Other Useful packages recently discovered.
octave
http://www.octave.org/
Open Source Matlab


Gnuplot
great drawing tool
http://www.gnuplot.info/


Boost, previous Generic Graph Component Library (GGCL), looks like a powerful c++ graph package

PathView

Great 3-D visulization, if we want to build a real cool galaxy of citation network ;-)
http://www.haydenplanetarium.org/hp/vo/partiview/

R
http://www.r-project.org/
statistics package with a good social network analysis module

install webdot/graphviz/tomcat/apache at intrepid:/home/liu_x/tool
Explore Java matrix/Graph packages

General Java matrix/math packages:
http://math.nist.gov/javanumerics/

It has many useful links to other java math projects.

Colt package:
It looks powerful but I did not find a graph theory API
http://hoschek.home.cern.ch/hoschek/colt/index.htm

JDSL:
http://www.cs.brown.edu/cgc/jdsl/doc.html
It has limited graph algo implementation, including DFS, DijkstraPath. It's more like a teaching tool.


Graph Foundation Class for Java
http://www.alphaworks.ibm.com/tech/gfc
It has a more powerful Graph API, however the latest version is released 07/31/2000. There is no much activity going on there. And the interface is rather odd. It supports breath-first search though.

Install Tomcat 4.1.24/Apache 2.0/jk2/GraphViz, many documents are incomplete or not work at all

Here are two useful links
http://www.greenfieldresearch.ca/technical/jk2_config.html
http://www.pixelfreak.net/howto/apache2_jk2_tomcat/socket.html

Steps:
--Compile Apache with so enabled
./configure --prefix=/usr/local/apache2 --enable-ssl --enable-module=so

--Install Tomcat
Downlod jk2 and compile
cd to /usr/local/src/jk2/jakarta-tomcat-connectors-jk2-2.0.2-src/jk/native2 and run configure with the following options...
./configure --with-apxs2=/bin/apxs --with-tomcat41= --with-java-home= --with-jni --with-pcre

--copy .so files to apache modules directory

--Config httpd.conf
LoadModule jk2_module modules/mod_jk2.so

--create workers.properties at $apache/conf
Define the communication channel
[shm]
file=/home/liu_x/tool/apache2/logs/jk2.shm
[channel.socket:localhost:8009]
info=Ajp13 forwarding over socket
tomcatId=localhost:8009

[ajp13:localhost:8009]
channel=channel.socket:localhost:8009

# Map the Tomcat examples webapp to the Web server uri space
[uri:/examples/*]
worker=ajp13:localhost:8009

--create jk2.properties at $tomcat/conf

shm.file=/home/liu_x/tool/apache2/logs/jk2.shm

-- Start tomcat first, and then start Apache.