;color:black">GeneNetwork's <a href=
-                "http://artemis.uthsc.edu" target="_blank" class="fs14"><small>Time
-                Machine</small></a> links to earlier versions that correspond to specific
-                publication dates.</p>
-              </blockquote>
-            </td>
-          </tr>
-        </table>
-      </td>
-    </tr>
-    <!-- End of body -->
-    <script src="/javascript/searchtip.js" type="text/javascript">
-    </script>
-    <script type="text/javascript">
-      $(document).ready(function () {
-                initialDatasetSelection();
-        });
-    </script>
-{% endblock %}
+                    <p>To try them out copy these examples into the search field:</p>
+
+                      <ul>
+                        <li><b>POSITION=(chr1 25 30)</b> finds genes, markers, or transcripts on
+                        chromosome 1 between 25 and 30 Mb.</li>
 
+                        <li><b>MEAN=(15 16) LRS=(23 46)</b> in the <b>Combined</b> field finds
+                        highly expressed genes (15 to 16 log2 units) AND with peak <a href=
+                        "http://www.genenetwork.org/glossary.html#L" target="_blank">LRS</a>
+                        linkage between 23 and 46.</li>
+
+                        <li><b>RIF=mitochondrial</b> searches RNA databases for <a href=
+                        "http://www.ncbi.nlm.nih.gov/projects/GeneRIF/GeneRIFhelp.html" target="_blank">
+                        GeneRIF</a> links.</li>
+
+                        <li><b>WIKI=nicotine</b> searches <a href=
+                        "http://www.genenetwork.org/webqtl/main.py?FormID=geneWiki" target="_blank">
+                        GeneWiki</a> for genes that you or other users have annotated
+                        with the word <i>nicotine</i>.</li>
+
+                        <li><b>GO:0045202</b> searches for synapse-associated genes listed in the
+                        <a href="http://www.godatabase.org/cgi-bin/amigo/go.cgi" target="_blank">
+                            Gene Ontology</a>.</li>
+
+                        <li><b>GO:0045202 LRS=(9 99 Chr4 122 155) cisLRS=(9 999 10)</b>
+                        finds synapse-associated genes with <a href=
+                        "http://www.genenetwork.org/glossary.html#E" target="_blank">
+                        cis eQTL</a> on Chr 4 from 122 and 155 Mb with LRS scores
+                        between 9 and 999.</li>
+
+                        <li><b>RIF=diabetes LRS=(9 999 Chr2 100 105) transLRS=(9 999 10)</b>
+                        finds diabetes-associated transcripts with peak <a href=
+                        "http://www.genenetwork.org/glossary.html#E" target="_blank">
+                        trans eQTLs</a> on Chr 2 between 100 and 105 Mb with LRS
+                        scores between 9 and 999.</li>
+                      </ul>
+                </section>
+
+                <section id="tour-info">
+                    <div class="page-header">
+                        <h1>Tour and more info</h1>
+                    </div>
+
+                    <h3>Thirty minute tour</h3>
+                    <p>
+                      Take the 30 minute
+                      GeneNetwork <a href="http://www.genenetwork.org/tutorial/WebQTLTour/" target=
+                      "_blank" class="fs14">tour</a> that includes screen shots and
+                      typical steps in the analysis.
+                    </p>
+
+                    <h3>Even more info</h3>
+                    <p>
+                      For information about
+                      resources and methods, select the Info buttons next to the Group
+                      and Database fields above.
+                    </p>
+
+                      <p>The <a href=
+                      "/conditionsofUse.html" target="_blank">conditions</a>
+                      and <a href="/statusandContact.html" target="_blank">contact
+                      </a> pages have information on the status of data sets
+                      and advice on their use and citation.</p>
+
+                </section>
+
+                <section id="websites">
+                    <div class="page-header">
+                        <h1>Affiliates and mirrors</h1>
+                    </div>
+                    <h3>Websites affiliated with GeneNetwork</h3>
+                    <ul>
+                        <li><a href="http://ucscbrowser.genenetwork.org/" target="_blank">Genome
+                        browser</a> at UTHSC</li>
+
+                        <li><a href="http://galaxy.genenetwork.org/" target="_blank">Galaxy</a> at
+                        UTHSC</li>
+
+                        <li>GeneNetwork at <a href="http://ec2.genenetwork.org/" target="_blank">Amazon
+                        Cloud (EC2)</a></li>
+
+                        <li>GeneNetwork Source Code at <a href=
+                        "http://sourceforge.net/projects/genenetwork/" target="_blank">SourceForge</a></li>
+
+                        <li>GeneNetwork Source Code at <a href=
+                        "https://github.com/genenetwork/genenetwork" target="_blank">GitHub</a></li>
+                    </ul>
+                    <h3>Mirror and development sites</h3>
+                    <ul>
+                        <li><a href="http://www.genenetwork.org/" target="_blank">
+                        Main GN site</a> at UTHSC</li>
+
+                        <li><a href="http://www.genenetwork.waimr.uwa.edu.au/" target="_blank">
+                        Australia</a> at the UWA</li>
+
+                        <li><a href="http://gn.genetics.ucla.edu/" target="_blank">
+                        California</a> at UCLA</li>
+
+                        <li><a href="http://genenetwork.helmholtz-hzi.de/" target="_blank">
+                        Germany</a> at the HZI</li>
+
+                        <li><a href="https://genenetwork.hubrecht.eu/" target="_blank">
+                        Netherlands</a> at the Hubrecht
+                        (development)</li>
+
+                        <li><a href="http://genenetwork.memphis.edu/" target="_blank">
+                        Memphis</a> at the U of M</li>
+
+                        <li><a href="http://webqtl.bic.nus.edu.sg/" target="_blank">
+                        Singapore</a> at the NUS</li>
+
+                        <li><a href="http://genenetwork.epfl.ch/" target="_blank">
+                        Switzerland</a> at the EPFL</li>
+                    </ul>
+                    <h3>History and archive</h3>
+
+                    <p>The
+                    <a href="http://artemis.uthsc.edu" target="_blank">
+                        time machine</a>
+                    has earlier versions that correspond to specific publication dates.
