<commit_before><html>
<head>
<meta name="order" content="4" />
<title>Public MySQL Server</title>
</head>

<body>

<h1>The Ensembl public MySQL Servers</h1>

<p>
For large amounts of data and more detailed analysis, we recommend you
use our publicly-accessible MySQL
server, <strong>ensembldb.ensembl.org</strong>, which you can access
as user 'anonymous'. A second
server, <strong>martdb.ensembl.org</strong> provides public access to
the BioMart databases.
</p>

<p>
There are two options for retrieving data from the Ensembl databases:
</p>

<dl>

<dt>Perl API</dt>

<dd>
<p>
The easiest option is to use the
Ensembl <a href="/info/data/api.html">Perl API</a>. The API uses an
object-oriented approach to model real biological objects such as
genes, transcripts and 'slices' of DNA sequence, making it
straightforward for you to write scripts that retrieve and analyze
data.
</p>

<pre class="code">
# find gene stable ids corresponding to the MGI symbol 'Tyr' my
$gene_adaptor = $dbCore-&gt;get_GeneAdaptor(); my @genes = @{
$gene_adaptor-&gt;fetch_all_by_external_name('Tyr') };
</pre>

<p>
Additional code examples and suggestions can be found in the
various <a href="/info/website/tutorials/">API tutorials</a> and the 
<a href="http://listserver.ebi.ac.uk/mailing-lists-archives/ensembl-dev/threads.html"
rel="external">ensembl-dev mailing list archives</a>.
</p>
</dd>

<dt>MySQL client</dt>

<dd>
<p>
Alternatively, you can use a
MySQL <a href="http://dev.mysql.com/downloads/mysql/">client
program</a> to query the database directly. However this does require
knowledge of the complex <a href="/info/docs/api/">database
schemas</a> used by Ensembl, so we only recommend it if you are unable
to install our API (e.g. if you have no access to Perl). Also note
that direct MySQL queries on the database are not suited to retrieve
sequences. To retrieve sequences please use the Perl API.
</p>
</dd>

</dl>

<p>
For <strong>BioMart</strong> access, we strongly recommend that you
use the <a href="/Multi/martview">martview web interface</a>, as the
mart databases contain very many tables of denormalised data. Data can
also be retrieved from BioMart programmatically, using
the <a href="http://www.biomart.org/martservice.html">Mart XML-based
webservice</a>.
</p> 

<h2>Summary of servers and ports</h2>

<p>
<strong>Important note:</strong> Because we are serving databases on
both MySQL4 and MySQL5, not all MySQL instances use the default port;
please ensure that you specify the correct port when trying to
connect. In addition, if your computer is behind a
<strong>firewall</strong>, outgoing TCP/IP connections to the
corresponding ports need to be allowed, too. Otherwise connections
will not be established.
</p>

<table class="ss tint">

<tr>
<th>Server</th>
<th>User</th>
<th>Password</th>
<th class="center">Up to version 47</th>
<th class="center">Version 48 onwards</th>
</tr>

<tr>
<td>ensembldb.ensembl.org</td>
<td>anonymous</td>
<td>-</td>
<td class="center">3306</td>
<td class="center">5306</td>
</tr>

<tr class="bg2">
<td>martdb.ensembl.org</td>
<td>anonymous</td>
<td>-</td>
<td class="center">3316</td>
<td class="center">5316</td>
</tr>

</table>

</body>
</html><commit_msg>*** empty log message ***<commit_after><html>
<head>
<meta name="order" content="4" />
<title>Public MySQL Server</title>
</head>

<body>

<h1>The Ensembl public MySQL Servers</h1>

<p>
For large amounts of data and more detailed analysis, we recommend you
use one of our publicly-accessible MySQL
servers <strong>ensembldb.ensembl.org</strong> or <strong>useastdb.ensembl.org</strong> which you can access
as user 'anonymous'. A third 
server, <strong>martdb.ensembl.org</strong> provides public access to
the BioMart databases.
</p>

<p>
There are two options for retrieving data from the Ensembl databases:
</p>

<dl>

<dt>Perl API</dt>

<dd>
<p>
The easiest option is to use the
Ensembl <a href="/info/data/api.html">Perl API</a>. The API uses an
object-oriented approach to model real biological objects such as
genes, transcripts and 'slices' of DNA sequence, making it
straightforward for you to write scripts that retrieve and analyze
data.
</p>

<pre class="code">
# find gene stable ids corresponding to the MGI symbol 'Tyr' my
$gene_adaptor = $dbCore-&gt;get_GeneAdaptor(); my @genes = @{
$gene_adaptor-&gt;fetch_all_by_external_name('Tyr') };
</pre>

<p>
Additional code examples and suggestions can be found in the
various <a href="/info/website/tutorials/">API tutorials</a> and the 
<a href="http://listserver.ebi.ac.uk/mailing-lists-archives/ensembl-dev/threads.html"
rel="external">ensembl-dev mailing list archives</a>.
</p>
</dd>

<dt>MySQL client</dt>

<dd>
<p>
Alternatively, you can use a
MySQL <a href="http://dev.mysql.com/downloads/mysql/">client
program</a> to query the database directly. However this does require
knowledge of the complex <a href="/info/docs/api/">database
schemas</a> used by Ensembl, so we only recommend it if you are unable
to install our API (e.g. if you have no access to Perl). Also note
that direct MySQL queries on the database are not suited to retrieve
sequences. To retrieve sequences please use the Perl API.
</p>
</dd>

</dl>

<p>
For <strong>BioMart</strong> access, we strongly recommend that you
use the <a href="/Multi/martview">martview web interface</a>, as the
mart databases contain very many tables of denormalised data. Data can
also be retrieved from BioMart programmatically, using
the <a href="http://www.biomart.org/martservice.html">Mart XML-based
webservice</a>.
</p> 

<h2>Summary of servers and ports</h2>

<p>
<strong>Important note:</strong> Because we are serving databases on
both MySQL4 and MySQL5, not all MySQL instances use the default port;
please ensure that you specify the correct port when trying to
connect. In addition, if your computer is behind a
<strong>firewall</strong>, outgoing TCP/IP connections to the
corresponding ports need to be allowed, too. Otherwise connections
will not be established.
</p>

<table class="ss tint">

<tr>
<th>Server</th>
<th>User</th>
<th>Password</th>
<th class="center">Port</th>
<th class="left">Notes</th>
</tr>

<tr>
<td>ensembldb.ensembl.org</td>
<td>anonymous</td>
<td>-</td>
<td class="center">3306</td>
<td class="left">Up to ensembl <strong>47</strong> ONLY</td>
</tr>

<tr>
<td>ensembldb.ensembl.org</td>
<td>anonymous</td>
<td>-</td>
<td class="center">5306</td>
<td class="left">From ensembl <strong>48</strong> onwards ONLY</td>
</tr>
<tr class="bg2">


<tr>
<td>useastdb.ensembl.org</td>
<td>anonymous</td>
<td>-</td>
<td class="center">5306</td>
<td class="left"><strong>Current</strong> ensembl version with <strong>Previous</strong> ensembl version ONLY</td>
</tr>

<td>martdb.ensembl.org</td>
<td>anonymous</td>
<td>-</td>
<td class="center">3316</td>
<td class="left">Up to ensembl <strong>47</strong> ONLY</td>
</tr>
<td>martdb.ensembl.org</td>
<td>anonymous</td>
<td>-</td>
<td class="center">5316</td>
<td class="left">From ensembl <strong>48</strong> onwards ONLY</td>
</tr>

</table>

</body>
</html>
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