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wormbase.conf
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######################################################
#
# WormBase Default Configuration
#
# This file contains defaults for the WormBase application.
# It should not be edited. Should you wish to over-ride any
# variables, provide them in a local configuration file
# according to the following rules.
#
# Configuration file precedence (highest to lowest)
#
# 1. Via environment variable provided on the command line
# or in the script/wormbase-init.sh script. For example, the following
# command will load $approot/wormbase_staging.conf with the highest
# precedence.
#
# CATALYST_CONFIG_LOCAL_SUFFIX=staging ./script/wormbase_server.pl -p 8000
#
# 2. Alternatively, provide a local configuration file
# $approot/wormbase_local.conf
#
# 3. This file:
# $approot/wormbase.conf
#
######################################################
######################################################
#
# General
#
######################################################
site_name = WormBase
site_byline = Nematode Information Resource
# Are we a (development|mirror|local|production) site?
# Used to determine whcih javascript to use.
installation_type = development
# Version information
version = 0.02
perl_version = 5.010000
codename = Saag Paneer
# For providing Google maps on strain pages
google_api_key = ABQIAAAAX6AZGEUlM28m4mzs0PsGkhRVfLFVmRFz44kSxZwC_XT2TLrxixTVyjZlGBxla25vFXfsh17xrvYj0g
# These all need to be reset and moved outside of version control
facebook_secret_key = a7c919f6d562e140cb6baebe8c7e4a80
facebook_app_id = 145770318837275
twitter_consumer_key = dORNthy42qJmltFfBEplQ
twitter_consumer_secret = ZT89nA5lmc3hGSre14dHSGCcciEPFpOWwCabaM8VUE
# Datomic to catayl location
# rest_server = "http://rest-dev.wormbase.org" # alias for stable development instance
# rest_server = "http://10.0.0.243:3000" # stable development instance (AWS private IP)
# rest_server = "http://54.152.75.107:3000" # stable development instance (AWS public IP)
# rest_server = "http://rest.wormbase.org" # production instance
rest_server = "http://wormbase-rest-ws277.us-east-1.elasticbeanstalk.com" # production instance (probably over AWS public IP) # this value can be overriden in the wormbase_staging.conf
# new search API endpoint
search_server = "http://wormbase-search-ws277.us-east-1.elasticbeanstalk.com"
# max ratio of traffic to divert to new search API (the remainig will go to Xapian)
max_ratio_elasticsearch_traffic = 0.3 # maybe overwritten in wormbase_staging.conf
# cached_rest_endpoints_expires_in = 20160 # minutes, for pre-caching
cached_rest_endpoints_expires_in = 5 # minutes, for production
precache_mode = 0 # turn this on during pre-caching step only
#intermine
intermine_server = "http://intermine.wormbase.org"
# This is the site-wide (dismissable) system message.
# The id is used to make sure a new message won't be hidden
<system_message>
message = "Welcome to WormBase - <a target=\"_blank\" href=\"/tools/support\">need help</a>?"
id = 6
</system_message>
survey_link = "http://www.wormbase.org"
# enable_ssl = 1;
# secure_uri_for will return the uri with the scheme https
# enable_ssl = 0;
# secure_uri_for will return the results of uri_for
enable_ssl = 0
# Are we using a front end proxy in front of our server?
# At WormBase, typically we are (except when running the Catalyst server itself)
using_frontend_proxy = 1
# BASE URL: Not required for default installations
# base = http://www.wormbase.org/
# For posting issues to github -
github_repo = "wormbase/website"
github_api_base = "http://upstream-proxy:3001" # go through the proxy via http, due to intermittent failure with https in starman running inside docker container
# uncomment this to activate WormMine
# Note: This will break log in functionality if WormMine is not running at this path:
wormmine_path = "tools/wormmine"
wormbase_release = "WS277"
parasite_release = "WBPS11" #override in lib/WormBase/Web.pm
shared_content_dir = "/usr/local/wormbase/website-shared-files/html"
