Along with xrate's annotation and training functionality, it provides web access to grammar state diagrams and substitution matrix bubbleplots.
Downloading the source code
The xREI source code is available from our anonymous cvs, to download use:
cvs -z3 -d:ext:email@example.com:/usr/local/cvs co xrei cvs -z3 -d:ext:firstname.lastname@example.org:/usr/local/cvs co xrei-scripts
xrei-scriptscontains the perl scripts which serve as xREI's backend.
Browsing the source code
Browse the source code repositories here:
The following notes are from experience configuring xREI under OS X and Debian Linux. ymmv under other OSes. These instructions presume that Apache2 and Perl5 are installed and functional on your system.
Before installing xREI, the following software packages should be installed, preferably via apt-get, rpm, macports or similar:
TeXLive 2007or equiv (note: the macports version under os x never worked for me, I recommend MacTeX)
TeX, dot and neato from
GraphVizand convert from
In addition xREI will require the following perl modules be installed:
xREI also requires DART.
Your sites-available/default or httpd.conf file should be modified to include a section that looks something like this:
<Directory "/var/www/xrei-scripts"> Options +ExecCGI [[Add Handler]] cgi-script .cgi .pl [[Set Env]] PERL5LIB /usr/local/biowiki/dart/perl [[Set Env]] MPINPUTS /usr/share/texmf-texlive/metapost/base </Directory>
xREI ConfigurationxREI expects xrei-scripts to live in
../xrei-scriptsby default, and for xrei.json to be in the same directory as
index.html. These can both be modified in the
xrei-vizrates.plexpects a directory
xrei-scriptsit can write
PostScriptfiles to. This directory should be cleaned out regularly with a cronjob. Once a night to once a week should be frequent enough, depending on use.
xrei.jsondefines the repositories that will be available to xREI, and is in a JSON format. An example configuration is included with xREI, including the directories containing xrate grammar files.
A quick tutorial on writing AJAX wrappers to Unix command-line tools can be found here: Dojo Perl Tutorial
- Barquist & Holmes: xREI: a phylo-grammar visualization webserver. Nucleic Acids Res. 2008;36:W65-9.
- Bendaña & Holmes: Colorstock, SScolor, Ratón: RNA alignment visualization tools. Bioinformatics 2008;24:579-80.
HistoryxREI development began during the 2007 Google Summer of Code, sponsored by NESCent. The original
SoCideas page can be found here.
-- Lars Barquist - 29 Feb 2008