Skip to content
Browse files

Updates for E75

  • Loading branch information...
1 parent af03d19 commit 48c81f6dc795f65e2811188f0377637967851a4f @nicklangridge nicklangridge committed Feb 24, 2014
View
4 conf/SiteDefs.pm
@@ -41,9 +41,9 @@ sub update_conf {
map {delete($SiteDefs::__species_aliases{$_}) } keys %SiteDefs::__species_aliases;
$SiteDefs::ENSEMBL_DATASETS = [];
- push (@{$SiteDefs::ENSEMBL_DATASETS}, "bacteria_$_") foreach (1..45);
+ #push (@{$SiteDefs::ENSEMBL_DATASETS}, "bacteria_$_") foreach (1..45);
- #$SiteDefs::ENSEMBL_DATASETS = ['bacteria_1', 'bacteria_10', 'bacteria_22'];
+ $SiteDefs::ENSEMBL_DATASETS = ['bacteria_1', 'bacteria_10', 'bacteria_22'];
$SiteDefs::ENSEMBL_PRIMARY_SPECIES = 'escherichia_coli_str_k_12_substr_mg1655';
$SiteDefs::__species_aliases{ 'escherichia_coli_str_k_12_substr_mg1655' } = [qw(bc)];
View
4 htdocs/components/10_SpeciesList.js
@@ -4,13 +4,11 @@ Ensembl.Panel.SpeciesList = Ensembl.Panel.extend({
init: function () {
this.base();
- var sitePrefix = $('[name="sitePrefix"]', this.el).val();
-
var ac = $("#species_autocomplete", this.el);
ac.autocomplete({
minLength: 3,
source: sitePrefix + '/Multi/Ajax/species_autocomplete',
- select: function(event, ui) { if (ui.item) Ensembl.redirect(sitePrefix + '/' + ui.item.production_name + '/Info/Index') },
+ select: function(event, ui) { if (ui.item) Ensembl.redirect('/' + ui.item.production_name + '/Info/Index') },
search: function() { ac.addClass('loading') },
response: function(event, ui) {
ac.removeClass('loading');
View
1 htdocs/index.html
@@ -14,7 +14,6 @@
<div class="plain-box access-box">
[[INCLUDE::/ssi/access.inc]]
</div>
- [[INCLUDE::/ssi/outline.inc]]
[[INCLUDE::/ssi/left_1.inc]]
[[INCLUDE::/ssi/left_2.inc]]
</div>
View
4 htdocs/ssi/about.inc
@@ -0,0 +1,4 @@
+<h2 class="first">Ensembl Bacteria</h2>
+<p>Over 6000 genome sequences from bacteria and archaea have been annotated and deposited in the public archives of the members of the <a href="http://www.insdc.org/">International Nucleotide Sequence Database Collaboration</a>. This site provides access to complete, annotated genomes from bacteria and archaea (present in the <a href="http://www.ebi.ac.uk/ena">European Nucleotide Archive</a>) through the Ensembl graphical user interface (genome browser). More details about the integration are provided <a href="/info/building/building_ensembl_bacteria.html">here</a></p>
+<p>Programmatic access is available through the Ensembl Perl and REST-ful APIs and through publicly accessible mysql databases, along with full data dumps (including DNA sequence and protein sequence in FASTA format, annotations in GTF format, and mysql dump files). Due to the large number of these databases, there is some modification to the APIs, and database and FTP site structure, compared to that used for other branches of the taxonomy (e.g. the storage of many genomes in one database; the provision of lookup services to identify genomes by INSDC identifiers, taxonomy identifiers, or partial names. <a href="/info/data/accessing_ensembl_bacteria.html">Full details are available here</a>.</p>
+<p>BioMart access is not available, but we are working on providing new, more powerful data mining tools to allow users to exploit these genomes. A selection of over 100 key bacterial genomes has been included in the pan-taxonomic Compara, and genes from all genomes are classified into families using HAMAP and PANTHER (<a href="/info/docs/compara/index.html">more details</a>)</p>
View
8 htdocs/ssi/access.inc
@@ -0,0 +1,8 @@
+<h1>Access to <b>9000</b> Bacterial Genomes</h1>
+
+<ul>
+ <li><b>Search for a gene</b> - type the name of a gene or other identifier into the search box above</li>
+ <li><b>Find a genome</b> - click in the 'browse a genome' box above and start typing your genome name to find matching genomes</li>