+                    </p>
+
+                    <h3>The next generation</h3>
+                       <p>Try the <a href=
+                      "http://alexandria.uthsc.edu/" target="_blank">
+                      development</a> site to explore experimental data and features.</p>
+                </section>
+            </div>
+        </div>
+    </div>
+
+        <!-- Footer
+    ================================================== -->
+    <footer class="footer">
+      <div class="container">
+        <p class="pull-right"><a href="#">Back to top</a></p>
+
+        <p>Launched in 1994 as
+        <A HREF="http://www.ncbi.nlm.nih.gov/pubmed?term=8043953">
+            The Portable Dictionary of the Mouse Genome</A> and in 2001 as WebQTL.
+        </p>
+        <p>Operated by
+            <A HREF="mailto:rwilliams@uthsc.edu">Rob Williams</A>,
+            <A HREF="mailto:lyan6@uthsc.edu">Lei Yan</A>,
+            <A HREF="mailto:zachary.a.sloan@gmail.com">Zachary Sloan</A>, and
+            <A HREF="mailto:acenteno@uthsc.edu" target="_blank">Arthur Centeno</A>.
+        </p>
+        <p>
+            Designed and coded by <a href="http://penguinpython.com">Sam Ockman</a>, Xiaodong Zhou,
+            Christian Fernandez,
+            Ning Liu, Rudi Alberts, Elissa Chesler, Jintao Wang, Kenneth Manly, Robert W. Williams,
+            and <A HREF="/credit.html">colleagues</A>.
+        </p>
+
+        <p>Built with <a href="http://twitter.github.com/bootstrap/">bootstrap</a>,
+            <a href="http://coffeescript.org/">coffeescript</a>,
+            <a href="http://flask.pocoo.org/">flask</a>,
+            <a href="http://en.wikipedia.org/wiki/Linux">linux</a>,
+            <a href="http://www.python.org/">python</a> and good intentions.
+        </p>
+        <p>Special thanks to CYP1A2 and AHR.</p>
+        <br />
+        <p>GeneNetwork is supported by:</p>
+        <UL>
+            <LI>
+                <a target="_blank" href="http://citg.uthsc.edu">
+                    The UT Center for Integrative and Translational Genomics
+                </A>
+            </li>
+            <LI><a target="_blank" href="http://www.iniastress.org">NIAAA</A>
+                Integrative Neuroscience Initiative on Alcoholism
+                (U01 AA016662, U01 AA013499, U24 AA013513, U01 AA014425)
+            </li>
+            <LI>
+                <a target="_blank"
+                   href="http://www.drugabuse.gov/about/organization/Genetics/geneexpression/index.html">NIDA</A>, <a class="smallsize" target="_blank" href="http://www.nimh.nih.gov/">NIMH</A>
+                   , and <a class="smallsize" target="_blank" href="http://www.niaaa.nih.gov/">
+                   NIAAA</A> (P20-DA 21131)
+            </li>
+            <LI>NCI <a target="_blank" href="http://emice.nci.nih.gov/">MMHCC</A> (U01CA105417) and
+                <a target="_blank" href="http://www.ncrr.nih.gov/">NCRR</A>
+                <a target="_blank" href="http://www.nbirn.net/TestBeds/Mouse/index.htm">BIRN</A>
+                (U24 RR021760)
+            </li>
+        </UL>
+        <!--</p>-->
+
+        <ul class="footer-links">
+          <li><a href="http://atlas.uthsc.edu/mailman/listinfo/genenetwork" target="_blank">Join the mailing list</a></li>
+          <!--<li><a href="#">Friend us on facebook</a></li>-->
+          <!--<li><a href="#">Follow us on twitter</a></li>-->
+        </ul>
+      </div>
+    </footer>
+
+    <script src="https://ajax.googleapis.com/ajax/libs/jquery/1.8.2/jquery.min.js"></script>
+    <script src="/static/packages/bootstrap/js/bootstrap.min.js"></script>
+    <script>
+            //http://stackoverflow.com/questions/11521763/bootstrap-scrollspy-not-working
+            var $window = $(window)
+            $('.bs-docs-sidenav').affix({
+              offset: {
+                top: function () { return $window.width() <= 980 ? 290 : 210 }
+              , bottom: 270
+              }
+            })
+    </script>
+    <!--<SCRIPT SRC="/javascript/webqtl.js"></SCRIPT>-->
+    <!--<script src="/static/new/javascript/dataset_menu_structure.json"></script>-->
+    <!--<script src="/static/new/javascript/dataset_select_items.js"></script>-->
+    <script src="/static/new/js_external/jquery.cookie.js"></script>
+    <script type="text/javascript" src="/static/new/js_external/json2.js"></script>
+    <script src="/static/new/javascript/dataset_select_menu.js"></script>
+</body>
+</html>
diff --git a/wqflask/wqflask/templates/new_index_page.html b/wqflask/wqflask/templates/new_index_page.html
deleted file mode 100644
index 695129a9..00000000
--- a/wqflask/wqflask/templates/new_index_page.html
+++ /dev/null
@@ -1,423 +0,0 @@
-<!DOCTYPE html>
-<html lang="en">
-<head>
-    <meta charset="utf-8">
-    <title>GeneNetwork</title>
-    <meta name="viewport" content="width=device-width, initial-scale=1.0">
-    <meta name="description" content="">
-    <meta name="author" content="">
-    <link REL="stylesheet" TYPE="text/css" href="/static/packages/bootstrap/css/bootstrap.min.css" />
-    <link REL="stylesheet" TYPE="text/css" href="/static/packages/bootstrap/css/bootstrap-responsive.min.css" />
-    <link REL="stylesheet" TYPE="text/css" href="/static/packages/bootstrap/css/docs.css" />
-
-    <!-- HTML5 shim, for IE6-8 support of HTML5 elements -->
-    <!--[if lt IE 9]>
-      <script src="http://html5shim.googlecode.com/svn/trunk/html5.js"></script>
-    <![endif]-->
-
-
-</head>
-
-<body data-spy="scroll" data-target=".bs-docs-sidebar">
-    <!-- Navbar
-    ================================================== -->
