LinkHub code release 8/12/2007

Linkhub is released in two ways:

(1) A fully functional VMware virtual machine. Simply download the tar file
for this, untar it, and import into either VMware Workstation, Server, or
Reader. It uses NAT for networking, so use http://localhost to access the
linkhub web gui; change the network settings if you would like to deploy
this virtual machine for your own data in a LinkHub instantation. See
http://hub.gersteinlab.org for information about how and where to download
the VMware virtual machine for LinkHub.

(2) Just the code (Perl, Javascript, html, apache conf file, etc.) needed
to run LinkHub. In this case, there are two main parts to the code.

	(i) Directory 'web' contains the server-side code and associated
	files for the LinkHub gui to run in Apache, including the example
	apache httpd.conf file (which has important settings for running
	index.cgi and also for mod_rewrite). index.cgi is the CGI script that
	runs the LinkHub gui.

	(ii) Directory 'update_maintain_database' contains numerous
	Perl scripts which are collectively used to maintain and update
	the LinkHub database. If you want to run your own instantiation
	of LinkHub, you will probably have your own data to put in it and
	so will need to write your own specific code for this --- but the
	scripts in 'update_maintain_database' can be used as a good guide.
	Module RESOURCE_MODULES/LinkHubUtil.pm contains a number of utility
	functions you might find useful. Also, the Perl scripts referenced
	and run by the shell script RESOURCE_MODULES/st_strgen.sh are all
	worth looking at, e.g. sprotTrembl.pl incorporates data from UniProt
	(which in our own LinkHub instantiation was our "backbone" content).
	Note also that the modules exact_match_proj/SeqSearch.pm and
	exact_match_proj/UniprotSeqSearch.pm are used to do efficient
	exact sequence matching (they work by building a dbm hash of
	sequences), e.g. in cross-referencing structural genomics targets
	from the PDB's targetdb web site to UniProt.

Finally, the file linkhub.sql contains the sql schema for the LinkHub database
in MySQL.