######################################################
#
# Debugging
#
######################################################
# debug: enable system-wide debugging; expects boolean
debug = 0
# debug_view: style of the view debugging. Off by default
# unless "debug" is set above and debug_view set to
# one of
# comment - send debugging statements as HTML comments
# browser - send debugging statements in formatted divs
# log - send to the error log file
debug_view =
# Enable fatal data stucture compliance. Rendering of
# widgets will fail if this is set to a true value.
fatal_non_compliance = 0
######################################################
#
# User Interface
#
######################################################
# Widget timing information.
# Enable display of timing, back end server,
# and cache information. You must also be an
# administrator. Uncommenting disables BOTH
# the collection and display of this information.
timer = 0
# Configuration of R visualization (barcharts, boxplots, other charts)
# FPKM Expression Chart (Gene page, Expression widget)
fpkm_expression_chart_xlabel = Measurement
fpkm_expression_chart_ylabel = FPKM
fpkm_expression_chart_width = 1280
fpkm_expression_chart_height = 1900
fpkm_expression_chart_height_shorter_if_less_than_X_facets = 4
fpkm_expression_chart_rotate = 1
fpkm_expression_chart_bw = 1
fpkm_expression_chart_facets = 1
########################################################
#
# FILE PATHS
#
########################################################
gbrowse_conf_dir = __path_to(conf)__/gbrowse
tmp_img_base = /tmp
# Where static movies live on the file system
static_movie_base = http://www.wormbase.org/img-static/movies/
# Where static images (such as the expression renders) live on the file system
# Note: This path served by Static::Simple as specified in Web.pm.
shared_html_base = /usr/local/wormbase/website-shared-files/html
# image_base_classic = /usr/local/wormbase/website-shared-files/html/images-website-classic
########################################################
#
# Cache
#
########################################################
<cache>
enabled 0
default couchdb
<couchdb>
enabled 0
# server 127.0.0.1:5984 # defaults
# The production couchdb is located at
# server couchdb.wormbase.org:443 # defaults
# Set this in your wormbase_local.conf if you'd like to use it.
# Note that you MUST specify the port even though it's on 80.
</couchdb>
<memcached>
enabled 0 # not used in code right now
expires 4 weeks
server 206.108.125.168:11211
server 206.108.125.175:11211
server 206.108.125.177:11211
server 206.108.125.178:11211
server 206.108.125.190:11211
</memcached>
<filecache>
enabled 0
root __path_to(root)__/tmp/cache
</filecache>
</cache>
########################################################
#
# EMAILS
#
########################################################
# Issue tracking and reporting
issue_email = [email protected]
# Registering a new account
register_email = [email protected]
# For sending emails
no_reply = [email protected]
