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diff --git a/web/webqtl/maintainance/updateMenuJS.py b/web/webqtl/maintainance/updateMenuJS.py
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+# 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
+# as published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+# See the GNU Affero General Public License for more details.
+#
+# This program is available from Source Forge: at GeneNetwork Project
+# (sourceforge.net/projects/genenetwork/).
+#
+# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
+# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
+#
+#
+#
+# This module is used by GeneNetwork project (www.genenetwork.org)
+#
+# Created by GeneNetwork Core Team 2010/08/10
+#
+# created by Lei Yan 02/08/2011
+import sys, os
+import MySQLdb
+import string
+
+
+
+abs_path = os.path.abspath(os.path.dirname(__file__))
+path1 = abs_path + "/.."
+path2 = abs_path + "/../../javascript"
+sys.path.insert(0, path1)
+
+#must import GN python files after add path
+from base import webqtlConfig
+
+# build MySql database connection
+con = MySQLdb.Connect(db=webqtlConfig.DB_NAME, host=webqtlConfig.MYSQL_SERVER, user=webqtlConfig.DB_USER, passwd=webqtlConfig.DB_PASSWD)
+cursor = con.cursor()
+cursor.execute("SELECT id,menuname FROM Species ORDER BY OrderId")
+results = list(cursor.fetchall())
+collectionsText = ""
+for result in results:
+ specieid = result[0]
+ speciename = result[1]
+ collectionsText += ("['" + speciename + "', ")
+ collectionsText += ("null, ")
+ collectionsText += ("null, ")
+ collectionsText += "\n"
+ cursor.execute("select name from InbredSet where speciesid=" + str(specieid))
+ results2 = list(cursor.fetchall())
+ for result2 in results2:
+ inbredsetName = result2[0]
+ if not cmp(inbredsetName, "BXD300"):
+ continue
+ collectionsText += "\t"
+ collectionsText += ("['" + inbredsetName + "', ")
+ collectionsText += ("'/webqtl/main.py?FormID=dispSelection&RISet=" + inbredsetName + "'], ")
+ collectionsText += "\n"
+ collectionsText += "],"
+ collectionsText += "\n"
+collectionsText = collectionsText.strip()
+
+jstext = """/*
+ --- menu items ---
+ note that this structure has changed its format since previous version.
+ additional third parameter is added for item scope settings.
+ Now this structure is compatible with Tigra Menu GOLD.
+ Format description can be found in product documentation.
+*/
+var MENU_ITEMS = [
+ ['menu_grp1', null, null,
+ ['GeneNetwork Intro', '/home.html'],
+ ['Enter Trait Data', '/webqtl/main.py?FormID=submitSingleTrait'],
+ ['Batch Submission', '/webqtl/main.py?FormID=batSubmit'],
+ ],
+ ['menu_grp2', null, null,
+ ['Search Databases', '/'],
+ ['Tissue Correlation', '/webqtl/main.py?FormID=tissueCorrelation'],
+ ['SNP Browser', '/webqtl/main.py?FormID=snpBrowser'],
+ ['Gene Wiki', '/webqtl/main.py?FormID=geneWiki'],
+ ['Interval Analyst', '/webqtl/main.py?FormID=intervalAnalyst'],
+ ['QTLminer', '/webqtl/main.py?FormID=qtlminer'],
+ ['GenomeGraph', '/dbResults.html'],
+ ['Trait Collections',null,null,
+%s
+ ],
+ ['Scriptable Interface', '/CGIDoc.html'],
+ /* ['Simple Query Interface', '/GUI.html'], */
+ ['Database Information',null,null,
+ ['Database Schema', '/webqtl/main.py?FormID=schemaShowPage'],
+ ],
+ ['Data Sharing', '/webqtl/main.py?FormID=sharing'],
+ ['Microarray Annotations', '/webqtl/main.py?FormID=annotation'],
+ ],
+ ['menu_grp3', null, null,
+ ['Movies','http://www.genenetwork.org/tutorial/movies'],
+ ['Tutorials', null, null,
+ ['GN Barley Tutorial','/tutorial/pdf/GN_Barley_Tutorial.pdf'],
+ ['GN Powerpoint', '/tutorial/ppt/index.html']],
+ ['HTML Tour','/tutorial/WebQTLTour/'],
+ ['FAQ','/faq.html'],
+ ['Glossary of Terms','/glossary.html'],
+ ['GN MediaWiki','http://wiki.genenetwork.org/'],
+ ],
+ ['menu_grp4', '/whats_new.html'
+ ],
+ ['menu_grp5', '/reference.html'
+ ],
+ ['menu_grp6', null, null,
+ ['Conditions and Limitation', '/conditionsofUse.html'],
+ ['Data Sharing Policy', '/dataSharing.html'],
+ ['Status and Contacts', '/statusandContact.html'],
+ ['Privacy Policy', '/privacy.html'],
+ ],
+ ['menu_grp8', '/links.html'
+ ],
+];
+"""
+
+# create menu_items.js file
+fileHandler = open(path2 + '/menu_items.js', 'w')
+fileHandler.write(jstext % collectionsText)
+fileHandler.close()