+ <li><a href="/info/about/species.html">View full list of all Ensembl Bacteria species</a></li>
+ <li><a href="/info/data/accessing_ensembl_bacteria.html">Access Ensembl Bacteria programmatically</a></li>
+</ul>
View
6 htdocs/ssi/advert.inc
@@ -0,0 +1,6 @@
+<h2 class="title"><img style="float: right;" alt="microme" src="/img/microme.png" height="20" width="104" />Microme Workshop on Microbial Metabolism</h2>
+<p><span class="date-display-start">Tuesday, October 8, 2013</span><span class="date-display-separator"> - </span><span class="date-display-end">Thursday, October 10, 2013</span><span class="postal-code">&nbsp;</span> at <a href="https://www.ebi.ac.uk/about/travel">EMBL-EBI</a></p>
+<p><span class="postal-code">Registration Deadline: Friday, August 9, 2013<br /></span></p>
+<p>Partners from the <a href="http://www.microme.eu/">Microme</a> project will teach in a number of practical workshop sessions aimed at guiding the participants through the complexities of networks of metabolites and biochemical pathways within the current knowledge.</p>
+<p>For more details, <a href="http://www.ebi.ac.uk/training/course/bacterial-genomics">click here</a></p>
+<h2></h2>
View
7 htdocs/ssi/microme.inc
@@ -0,0 +1,7 @@
+<p>
+ Ensembl Bacteria has been developed with the support of the <a href="http://www.microme.eu">Microme</a> project, a resource for bacterial metabolism.
+</p>
+<p>
+ <a href="http://www.microme.eu"><img align="absmiddle" src="img/microme.png" width="104" height="20" alt="" /></a>
+ <a style="padding-left:15px" href="http://cordis.europa.eu/fp7/dc/index.cfm"><img align="absmiddle" src="img/eu-fp7.png" width="87" height="30" alt="" title="Seventh Framework Programme (FP7)" /></a>
+</p>
View
13 htdocs/ssi/whatsnew.html
@@ -0,0 +1,13 @@
+<h2 class="first">What's new in release 18</h2>
+<p>
+Release 18 of Ensembl Bacteria has been loaded from EMBL-Bank release 115 into 27 multispecies Ensembl v71 databases. The current dataset contains 6,306 genomes (6,047 eubacteria and 162 archaea) containing 20,630,403 protein coding genes loaded from 508,569 INSDC entries.<ul>
+ <li>Generated stable IDs now have the prefix EB in place of ENA. The web interface provides mappings between all old and new identifiers (including pre-EG17 identifiers where available).</li>
+ <li>Issue where some assemblies consisted of annotated WGSs rather than supercontig/chromosome now addressed.</li>
+ <li>Addition of cross-references to Rhea.</li>
+</ul>
+</p>
+
+<!--
+<h3>Future Releases</h3>
+<p>Detailed notes for Release 18 of Ensembl Genomes can be found <a href="http://www.ensemblgenomes.org/info/release18" _mce_href="http://www.ensemblgenomes.org/info/release18"> here</a>.</p>
+-->
View
3,980 modules/Bio/EnsEMBL/CircularSlice.pm
0 additions, 3,980 deletions not shown because the diff is too large. Please use a local Git client to view these changes.
View
9 modules/EnsEMBL/Web/Document/HTML/GenomeCollectionsList.pm 100644 → 100755
@@ -24,11 +24,11 @@ use strict;
use warnings;
sub render {
- return sprintf( qq{
+ return qq{
<div class="home-search-flex">
<div id="species_list" class="js_panel">
<input type="hidden" class="panel_type" value="SpeciesList" />
- <input type="hidden" name="sitePrefix" value="%s" />
+ <input type="hidden" name="sitePrefix" value="" />
<h3 class="first">Search for a genome</h3>
<form id="species_autocomplete_form" action="/info/about/species.html" style="margin-bottom:5px" method="get">
<div>
@@ -39,9 +39,8 @@ sub render {
e.g. type <b>esc</b> to find Escherichia
</p>
</div>
- </div>},
- $SiteDefs::SITE_PREFIX
- );
+ </div>
+ };
}
1;

0 comments on commit 48c81f6

Please sign in to comment.
Something went wrong with that request. Please try again.