########################################################
#
# GBrowse
#
########################################################
# Sets a redirect within Catalyst to GBrowse. Also needs
# the "genome" tool uncommented below.
#
# For example, when you want to redirect
# http://dev.wormbase.org:4455/tools/genome/gbrowse/c_elegans
# to
# http://dev.wormbase.org:4466/cgi-bin/gb2/gbrowse/c_elegans
# then set
# gbrowse_base_uri = http://dev.wormbase.org:4466/cgi-bin/gb2/gbrowse
#
# No trailing "/" character permitted.
gbrowse_base_uri = http://dev.wormbase.org:10006/tools/genome/gbrowse
<WormBase::Web::Controller::GBrowse>
cgi_root_path test
cgi_dir cgi-bin/gb2
# cgi_chain_root /optional/private/path/to/Chained/root
# cgi_file_pattern *
# or regex
cgi_file_pattern /gbrowse/
<CGI>
# username_field username # used for REMOTE_USER env var
pass_env PERL5LIB
pass_env PATH
pass_env /^WORMBASE_/
pass_env GB_HOME
# pass_env GBROWSE_CONF
</CGI>
</WormBase::Web::Controller::GBrowse>
########################################################
#
# API & REST CONFIGURATION
# Should probably be Controller::REST
#
########################################################
<api>
<content_type>
application/json = json
text/xml = xml
text/x-yaml = yml
text/html = html
text/csv = csv
</content_type>
</api>
########################################################
# Authentication&Authorization: Configuration in Web.pm
########################################################
#<authentication>
# default_realm = members
# <realms>
# <members>
# <credential>
# </credential>
# <store>
# class = DBIx::Class
# user_model = Schema::User
# role_relation = roles
# role_field = role
# #ignore_fields_in_find = remote_name
# #use_userdata_from_session = 1,
# </store>
# </members>
# <openid>
# <credential>
# class = OpenID
# ua_class = LWP::UserAgent
# <extensions>
# http://openid.net/extensions/sreg/1.1
# required = email
# optional = fullname nickname timezone
# </extensions>
# </credential>
# </openid>
# </realms>
#</authentication>
<Model::Schema>
schema_class = WormBase::Schema
<connect_info>
# dsn = dbi:mysql:wormbase_user:hostname=localhost
# user = wormbase
# password =
# You can find production here although you won't
# be able to access it unless specifically granted
# permissions.
dsn = dbi:mysql:wormbase_user:hostname=mysql.wormbase.org
user = wormbase
password = sea3l3ganz
</connect_info>
</Model::Schema>
password_reset_expires = 86400 # 24 hours
<Model::Mendeley>
<args>
consumer_key = f67b2a45de14e07cc9658f779dd22a5804d32335b
consumer_secret = 1bd1255a50325e72840d33ae8decac11
authorization_url = http://api.mendeley.com/oauth/authorize/
request_token_url = http://api.mendeley.com/oauth/request_token/
access_token_url = http://api.mendeley.com/oauth/access_token/
</args>
</Model::Mendeley>
########################################################
#
# Database Locations and Authorization
#
# By default, we use remote data sources for
# convenience but expect this to be overriden
# by the wormbase_local.conf.
#
########################################################
<Model::WormBaseAPI>
class = WormBase::API
<args>
<pre_compile>
base = /usr/local/wormbase/databases
gene = /gene
position_matrix = /position_matrix
# These are all old precompiled files from CompileGeneResources. None are
# in use any longer
# rnai_details_file = rnai_data.txt
# gene_rnai_phene_file = gene_rnai_pheno.txt
# gene_variation_phene_file = variation_data.txt
# phenotype_name_file = phenotype_id2name.txt
# gene_xgene_phene_file = gene_xgene_pheno.txt
pm_id2consensus_seq_file = pm_id2consensus_seq.txt
pm_id2source_pm_file = pm_id2source_pm.txt
image_file_base = ${shared_html_base}
gene_expression_path = /img-static/virtualworm/Gene_Expr_Renders
expression_object_path = /img-static/virtualworm/Expr_Object_Renders
picture = /img-static/pictures
</pre_compile>
conf_dir = __path_to(conf)__/
# Temporary directory in filesystem space
# tmp_base = __path_to(root)__/tmp/
# tmp_base = /tmp/wormbase/
# In production, this is an nfs mount
tmp_base = /usr/local/wormbase/tmp
#different tools WB provides
<tool>
<blast_blat>
base = /usr/local/wormbase/databases
blast = /blast
blat = /blat
SCORE_KEY_IMAGE = score_key.png
HSP_GENOME_LINK_PART_LIMIT = 10
HSP_ALIGNMENT_IMAGE_LIMIT = 10
BLAST_EXEC_DIR = /usr/local/wormbase/services/blast
BLAT_CLIENT = /usr/local/wormbase/services/blat/bin/blat
#BLAT_CLIENT = /usr/local/wormbase/services/blat/bin/gfClient
</blast_blat>
epic
epcr
# The 'genome' tools is used in conjunction with the 'gbrowse_base_uri' setting. More details there.
# genome
gmap
# nearby_genes
nucleotide_aligner
protein_aligner
tree
rnaseq_plot
schema
queries
<ontology_browser>
association_count_file = /usr/local/wormbase/databases/%s/ontology/%s_association.%s.wb