-    <div class="navbar navbar-inverse navbar-fixed-top">
-      <div class="navbar-inner">
-        <div class="container">
-          <button type="button" class="btn btn-navbar" data-toggle="collapse" data-target=".nav-collapse">
-            <span class="icon-bar"></span>
-            <span class="icon-bar"></span>
-            <span class="icon-bar"></span>
-          </button>
-          <a class="brand" href="/">GeneNetwork</a>
-          <div class="nav-collapse collapse">
-            <ul class="nav">
-              <li class="active">
-                <a href="/">Home</a>
-              </li>
-              <li class="dropdown">
-                <a id="drop1" href="#" role="button" class="dropdown-toggle" data-toggle="dropdown">
-                    Search <b class="caret"></b>
-                </a>
-                    <ul class="dropdown-menu" role="menu" aria-labelledby="drop1">
-                        <li><a tabindex="-1" href="/webqtl/main.py?FormID=tissueCorrelation">Tissue Corrleation</a></li>
-                        <li><a tabindex="-1" href="/webqtl/main.py?FormID=snpBrowser">SNP Browser</a></li>
-                        <li class="divider"></li>
-                        <li><a tabindex="-1" href="/webqtl/main.py?FormID=geneWiki">Gene Wiki</a></li>
-                    </ul>
-              </li>
-              <li class="">
-                <a href="#">Help</a>
-              </li>
-              <li class="">
-                <a href="/whats_new">News</a>
-              </li>
-              <li class="">
-                <a href="./reference.html">References</a>
-              </li>
-              <li class="">
-                <a href="./policies">Policies</a>
-              </li>
-              <li class="">
-                <a href="./links">Links</a>
-              </li>
-            </ul>
-          </div>
-        </div>
-      </div>
-    </div>
-
-    <header class="jumbotron subhead" id="overview">
-        <div class="container">
-            <h1>GeneNetwork</h1>
-            <p class="lead">Open source bioinformatics for systems genetics<br />
-            Brought to you by the University of Tennessee</p>
-        </div>
-    </header>
-
-
-    <div class="container">
-        <div class="row">
-            <div class="span3 bs-docs-sidebar">
-              <ul class="nav nav-list bs-docs-sidenav">
-                <li><a href="#search"><i class="icon-chevron-right"></i> Search</a></li>
-                <li><a href="#getting-started"><i class="icon-chevron-right"></i> Getting started</a></li>
-                <li><a href="#advanced"><i class="icon-chevron-right"></i> Advanced commands</a></li>
-                <li><a href="#tour-info"><i class="icon-chevron-right"></i> Tour and more info</a></li>
-                <li><a href="#websites"><i class="icon-chevron-right"></i> Affiliates and mirrors</a></li>
-              </ul>
-            </div>
-
-            <div class="span9">
-                <section id="search">
-                    <div class="page-header">
-                        <h1>Select and search</h1>
-                    </div>
-                    <form method="get" action="/search"  name="SEARCHFORM">
-                        <fieldset>
-                            <!--<legend>Select and Search</legend>-->
-                            <label for="species">Species:</label>
-                                <select name="species" id="species" class="input-xlarge ds_selector">
-                                </select>
-
-                            <div class="input-append">
-                                <label for="group">Group: </label>
-                                    <select name="group" id="group" class="input-xlarge ds_selector"></select>
-                                    <!--<i class="icon-question-sign"></i>-->
-                                    <input type="button" class="btn" value="Info" id="group_info" />
-                            </div>
-
-
-                            <label for="tissue">Type:</label>
-                                <select name="type" id="type" class="input-xlarge ds_selector"></select>
-
-                            <div class="input-append">
-                                <label for="dataset">Dataset:</label>
-                                    <select name="dataset" id="dataset" class="input-xlarge"></select>
-                                    <input type="button" class="btn" value="Info" id="dataset_info" />
-                            </div>
-                            <!--  USER HELP   -->
-
-
-                                <!--<p >Databases marked with <b>**</b>-->
-                                <!--      suffix are not public yet.<br>-->
-                                <!--     Access requires <a href="/account.html" target=-->
-                                <!--      "_blank" class="fs14">user login</a>.</p>-->
-
-                                <!--  GET ANY  SEARCH -->
-
-                            <label for="tfor">Search:</label>
-
-                            <input class="search-query input-xlarge"
-                                id="tfor" name="search_terms"
-                                type="text" maxlength="500">
-
-                            <!--  GET ANY HELP   -->
-
-                            <p>Enter terms, genes, ID numbers in the
-                                  <b>Search</b> field<br>
-                                  Use <b>*</b> or <b>?</b> wildcards (Cyp*a?,
-                                  synap*)<br>
