= VectorBase Expression Map =

Author: Bob MacCallum

This software is released under the GPL.
See gpl.txt for details.

Third party Javascript libraries Scriptaculous and Raphael
are included for convenience only.  Please see the licences
in their respective source files:

web/controls.js web/dragdrop.js web/effects.js
web/scriptaculous.js web/slider.js web/raphael-min.js
web/stereotabs.js

We are VERY grateful to the developers of these libaries.

== What is this? ==

Scripts for generating and displaying a self-organising map of gene
expression data from multiple experiments.

Documentation for running the pipeline in-house at VectorBase is
available here: http://wiki.vectorbase.org/index.php/Expression_maps

== What's included? ==

=== sql/schema.sql ===
This is the schema for the database - load it before starting any scripts.

=== scripts/cluster-continuous-data.pl ===
This is the main script for generating the map.

=== scripts/run-go-ora.pl ===
This runs the ermineJ GO enrichment analysis
(http://www.chibi.ubc.ca/ermineJ/) on the genes in each map cluster
and loads the results into the database

=== web/map.cgi ===
The new web front end.  Makes heavy AJAX use of web/json.cgi.
web/index.cgi is the old Web1.0 front end (more functionality but
very clunky).

== What's not included ==

Software for generating/normalising the input expression data matrix.
Example input data can be found on the VectorBase download
site: http://www.vectorbase.org/GetData/Downloads/?&type=Expression&archive_status=current ("shifted-means" files).

The gene annotation file ('biomart.txt'), needed for the GO enrichment
analysis and the web interface, is not provided, nor is an example of
these files.  It is, however, a tab-delimited file which has the
following column headings: 'Ensembl Gene ID', 'Description',
'Anopheles symbol', 'GO ID', 'GO description', 'Interpro ID',
'Interpro Description'.