Programming and Modeling Tools

Python

Tools:

• Python 2.6.4
• NumPy 1.4.0 and SciPy 0.7.1 (MATLAB-like numerical packages)
• NumPy download
• SciPy download
• Matplotlib 0.99.1 (MATLAB-like visualization package)
• NetworkX 1.0rc1
• Pajek - Program for large network analysis

Guides:

• Beginner's Guide to Python
• Python 2.6.4 Documentation
• Python 2.6.4 Library Reference
• NumPy and SciPy Documentation
• NumPy Tutorial
• NumPy Functions by Category
• SciPy Tutorial
• Matplotlib Screenshots and Sample Codes
• Matplotlib Documentation
• NetworkX Tutorial
• NetworkX Reference

Java

Tools:

• Eclipse IDE
• Frevo - Framework for evolutionary design of complex systems

However, quick visualization in Java is a pain without appropriate tools. There is a nice discussion on Java Scientific Packages similar to SciPy at [1]

In summary, the proposed packages for Java which could be interesting are:

• Apache Commons Math
• Java Numerics
• Colt
• Matlib
• Java Scientific Library
• JFreeChart
• JScience
• jHepWork

Graph and Network Analysis Tools

JGraphT

JGraphT is a free Java graph library that provides mathematical graph-theory objects and algorithms. JGraphT supports various types of graphs including:

• directed and undirected graphs.
• graphs with weighted / unweighted / labeled or any user-defined edges.
• various edge multiplicity options, including: simple-graphs, multigraphs, pseudographs.
• unmodifiable graphs - allow modules to provide "read-only" access to internal graphs.
• listenable graphs - allow external listeners to track modification events.
• subgraphs graphs that are auto-updating subgraph views on other graphs.
• all compositions of above graphs.

Although powerful, JGraphT is designed to be simple and type-safe (via Java generics). For example, graph vertices can be of any objects. You can create graphs based on: Strings, URLs, XML documents, etc; you can even create graphs of graphs! This code example shows how.