-                                  Use <b>quotes</b> for terms such as <i>"tyrosine
-                                  kinase"</i></p>
-
-                                <!--  SEARCH, MAKE DEFAULT, ADVANCED SEARCH -->
-
-
-                               <input id="btsearch" type="submit"
-                                class="btn btn-primary" value="Search">
-
-                                <input type="button" class="btn" value="Make Default"
-                                       id="make_default">
-
-                                <input type="button" class=
-                                    "btn" value="Advanced Search" onclick=
-                                    "javascript:window.open('/index3.html', '_self');">
-
-                                <input type="hidden" name="FormID" value="searchResult"> <input type=
-                                "hidden" name="RISet" value="BXD">
-                        </fieldset>
-                    </form>
-                </section>
-
-                <section id="getting-started">
-                    <div class="page-header">
-                        <h1>Getting started</h1>
-                    </div>
-
-                <ol style="font-size:12px;font-family:verdana;color:black">
-                  <li>Select <b>Species</b> (or All)</li>
-
-                  <li>Select <b>Group</b> (a specific sample)</li>
-
-                  <li>Select <b>Type</b> of data:
-
-                    <ul>
-                      <li>Phenotype (traits)</li>
-
-                      <li>Genotype (markers)</li>
-
-                      <li>Expression (mRNAs)</li>
-                    </ul>
-                  </li>
-
-                  <li>Select a <b>Database</b></li>
-
-                  <li>Enter terms in the search field: words,
-                  genes, ID numbers, probes, advanced search commands</li>
-
-                  <li>Click the <b>Search</b> button</li>
-
-                  <li>Optional: Use the <b>Make Default</b> button to save your preferences</li>
-                </ol>
-
-                <h3>User Guide</h3>
-                <h5>Read the
-                <a href="http://www.genenetwork.org/index4.html" target="_blank">
-                    user guide</a>.</h5>
-
-                </section>
-
-
-                <section id="advanced">
-                    <div class="page-header">
-                        <h1>Advanced commands</h1>
-                    </div>
-
-                    <p>GeneNetwork supports a variety of advanced searches.</p>
-
-                    <p>To try them out copy these examples into the search field:</p>
-
-                      <ul>
-                        <li><b>POSITION=(chr1 25 30)</b> finds genes, markers, or transcripts on
-                        chromosome 1 between 25 and 30 Mb.</li>
-
-                        <li><b>MEAN=(15 16) LRS=(23 46)</b> in the <b>Combined</b> field finds
-                        highly expressed genes (15 to 16 log2 units) AND with peak <a href=
-                        "http://www.genenetwork.org/glossary.html#L" target="_blank">LRS</a>
-                        linkage between 23 and 46.</li>
-
-                        <li><b>RIF=mitochondrial</b> searches RNA databases for <a href=
-                        "http://www.ncbi.nlm.nih.gov/projects/GeneRIF/GeneRIFhelp.html" target="_blank">
-                        GeneRIF</a> links.</li>
-
-                        <li><b>WIKI=nicotine</b> searches <a href=
-                        "http://www.genenetwork.org/webqtl/main.py?FormID=geneWiki" target="_blank">
-                        GeneWiki</a> for genes that you or other users have annotated
-                        with the word <i>nicotine</i>.</li>
-
-                        <li><b>GO:0045202</b> searches for synapse-associated genes listed in the
-                        <a href="http://www.godatabase.org/cgi-bin/amigo/go.cgi" target="_blank">
-                            Gene Ontology</a>.</li>
-
-                        <li><b>GO:0045202 LRS=(9 99 Chr4 122 155) cisLRS=(9 999 10)</b>
-                        finds synapse-associated genes with <a href=
-                        "http://www.genenetwork.org/glossary.html#E" target="_blank">
-                        cis eQTL</a> on Chr 4 from 122 and 155 Mb with LRS scores
-                        between 9 and 999.</li>
-
-                        <li><b>RIF=diabetes LRS=(9 999 Chr2 100 105) transLRS=(9 999 10)</b>
-                        finds diabetes-associated transcripts with peak <a href=
-                        "http://www.genenetwork.org/glossary.html#E" target="_blank">
-                        trans eQTLs</a> on Chr 2 between 100 and 105 Mb with LRS
-                        scores between 9 and 999.</li>
-                      </ul>
-                </section>
-
-                <section id="tour-info">
-                    <div class="page-header">
-                        <h1>Tour and more info</h1>
-                    </div>
-
-                    <h3>Thirty minute tour</h3>
-                    <p>
-                      Take the 30 minute
-                      GeneNetwork <a href="http://www.genenetwork.org/tutorial/WebQTLTour/" target=
-                      "_blank" class="fs14">tour</a> that includes screen shots and
-                      typical steps in the analysis.
-                    </p>
-
-                    <h3>Even more info</h3>
-                    <p>
-                      For information about
-                      resources and methods, select the Info buttons next to the Group
-                      and Database fields above.
