REDAME for TaxInspector

GENERAL

This is a browser for taxonomy databases originally designed to enable
taxonomy browsing as a plugin function for the Pedro tool (see links).

In the version 1.0 release, it browses the NCBI Taxonomy by loading the
tree from the flat files supplied by the NCBI into a local HSQLDB database.

INSTALLATION

This is handled by the IzPack installer.  Simply run
  java -jar TaxInspectorInstaller.jar

You will need Java installed, of course!

REQUIREMENTS

You need to be able to make direct FTP or HTTP connections to fetch the data
files.
You will need around 100MB of disk space to hold the populated
database of taxonomy entries.

CONFIGURATION

There are various options you can set in the taxinspector.conf file.
See the comments in the supplied default file for more information.

You can overrride these settings by having an alternate personal 
configuration file named .taxinspector.conf in your home directory.

USING YOUR OWN DATABASE

Things can be speeded up by using MySQL as the database backend.

More info to come in this section.

WORKING WITHOUT A DIRECT NET CONNECTION

The is currently no support for FTP or HTTP proxies.  If the application
cannot fetch the files, it is possible to download the taxdmp.zip
file manually and then tell the program to use the local copy.  See the
taxinspector.conf file for details.

USING THE BROWSER AS A PEDRO PLUGIN

More info to come.  See the NOTES.txt in the source directory.

CREDITS AND LINKS

This project is now hosted at bioinformatics.org
http://bioinformatics.org/groups/?group_id=504

The development of this program was funded by the Natural Environment 
Research Council as part of the Environmental Genomics Thematic
Programme Datacentre
http://www.nerc.ac.uk
http://envgen.nox.ac.uk

The Pedro tool for creating input forms from XML schemata:
http://pedro.sf.net
 
IzPack is a free Java installer maker which is very nifty.
http://www.izforge.com/izpack

Kudos to Dave Hancock for suggesting the name of the tool.
http://www.davesweboflies.com
