Xrei Program

xREI

xREI (pron. "X-ray") is an AJAX web interface and visualization server for xrate and its grammar files.

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:anonymous@cvs.biowiki.org:/usr/local/cvs co xrei
cvs -z3 -d:ext:anonymous@cvs.biowiki.org:/usr/local/cvs co xrei-scripts

xrei

contains the javascript and html interface files, while

xrei-scripts

contains the perl scripts which serve as xREI's backend.

Browsing the source code

Browse the source code repositories here:

• BiowikiCvsDir:xrei
• BiowikiCvsDir:xrei-scripts

Installation notes

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.

Dependencies

Before installing xREI, the following software packages should be installed, preferably via apt-get, rpm, macports or similar:

• TeXLive 2007

  or equiv (note: the macports version under os x never worked for me, I recommend MacTeX)

• ImageMagick

• GraphViz

All executables should be installed within the root/default path, /usr/bin or /usr/local/bin are usually good choices under linux. By default, macports under OS X will require that you add /opt/local/bin to your path. xREI uses mpost, dvips, and latex from

TeX

, dot and neato from

GraphViz

and convert from

ImageMagick

.

In addition xREI will require the following perl modules be installed:

• GraphViz

• MIME::Base64
• JSON::Any

xREI also requires DART.

Apache Configuration

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 Configuration

xREI expects xrei-scripts to live in

../xrei-scripts

by default, and for xrei.json to be in the same directory as

index.html

. These can both be modified in the

init

function in

index.html

.

xrei-vizrates.pl

expects a directory

/temp

under

xrei-scripts

it can write

PostScript

files 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.json

xrei.json

defines 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.

Other information

A quick tutorial on writing AJAX wrappers to Unix command-line tools can be found here: Dojo Perl Tutorial

Papers

• 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.

History

xREI development began during the 2007 Google Summer of Code, sponsored by NESCent. The original

SoC

ideas page can be found here.

-- Lars Barquist - 29 Feb 2008