</ontology_browser>
<print>
PRO_EXEC = ./CutyCapt
</print>
</tool>
<database>
# tmp directory for sockets and lock files.
# This *must* be distinct from above since
# to prevent collisions of lock files in production.
tmp = /tmp/wormbase/
<acedb>
# Acedb configuration
delay = 600
reconnect = 5
# host = localhost mining.wormbase.org
host = localhost
port = 2005
user =
pass =
root = /usr/local/wormbase/acedb/wormbase
# cache_root = __path_to(root)__/cache
# cache_expires = 3 weeks
# cache_size = 100000000
# cache_auto_purge_interval =
</acedb>
<mysql>
delay = 600
reconnect = 3
host = rdbms.wormbase.org
# host = 10.0.0.181
user = wormbase
pass = sea3l3ganz
<data_sources>
clustal = 1
</data_sources>
</mysql>
<gff>
# MySQL configuration
delay = 600
reconnect = 3
# TODO: remove localhost when databases get copied over
host = rdbms.wormbase.org
# host = 10.0.0.181
user = wormbase
pass = sea3l3ganz
<data_sources>
<b_malayi>
adaptor = DBI::mysql
bioproject = PRJNA10729
</b_malayi>
<c_angaria>
adaptor = DBI::mysql
bioproject = PRJNA51225
</c_angaria>
<c_brenneri>
adaptor = DBI::mysql
bioproject = PRJNA20035
</c_brenneri>
<c_briggsae>
adaptor = DBI::mysql
bioproject = PRJNA10731
</c_briggsae>
<c_elegans>
adaptor = DBI::mysql
bioproject = PRJNA13758
</c_elegans>
<c_elegans_pmap>
adaptor = DBI::mysql
</c_elegans_pmap>
<c_elegans_gmap>
adaptor = DBI::mysql
</c_elegans_gmap>
<c_inopinata>
adaptor = DBI::mysql
bioproject = PRJDB5687
</c_inopinata>
<c_japonica>
adaptor = DBI::mysql
bioproject = PRJNA12591
</c_japonica>
<c_latens>
adaptor = DBI::mysql
bioproject = PRJNA248912
</c_latens>
<c_nigoni>
adaptor = DBI::mysql
bioproject = PRJNA384657
</c_nigoni>
<c_remanei>
adaptor = DBI::mysql
bioproject = PRJNA53967
</c_remanei>
<c_tropicalis>
adaptor = DBI::mysql
bioproject = PRJNA53597
</c_tropicalis>
<o_tipulae>
adaptor = DBI::mysql
bioproject = PRJEB15512
</o_tipulae>
<o_volvulus>
adaptor = DBI::mysql
bioproject = PRJEB513
</o_volvulus>
<p_pacificus>
adaptor = DBI::mysql
bioproject = PRJNA12644
</p_pacificus>
<p_redivivus>
adaptor = DBI::mysql
bioproject = PRJNA186477
</p_redivivus>
<s_ratti>
adaptor = DBI::mysql
bioproject = PRJEB125
</s_ratti>
<t_muris>
adaptor = DBI::mysql
bioproject = PRJEB126
</t_muris>
</data_sources>
</gff>
</database>
</args>
</Model::WormBaseAPI>
########################################################
#
#
# Plugins
#
#
############################################################
# Error reporting disabled automatically on
# instances with installation_type=development
<stacktrace>
enable 1
</stacktrace>
<Plugin::ErrorCatcher>
enable 1
context 2
</Plugin::ErrorCatcher>
<Plugin::ErrorCatcher::Email>
from [email protected]
use_tags 1
subject [WB] App error on %h in %F
</Plugin::ErrorCatcher::Email>
# Session database
#<Plugin::Session>
# expires = 3600
# dbi_dbh = Schema
# dbi_table = sessions
# dbi_id_field = session_id
# dbi_data_field = session_data
# dbi_expires_field = expires
#</Plugin::Session>
# Which hash elements of the data structure to return in JSON renders?
<View::JSON>
expose_stash = data
</View::JSON>
########################################################
#
#
# NAVBAR configuration
#
#
############################################################
<nav_bar>
<option>
id = about
title = About
url = /about\#01--10
description = WormBase is an international consortium of biologists and computer scientists
<nav_item>
id = general
title = General
<nav_item>
title = Mission Statement
url = /about\#0--10
</nav_item>
<nav_item>
title = Publications
</nav_item>
<nav_item>
title = FAQ
url = /about/Frequently_asked_questions
</nav_item>
</nav_item>
<nav_item>
id = people
title = People
<nav_item>
title = Advisory Board
url = /about/advisory_board
</nav_item>
<nav_item>
title = WormBase Staff
url = /about/staff\#01--10
</nav_item>
</nav_item>
<nav_item>
id = whats_new
title = What's New
<nav_item>
title = News (Blog)
url = http://blog.wormbase.org/
</nav_item>
<nav_item>
title = Release notes
url = /about/wormbase_release_current
</nav_item>
<nav_item>
title = Release Schedule
url = /about/release_schedule
</nav_item>
<nav_item>
title = Gene Name Changes
url = /\#012-34-5
</nav_item>
</nav_item>
<more>
<nav_item>
title = Want to know more about worm research?