-                    </p>
-
-                      <p>The <a href=
-                      "/conditionsofUse.html" target="_blank">conditions</a>
-                      and <a href="/statusandContact.html" target="_blank">contact
-                      </a> pages have information on the status of data sets
-                      and advice on their use and citation.</p>
-
-                </section>
-
-                <section id="websites">
-                    <div class="page-header">
-                        <h1>Affiliates and mirrors</h1>
-                    </div>
-                    <h3>Websites affiliated with GeneNetwork</h3>
-                    <ul>
-                        <li><a href="http://ucscbrowser.genenetwork.org/" target="_blank">Genome
-                        browser</a> at UTHSC</li>
-
-                        <li><a href="http://galaxy.genenetwork.org/" target="_blank">Galaxy</a> at
-                        UTHSC</li>
-
-                        <li>GeneNetwork at <a href="http://ec2.genenetwork.org/" target="_blank">Amazon
-                        Cloud (EC2)</a></li>
-
-                        <li>GeneNetwork Source Code at <a href=
-                        "http://sourceforge.net/projects/genenetwork/" target="_blank">SourceForge</a></li>
-
-                        <li>GeneNetwork Source Code at <a href=
-                        "https://github.com/genenetwork/genenetwork" target="_blank">GitHub</a></li>
-                    </ul>
-                    <h3>Mirror and development sites</h3>
-                    <ul>
-                        <li><a href="http://www.genenetwork.org/" target="_blank">
-                        Main GN site</a> at UTHSC</li>
-
-                        <li><a href="http://www.genenetwork.waimr.uwa.edu.au/" target="_blank">
-                        Australia</a> at the UWA</li>
-
-                        <li><a href="http://gn.genetics.ucla.edu/" target="_blank">
-                        California</a> at UCLA</li>
-
-                        <li><a href="http://genenetwork.helmholtz-hzi.de/" target="_blank">
-                        Germany</a> at the HZI</li>
-
-                        <li><a href="https://genenetwork.hubrecht.eu/" target="_blank">
-                        Netherlands</a> at the Hubrecht
-                        (development)</li>
-
-                        <li><a href="http://genenetwork.memphis.edu/" target="_blank">
-                        Memphis</a> at the U of M</li>
-
-                        <li><a href="http://webqtl.bic.nus.edu.sg/" target="_blank">
-                        Singapore</a> at the NUS</li>
-
-                        <li><a href="http://genenetwork.epfl.ch/" target="_blank">
-                        Switzerland</a> at the EPFL</li>
-                    </ul>
-                    <h3>History and archive</h3>
-
-                    <p>The
-                    <a href="http://artemis.uthsc.edu" target="_blank">
-                        time machine</a>
-                    has earlier versions that correspond to specific publication dates.
-                    </p>
-
-                    <h3>The next generation</h3>
-                       <p>Try the <a href=
-                      "http://alexandria.uthsc.edu/" target="_blank">
-                      development</a> site to explore experimental data and features.</p>
-                </section>
-            </div>
-        </div>
-    </div>
-
-        <!-- Footer
-    ================================================== -->
-    <footer class="footer">
-      <div class="container">
-        <p class="pull-right"><a href="#">Back to top</a></p>
-
-        <p>Launched in 1994 as
-        <A HREF="http://www.ncbi.nlm.nih.gov/pubmed?term=8043953">
-            The Portable Dictionary of the Mouse Genome</A> and in 2001 as WebQTL.
-        </p>
-        <p>Operated by
-            <A HREF="mailto:rwilliams@uthsc.edu">Rob Williams</A>,
-            <A HREF="mailto:lyan6@uthsc.edu">Lei Yan</A>,
-            <A HREF="mailto:zachary.a.sloan@gmail.com">Zachary Sloan</A>, and
-            <A HREF="mailto:acenteno@uthsc.edu" target="_blank">Arthur Centeno</A>.
-        </p>
-        <p>
-            Designed and coded by <a href="http://penguinpython.com">Sam Ockman</a>, Xiaodong Zhou,
-            Christian Fernandez,
-            Ning Liu, Rudi Alberts, Elissa Chesler, Jintao Wang, Kenneth Manly, Robert W. Williams,
-            and <A HREF="/credit.html">colleagues</A>.
-        </p>
-
-        <p>Built with <a href="http://twitter.github.com/bootstrap/">bootstrap</a>,
-            <a href="http://coffeescript.org/">coffeescript</a>,
-            <a href="http://flask.pocoo.org/">flask</a>,
-            <a href="http://en.wikipedia.org/wiki/Linux">linux</a>,
-            <a href="http://www.python.org/">python</a> and good intentions.
