View source for Programming and Modeling Tools

== Python ==

Tools:
* [http://www.python.org/ Python 2.6.4]
* [http://www.scipy.org/ NumPy 1.4.0 and SciPy 0.7.1 (MATLAB-like numerical packages)]
* [http://sourceforge.net/projects/numpy/files/ NumPy download]
* [http://sourceforge.net/projects/scipy/files/ SciPy download]
* [http://matplotlib.sourceforge.net/ Matplotlib 0.99.1 (MATLAB-like visualization package)]
* [http://networkx.lanl.gov/ NetworkX 1.0rc1]
* [http://vlado.fmf.uni-lj.si/pub/networks/pajek/ Pajek - Program for large network analysis]


Guides:
* [http://wiki.python.org/moin/BeginnersGuide Beginner's Guide to Python]
* [http://www.python.org/doc/2.6.4/ Python 2.6.4 Documentation]
* [http://docs.python.org/library/index.html Python 2.6.4 Library Reference]
* [http://docs.scipy.org/doc/ NumPy and SciPy Documentation]
* [http://www.scipy.org/Tentative_NumPy_Tutorial NumPy Tutorial]
* [http://www.scipy.org/Numpy_Functions_by_Category NumPy Functions by Category]
* [http://www.scipy.org/SciPy_Tutorial SciPy Tutorial]
* [http://matplotlib.sourceforge.net/users/screenshots.html Matplotlib Screenshots and Sample Codes]
* [http://matplotlib.sourceforge.net/contents.html Matplotlib Documentation]
* [http://networkx.lanl.gov/tutorial/index.html NetworkX Tutorial]
* [http://networkx.lanl.gov/reference/index.html NetworkX Reference]

== Java ==

Tools:
* [http://www.eclipse.org Eclipse IDE]
* [http://www.frevotool.tk/ 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
[http://stackoverflow.com/questions/482305/java-scientific-packages-similar-to-scipy]

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

See also our [[Data Visualization with Java|detailed report on data visualization in Java]].

== Graph and Network Analysis Tools ==

===JGraphT===

[http://jgrapht.sourceforge.net/ 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.