Software:

The R Project - R is a language and environment for statistical computing and graphics. It is a GNU project which is similar to the S language and environment which was developed at Bell Laboratories (formerly AT&T, now Lucent Technologies) by John Chambers and colleagues. R can be considered as a different implementation of S. There are some important differences, but most code written for S runs unaltered under R.

Perfuse - supports a rich set of features for data modeling, visualization, and interaction. It provides optimized data structures for tables, graphs, and trees, a host of layout and visual encoding techniques, and support for animation, dynamic queries, integrated search, and database connectivity.

MIM - MIM is currently among the world's leading software for graphical modelling. It has been applied in sociology, psychology, epidemiology, clinical trials, engineering, molecular genetics, market research and many other fields.

GBrowse java browser at University of Arizona - The Java GBrowse is a Java Applet-based implementation of the original CGI-based GMOD GBrowse web application developed by GMOD. Although similar to the CGI-based GBrowse application, Java GBrowse has some new functionality, including more search options, and a modified navigation interface. With a few exceptions, Java GBrowse can be used with the same configuration and database as the original CGI-based GBrowse.

GENA Gene Name Dictionary - University of Tokyo BioTermNet tool for looking up gene names for seven species.

Genome Browser - These tools are at The Generic Model Organism Database (GMOD) Project, which is a largely open source project to develop a complete set of software for creating and administering a model organism database, the apollo and gbrowse tools are helpful.