-        </p>
-        <p>Special thanks to CYP1A2 and AHR.</p>
-        <br />
-        <p>GeneNetwork is supported by:</p>
-        <UL>
-            <LI>
-                <a target="_blank" href="http://citg.uthsc.edu">
-                    The UT Center for Integrative and Translational Genomics
-                </A>
-            </li>
-            <LI><a target="_blank" href="http://www.iniastress.org">NIAAA</A>
-                Integrative Neuroscience Initiative on Alcoholism
-                (U01 AA016662, U01 AA013499, U24 AA013513, U01 AA014425)
-            </li>
-            <LI>
-                <a target="_blank"
-                   href="http://www.drugabuse.gov/about/organization/Genetics/geneexpression/index.html">NIDA</A>, <a class="smallsize" target="_blank" href="http://www.nimh.nih.gov/">NIMH</A>
-                   , and <a class="smallsize" target="_blank" href="http://www.niaaa.nih.gov/">
-                   NIAAA</A> (P20-DA 21131)
-            </li>
-            <LI>NCI <a target="_blank" href="http://emice.nci.nih.gov/">MMHCC</A> (U01CA105417) and
-                <a target="_blank" href="http://www.ncrr.nih.gov/">NCRR</A>
-                <a target="_blank" href="http://www.nbirn.net/TestBeds/Mouse/index.htm">BIRN</A>
-                (U24 RR021760)
-            </li>
-        </UL>
-        <!--</p>-->
-
-        <ul class="footer-links">
-          <li><a href="http://atlas.uthsc.edu/mailman/listinfo/genenetwork" target="_blank">Join the mailing list</a></li>
-          <!--<li><a href="#">Friend us on facebook</a></li>-->
-          <!--<li><a href="#">Follow us on twitter</a></li>-->
-        </ul>
-      </div>
-    </footer>
-
-    <script src="https://ajax.googleapis.com/ajax/libs/jquery/1.8.2/jquery.min.js"></script>
-    <script src="/static/packages/bootstrap/js/bootstrap.min.js"></script>
-    <script>
-            //http://stackoverflow.com/questions/11521763/bootstrap-scrollspy-not-working
-            var $window = $(window)
-            $('.bs-docs-sidenav').affix({
-              offset: {
-                top: function () { return $window.width() <= 980 ? 290 : 210 }
-              , bottom: 270
-              }
-            })
-    </script>
-    <!--<SCRIPT SRC="/javascript/webqtl.js"></SCRIPT>-->
-    <!--<script src="/static/new/javascript/dataset_menu_structure.json"></script>-->
-    <!--<script src="/static/new/javascript/dataset_select_items.js"></script>-->
-    <script src="/static/new/js_external/jquery.cookie.js"></script>
-    <script type="text/javascript" src="/static/new/js_external/json2.js"></script>
-    <script src="/static/new/javascript/dataset_select_menu.js"></script>
-</body>
-</html>
diff --git a/wqflask/wqflask/templates/old_index_page.html b/wqflask/wqflask/templates/old_index_page.html
new file mode 100644
index 00000000..db0b2d9e
--- /dev/null
+++ b/wqflask/wqflask/templates/old_index_page.html
@@ -0,0 +1,320 @@
+{% extends "base.html" %}
+{% block title %}GeneNetwork{% endblock %}
+{% block content %} 
+  <!-- Start of body -->
+    <tr>
+      <td bgcolor="#EEEEEE" class="solidBorder">
+        <table width="100%" cellspacing="0" cellpadding="5">
+          <tr>
+            <td valign="top" width="40%" align="left" height="10" bgcolor="#EEEEEE">
+              <p style="font-size:18px;font-family:verdana;color:black"><b>Select and
+              Search</b></p>
+
+              <form method="get" action="/search" class="form-search" name="SEARCHFORM">
+                <table width="100%">
+                  <!--  SPECIES  SELECTION -->
+
+                  <tr>
+                    <td align="right" height="35" style=
+                    "font-size:14px;font-family:verdana;color:black" width="16%">
+                    <b>Species:</b></td>
+
+                    <td width="3%"></td>
+
+                    <td nowrap width="85%" align="left">
+                      <div id="menu0">
+                        <select name="species" size="1" id="species" onchange=
+                        "fillOptions('species');">
+                          </select>
+                      </div>
+                    </td>
+                  </tr><!--  GROUP  SELECTION -->
+
+                  <tr>
+                    <td align="right" height="35" style=
+                    "font-size:14px;font-family:verdana;color:black"><b>Group:</b></td>
+
+                    <td width="3%"></td>
+
+                    <td nowrap width="85%" align="left">
+                      <div id="menu1">
+                        <select name="cross" size="1" id="cross" onchange="fillOptions('cross');">
+                          </select> <input type="button" class="btn" value="Info" onclick=
+                          "javascript:crossinfo();">
+                      </div>
+                    </td>
+                  </tr><!--  TYPE  SELECTION -->
+
+                  <tr>
+                    <td align="right" height="35" style=
+                    "font-size:14px;font-family:verdana;color:black"><b>Type:</b></td>
+
+                    <td width="3%"></td>
+
+                    <td nowrap width="85%" align="left">
+                      <div id="menu2">
+                        <select name="tissue" size="1" id="tissue" onchange=
+                        "fillOptions('tissue');">
+                          </select>
+                      </div>
+                    </td>
+                  </tr><!--  DATABASE  SELECTION -->
+
+                  <tr>
+                    <td align="right" height="35" style=
+                    "font-size:14px;font-family:verdana;color:black"><b>Database:</b></td>
+
+                    <td width="3%"></td>
+
+                    <td nowrap width="85%" align="left">
+                      <div id="menu3">
+                        <select name="database" size="1" id="database">
+                          </select> <input type="submit" class="btn" value="Info" name=
+                          "info_database">
+                      </div>
+                    </td>
+                  </tr><!--  USER HELP   -->
+
+                  <tr>
+                    <td align="right" height="20" width="10%"></td>
+
