BioJava is an open-source project dedicated to providing a Java framework for processing biological data. It provides analytical and statistical routines, parsers for common file formats and allows the manipulation of sequences and 3D structures. The goal of the Biojava project is to facilitate rapid application development of bioinformatics and I was a significant contributor of this project.
A Statistical Online Model Checker for Biological Pathway Models, based on the PLTLs formalism for expressing the rules/properties to be checked. MIRACH can currently check pathways models written in popular formats such as CSML or SBML.
Sirius Prediction System Builder (Sirius PSB) is a software package designed to enable biologists with little or no computing knowledge to carry out sequence analysis using computational methods with ease and speed via a graphical user interface. Built into the software is the ability to build high-quality prediction models, visualization, multi-dimensional protein search, and more.