ProteomeCommons.org IO Framework is a proper Java framework for handling spectra and peak lists. The framework can read and write to a number of different spectra and peak list formats, and it provides a simple, intuitive Java object model for working with spectra or peak lists. All classes support two methods of handling peak list and spectrum data: in-memory or stream. The goal of this framework is to support all the popular MS and MSMS data formats, and to eliminate any time or effort involved in figuring out how to read and write peak list or spectrum files.
Pulga is a program for numerical simulation of dynamical systems. It is designed to provide a way for students and researchers who study dynamical systems to model them on a computer and analyze them numerically without the difficulty of traditional computer programming languages.
Kabeja is a Java library for parsing CAD data (i.e. Autodesk's DXF format) and converting to SVG (dxf2svg). You can use Kabeja from the command line or embed it into your application. It includes a plain DXF2SVGViewer and integration into the Cocoon XML Web development framework and the Inkscape SVG editor.
Erudite is an application for training and testing back propogation neural networks using the ANNeML (Artifical Neural Network Markup Language) XML format. It supports testing and training neural nets with CSV files and has support for randomized training sets, optional adapting learning rate, sigmoid or hyperbolic tangent transfer functions, optional bias and weight adjustment locking, and more.