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	<li><a href="#berkeleydb">The Berkeleydb Backend</a>
	    <ol>
	      <li><a href="#bp_seqfeature_load">The bp_seqfeature_load.pl script</a>
	    </ol>
	<li><a href="#mysql">The MySQL Backend</a>
	<li><a href="#other_backends">Other Backends</a>
      </ol>
  <li><a href="#multiple_databases">Multiple Database Backends</a>
  <li><a href="#conclusion">Conclusion</a>
</ol>

<h2><a name="basics">1. The Basics</a></h2>

<p>

We will be working with simulated Volvox genome annotation data.  The
database will be named "volvox" and GBrowse will be invoked with this
URL:

<blockquote
class="example"><pre>http://localhost/cgi-bin/gbrowse2/gbrowse/volvox</pre></blockquote>

<p>

These directories contain data files used during the tutorial:

<dl>
  <dt><a href="data_files/">data_files</a>
  <dd>DNA and features files to load into the local database.
      <p>
  <dt><a href="conf_files/">conf_files</a>
  <dd>GBrowse configuration files for you to take and modify.
</dl>

<p>

To introduce you to the system we will be using a file-based database
which allows GBrowse to run directly off text files.  To prepare this
database for use, find the GBrowse databases directory which was
created in your Apache web server directory at the time of
installation.  It should be located at
<b>/var/lib/gbrowse2/databases</b>, but check to make sure.

<p>

Similarly, check that you can find the gbrowse.conf configuration
directory.  It should be located at <b>/etc/gbrowse2</b> and contain the main
configuration file "GBrowse.conf" and the example yeast genome
datasource file "yeast_simple.conf" (among several others).

<p>

Now you will change the permissions of the database and configuration
directories so that you can write to them without root privileges.
This is only an issue on Unix systems, and Windows users can safely
ignore this step.

<blockquote class="example"><pre>
% <b>su</b>
Password: <b>*********</b>
# <b>chown my_user_name /var/lib/gbrowse2/databases</b>
# <b>chown my_user_name /etc/gbrowse2</b>
# <b>exit</b>
%
</pre></blockquote>

<p>

(Be sure to replace "my_user_name" with your login name!)

<p>

Now look around inside the databases directory.  There should be a
single subdirectory named "yeast_chr1+2". The yeast subdirectory is
where the example yeast chromosomes 1 and 2 data set is stored.

<p>

You will create an empty volvox subdirectory, and make it world
writable.  On Unix systems:

<blockquote class="example"><pre>
% <b>cd /var/lib/gbrowse2/databases</b>
% <b>mkdir volvox</b>
% <b>chmod go+rwx volvox</b>
</pre></blockquote>

<p>

<blockquote> <i>NOTE: The "%" sign in these examples is the
command-line prompt.  On Windows systems, the command-line prompt is
something like C:\Program Files\Apache
Group\Apache2\htdocs\databases&gt;.  Unix systems are more
variable, but the prompt usually ends with a "%" or a "#".  In all the
examples in this tutorial, what you type is rendered in
<b>boldface</b>, while prompts and command-line results are shown in
medium typeface.</i> </blockquote>

<p>

On Windows systems, use the file manager ("Explorer") to create a new
folder named "volvox."  If you are using Windows NT, 2000 or XP, right
click on the new folder and grant write privileges to all.

<p>

You'll now put the first of several data files into the volvox
database directory.  In the <a href="data_files/">data_files</a>
subdirectory of this tutorial you will find the file <a
href="data_files/volvox_remarks.gff3">volvox_remarks.gff3</a>.  Copy this into the
volvox database directory.  On Unix systems:

<blockquote class="example">
<pre>
% <b>cd /var/www/gbrowse2</b>
% <b>cp tutorial/data_files/volvox_remarks.gff3 /var/lib/gbrowse2/databases/volvox</b>
</pre>
</blockquote>

<p>

On Windows systems, use Explorer to copy the file into the volvox