+                    <td width="3%"></td>
+
+                    <td align="left" width="85%">
+                      <p class="fs12">&nbsp;&nbsp;&nbsp;&nbsp;Databases marked with <b>**</b>
+                      suffix are not public yet.<br>
+                      &nbsp;&nbsp;&nbsp;&nbsp;Access requires <a href="/account.html" target=
+                      "_blank" class="fs14"><small>user login</small></a>.</p>
+                    </td>
+                  </tr><!--  GET ANY  SEARCH -->
+
+                  <tr>
+                    <td align="right" height="35" nowrap="on" style=
+                    "font-size:14px;font-family:verdana;color:black" width="10%">
+                    <b>Search:</b></td>
+
+                    <td width="3%"></td>
+
+                    <td nowrap width="85%" align="left"><input class="input-medium search-query"
+                    id="tfor" name="search_terms" style=
+                    "width:420px; background-color:white; font-family:verdana; font-size:14px"
+                    type="text" maxlength="500"></td>
+                  </tr><!--  GET ANY HELP   -->
+
+                  <tr>
+                    <td align="right" height="20" width="10%"></td>
+
+                    <td width="3%"></td>
+
+                    <td width="85%" align="left">
+                      <p class="fs12">&nbsp;&nbsp;&nbsp;&nbsp;Enter terms, genes, ID numbers in the
+                      <b>Search</b> field.<br>
+                      &nbsp;&nbsp;&nbsp;&nbsp;Use <b>*</b> or <b>?</b> wildcards (Cyp*a?,
+                      synap*).<br>
+                      &nbsp;&nbsp;&nbsp;&nbsp;Use <b>quotes</b> for terms such as <i>"tyrosine
+                      kinase"</i>.</p>
+                    </td>
+                  </tr><!--  SEARCH, MAKE DEFAULT, ADVANCED SEARCH -->
+
+                  <tr align="center">
+                    <td width="3%"></td>
+
+                    <td width="3%"></td>
+
+                    <td align="left" height="40" colspan="3"><input id="btsearch" type="submit"
+                    class="btn btn-primary" value="Search">&nbsp;&nbsp;&nbsp;&nbsp; <input type=
+                    "button" class="btn" value="Make Default" onclick=
+                    "setDefault(this.form);">&nbsp;&nbsp;&nbsp;&nbsp; <input type="button" class=
+                    "btn" value="Advanced Search" onclick=
+                    "javascript:window.open('/index3.html', '_self');"></td>
+                  </tr>
+                </table><input type="hidden" name="FormID" value="searchResult"> <input type=
+                "hidden" name="RISet" value="BXD"> <script src="/javascript/selectDatasetMenu.js"
+                type="text/javascript">
+</script>
+              </form><!--  QUICK HELP  -->
+
+              <p>&nbsp;______________________________________________________</p>
+
+              <p style="font-size:13px;font-family:verdana;color:black"><b>&nbsp; Quick HELP
+              Examples and</b> <a href="http://www.genenetwork.org/index4.html" target="_blank"
+              class="fs14"><b>User's Guide</b></a></p>&nbsp;&nbsp;You can also use advanced
+              commands. Copy these simple examples<br>
+              &nbsp;&nbsp;into the <b>Get Any</b> or <b>Combined</b> search fields:
+
+              <ul style="font-size:12px;font-family:verdana;color:black">
+                <li><b><i>POSITION=(chr1 25 30)</i></b> finds genes, markers, or transcripts on
+                chromosome 1 between 25 and 30 Mb.</li>
+
+                <li><b><i>MEAN=(15 16) LRS=(23 46)</i></b> in the <b>Combined</b> field finds
+                highly expressed genes (15 to 16 log2 units) AND with peak <a href=
+                "http://www.genenetwork.org/glossary.html#L" target="_blank" class=
+                "fs14"><small>LRS</small></a> linkage between 23 and 46.</li>
+
+                <li><b><i>RIF=mitochondrial</i></b> searches RNA databases for <a href=
+                "http://www.ncbi.nlm.nih.gov/projects/GeneRIF/GeneRIFhelp.html" target="_blank"
+                class="fs14"><small>GeneRIF</small></a> links.</li>
+
+                <li><b><i>WIKI=nicotine</i></b> searches <a href=
+                "http://www.genenetwork.org/webqtl/main.py?FormID=geneWiki" target="_blank" class=
+                "fs14"><small>GeneWiki</small></a> for genes that you or other users have annotated
+                with the word <i>nicotine</i>.</li>
+
+                <li><b><i>GO:0045202</i></b> searches for synapse-associated genes listed in the
+                <a href="http://www.godatabase.org/cgi-bin/amigo/go.cgi" target="_blank" class=
+                "fs14"><small>Gene Ontology</small></a>.</li>
+
+                <li><b><i>GO:0045202 LRS=(9 99 Chr4 122 155) cisLRS=(9 999 10)</i></b><br>
+                in <b>Combined</b> finds synapse-associated genes with <a href=
+                "http://www.genenetwork.org/glossary.html#E" target="_blank" class=
+                "fs14"><small>cis eQTL</small></a> on Chr 4 from 122 and 155 Mb with LRS scores
+                between 9 and 999.</li>
+
+                <li><b><i>RIF=diabetes LRS=(9 999 Chr2 100 105) transLRS=(9 999 10)</i></b><br>
+                in <b>Combined</b> finds diabetes-associated transcripts with peak <a href=
+                "http://www.genenetwork.org/glossary.html#E" target="_blank" class=
+                "fs14"><small>trans eQTLs</small></a> on Chr 2 between 100 and 105 Mb with LRS
+                scores between 9 and 999.</li>
+              </ul>
+            </td><!-- END OF FIND SELECTOR PULL-DOWN PANEL (LEFT SIDE)  -->
+            <!-- START OF TOP RIGHT PANEL  -->
+
+            <td valign="top" width="40%" bgcolor="#FFFFFF">
+              <p style="font-size:15px;font-family:verdana;color:black"><b>Websites Affiliated with
+              GeneNetwork</b></p>
+
+              <p style="font-size:12px;font-family:verdana;color:black"></p>
+
+              <ul>
+                <li><a href="http://ucscbrowser.genenetwork.org/" target="_blank">Genome
+                Browser</a> at UTHSC</li>
+
+                <li><a href="http://galaxy.genenetwork.org/" target="_blank">Galaxy</a> at
+                UTHSC</li>
+