<nav_item>
title = Caenorhabditis Genetics Center (CGC)
url = http://cbs.umn.edu/cgc/home
</nav_item>
<nav_item>
title = NEMABASE
url = http://www.ipm.ucdavis.edu/NEMABASE/
</nav_item>
<nav_item>
title = Nematode.net
url = http://nematode.net/NN3_frontpage.cgi
</nav_item>
<nav_item>
title = Nematodes.org
url = http://www.nematodes.org/
</nav_item>
<nav_item>
title = WormAtlas
url = http://www.wormatlas.org/
</nav_item>
<nav_item>
title = WormBook
url = http://www.wormbook.org/
</nav_item>
</nav_item>
</more>
</option>
<option>
id = directory
title = Directory
url = /search
description = Start here to access encyclopedic information about the worm genome and its genes, proteins, and other encoded features
<nav_item>
id = get_started
title = Get Started
<nav_item>
title = About the directory
url = /species/all\#0123--10
</nav_item>
</nav_item>
<nav_item>
id = search
title = Search
<nav_item>
title = Basic Search
url = /search/gene/
</nav_item>
<nav_item>
title = Advanced Search
url = /tools/queries
</nav_item>
</nav_item>
<nav_item>
id = browse
title = Browse
<nav_item>
id = by_species
title = By Species
url = /species/all\#0123--10
<nav_item>
species = c_elegans
</nav_item>
<nav_item>
species = b_malayi
</nav_item>
<nav_item>
species = c_brenneri
</nav_item>
<nav_item>
species = c_briggsae
</nav_item>
<nav_item>
species = c_japonica
</nav_item>
<nav_item>
species = c_remanei
</nav_item>
<nav_item>
species = o_volvulus
</nav_item>
<nav_item>
species = p_pacificus
</nav_item>
<nav_item>
species = s_ratti
</nav_item>
<nav_item>
species = t_muris
</nav_item>
<nav_item>
title = More…
url = /species/all\#0123--10
</nav_item>
</nav_item>
<nav_item>
id = by_resource
title = By Resource
url = /resources\#0123--10
<nav_item>
title = Databases
url = /resources\#3--10
</nav_item>
<nav_item>
resource = gene_class
</nav_item>
<nav_item>
resource = laboratory
</nav_item>
<nav_item>
title = Methods
url = /resources\#2--10
</nav_item>
<nav_item>
resource = motif
</nav_item>
<nav_item>
resource = paper
</nav_item>
<nav_item>
resource = person
</nav_item>
<nav_item>
resource = wbprocess
</nav_item>
<nav_item>
resource = reagents
</nav_item>
<nav_item>
resource = transposon_family
</nav_item>
</nav_item>
</nav_item>
<nav_item>
id = tools
title = Tools
<nav_item>
title = Schema Display
url = /tools/schema
</nav_item>
<nav_item>
title = Tree Display
url = /tools/tree
</nav_item>
<nav_item>
title = Submit Data
url = /about/userguide/submit_data#01--10
</nav_item>
</nav_item>
<more>
<nav_item>
title = Latest updates
<nav_item>
title = News (Blog)
url = http://blog.wormbase.org/
</nav_item>
<nav_item>
title = Release Schedule
url = /about/release_schedule
</nav_item>
</nav_item>
<nav_item>
title = Need help?