+                <li>GeneNetwork at <a href="http://ec2.genenetwork.org/" target="_blank">Amazon
+                Cloud (EC2)</a></li>
+
+                <li>GeneNetwork Source Codes at <a href=
+                "http://sourceforge.net/projects/genenetwork/" target="_blank">SourceForge</a></li>
+
+                <li>GeneNetwork Source Codes at <a href=
+                "https://github.com/genenetwork/genenetwork" target="_blank">GitHub</a></li>
+              </ul>
+
+              <p>____________________________</p>
+
+              <p style="font-size:15px;font-family:verdana;color:black"><b>Getting Started</b>
+              &nbsp;&nbsp;</p>
+
+              <ol style="font-size:12px;font-family:verdana;color:black">
+                <li>Select <b>Species</b> (or select All)</li>
+
+                <li>Select <b>Group</b> (a specific sample)</li>
+
+                <li>Select <b>Type</b> of data:
+
+                  <ul>
+                    <li>Phenotype (traits)</li>
+
+                    <li>Genotype (markers)</li>
+
+                    <li>Expression (mRNAs)</li>
+                  </ul>
+                </li>
+
+                <li>Select a <b>Database</b></li>
+
+                <li>Enter search terms in the <b>Get Any</b> or <b>Combined</b> field: words,
+                genes, ID numbers, probes, advanced search commands</li>
+
+                <li>Click on the <b>Search</b> button</li>
+
+                <li>Optional: Use the <b>Make Default</b> button to save your preferences</li>
+              </ol>
+
+              <p>____________________________</p>
+
+              <p style="font-size:14px;font-family:verdana;color:black"><b>How to Use
+              GeneNetwork</b></p>
+
+              <blockquote>
+                <p style="font-size:12px;font-family:verdana;color:black">Take a 20-40 minute
+                GeneNetwork <a href="http://www.genenetwork.org/tutorial/WebQTLTour/" target=
+                "_blank" class="fs14"><small>Tour</small></a> that includes screen shots and
+                typical steps in the analysis.</p>
+              </blockquote>
+
+              <blockquote>
+                <p style="font-size:12px;font-family:verdana;color:black">For information about
+                resources and methods, select the <img src=
+                "http://www.genenetwork.org/images/upload/Info.png" alt="INFO" border="0" valign=
+                "middle"> buttons.</p>
+
+                <p style="font-size:12px;font-family:verdana;color:black">Try the <a href=
+                "http://alexandria.uthsc.edu/" target="_blank" class=
+                "fs14"><small>Workstation</small></a> site to explore data and features that are
+                being implemented.</p>
+
+                <p style="font-size:12px;font-family:verdana;color:black">Review the <a href=
+                "/conditionsofUse.html" target="_blank" class="fs14"><small>Conditions</small></a>
+                and <a href="/statusandContact.html" target="_blank" class=
+                "fs14"><small>Contacts</small></a> pages for information on the status of data sets
+                and advice on their use and citation.</p>
+              </blockquote>
+
+              <p style="font-size:14px;font-family:verdana;color:black"><b>Mirror and Development
+              Sites</b></p>
+
+              <ul>
+                <li><a href="http://www.genenetwork.org/" target="_blank" style=
+                "font-size:12px;font-family:verdana;color:blue">Main GN site at UTHSC</a> (main
+                site)</li>
+
+                <li><a href="http://www.genenetwork.waimr.uwa.edu.au/" target="_blank" style=
+                "font-size:12px;font-family:verdana;color:blue">Australia at the UWA</a></li>
+
+                <li><a href="http://gn.genetics.ucla.edu/" target="_blank" style=
+                "font-size:12px;font-family:verdana;color:blue">California at UCLA</a></li>
+
+                <li><a href="http://genenetwork.helmholtz-hzi.de/" target="_blank" style=
+                "font-size:12px;font-family:verdana;color:blue">Germany at the HZI</a></li>
+
+                <li><a href="https://genenetwork.hubrecht.eu/" target="_blank" style=
+                "font-size:12px;font-family:verdana;color:blue">Netherlands at the Hubrecht</a>
+                (Development)</li>
+
+                <li><a href="http://genenetwork.memphis.edu/" target="_blank" style=
+                "font-size:12px;font-family:verdana;color:blue">Memphis at the U of M</a></li>
+
+                <li><a href="http://webqtl.bic.nus.edu.sg/" target="_blank" style=
+                "font-size:12px;font-family:verdana;color:blue">Singapore at the NUS</a></li>
+
+                <li><a href="http://genenetwork.epfl.ch/" target="_blank" style=
+                "font-size:12px;font-family:verdana;color:blue">Switzerland at the EPFL</a></li>
+              </ul>
+
+              <p style="font-size:14px;font-family:verdana;color:black"><b>History and
+              Archive</b></p>
+
+              <blockquote>
+                <p style="font-size:12px;font-family:verdana;color:black">GeneNetwork's <a href=
+                "http://artemis.uthsc.edu" target="_blank" class="fs14"><small>Time
+                Machine</small></a> links to earlier versions that correspond to specific
+                publication dates.</p>
+              </blockquote>
+            </td>
+          </tr>
+        </table>
+      </td>
+    </tr>
+    <!-- End of body -->
+    <script src="/javascript/searchtip.js" type="text/javascript">
+    </script>
+    <script type="text/javascript">
+      $(document).ready(function () {
+                initialDatasetSelection();
+        });
+    </script>
+{% endblock %}
+
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index d639ed07..629a5b15 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -33,13 +33,6 @@ def index_page():
     print("Sending index_page")
     return render_template("index_page.html")
 
-
-@app.route("/new")
-def new_index_page():
-    print("Sending index_page")
-
-    return render_template("new_index_page.html")
-
 @app.route("/data_sharing")
 def data_sharing_page():
     print("In data_sharing")