<nav_item>
title = Nematode Nomenclature
url = /about/userguide/nomenclature
</nav_item>
<nav_item>
title = User's Guide
url = /about/userguide/for_users
</nav_item>
<nav_item>
title = FAQ
url = /about/Frequently_asked_questions
</nav_item>
<nav_item>
title = HelpDesk
url = /tools/support
</nav_item>
</nav_item>
</more>
</option>
<option>
id = tools
title = Tools
url = /tools
description = Come explore WormBase's complex collection of information with a variety of bioinformatic tools and more
<nav_item>
id = get_started
title = Get Started
<nav_item>
title = About our tools
url = /about/userguide/for_users\#1--10
</nav_item>
</nav_item>
<nav_item>
id = general_search
title = General Search
<nav_item>
title = Basic Search
url = /search/gene/
</nav_item>
<nav_item>
title = Browse by Species
url = /species/all\#0123--10
</nav_item>
<nav_item>
title = Browse by Resource
url = /resources\#0123--10
</nav_item>
<nav_item>
title = Advanced Search
url = /tools/queries
</nav_item>
</nav_item>
<nav_item>
id = by_sequence
title = By Sequence
<nav_item>
title = BLAST/BLAT
url = /tools/blast_blat
</nav_item>
<nav_item>
title = e-PCR Search
url = /tools/epcr
</nav_item>
<nav_item>
title = GBrowse
url = /tools/genome/gbrowse/
</nav_item>
<nav_item>
title = Genetic Map
url = /tools/gmap
</nav_item>
<nav_item>
title = JBrowse
url = /tools/genome/jbrowse-simple/?data=data/c_elegans_PRJNA13758
</nav_item>
<nav_item>
title = Nucleotide Aligner
url = /tools/nucleotide_aligner
</nav_item>
<nav_item>
title = Protein Aligner
url = /tools/protein_aligner
</nav_item>
<nav_item>
title = Synteny Viewer
url = /tools/synteny/mercator/
</nav_item>
</nav_item>
<nav_item>
id = by_expression
title = By Expression
<nav_item>
title = SPELL
url = https://spell.wormbase.org/
</nav_item>
<nav_item>
title = Expression Dataset Locator
url = /tools/rnaseq/expression_dataset_locator.cgi
</nav_item>
<nav_item>
title = RNA-Seq FPKM Gene Search
url = /tools/rnaseq/fpkmmine.cgi
</nav_item>
</nav_item>
<nav_item>
id = by_literature
title = By Literature
<nav_item>
title = Resources: Papers
url = /resources/paper\#1-0-2
</nav_item>
<nav_item>
title = TextPresso
url = http://www.textpresso.org/celegans/
</nav_item>
</nav_item>
<nav_item>
id = by_object
title = By Object
<nav_item>
title = Schema Display
url = /tools/schema
</nav_item>
<nav_item>
title = Tree Display
url = /tools/tree
</nav_item>
</nav_item>
<nav_item>
id = data_mining_batch_queries
title = Data Mining and Batch Queries
<nav_item>
title = ParaSite BioMart
url = http://parasite.wormbase.org/biomart/martview
</nav_item>
<nav_item>
title = SimpleMine
url = /tools/mine/simplemine.cgi
</nav_item>
<nav_item>
title = Gene Set Enrichment Analysis
url = /tools/enrichment/tea/tea.cgi
</nav_item>
<nav_item>
title = WormMine
url = http://intermine.wormbase.org/tools/wormmine/begin.do
</nav_item>
</nav_item>
<nav_item>
id = for_parasites
title = For Parasites
<nav_item>
title = ParaSite
url = http://parasite.wormbase.org
</nav_item>
<nav_item>
title = ParaSite BioMart
url = http://parasite.wormbase.org/biomart/martview
</nav_item>
</nav_item>
<nav_item>
id = for_developers
title = For Developers
<nav_item>
title = Query Language
url = /tools/queries
</nav_item>
<nav_item>
title = WormBase APIs
url = /about/userguide/for_developers\#3--10
</nav_item>
<nav_item>
title = WormBase Assembly Hubs
url = /about/userguide/wormbasehubs\#0123--10
</nav_item>
</nav_item>
<nav_item>
id = by_ontology
title = By Ontology
<nav_item>
title = Ontology Browser
url = /tools/ontology_browser
</nav_item>
<nav_item>
title = Gene-pair Ontology Graph
url = /tools/soba/soba.cgi?action=Gene+Pair+to+SObA+Graph
</nav_item>
<nav_item>
title = Terms Ontology Graph
url = /tools/soba/soba.cgi?action=Terms+to+SObA+Graph
</nav_item>
</nav_item>
<more>
<nav_item>
title = Top 3 most used tools