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.
Amiba is a Gene Expression Programming (GEP) framework for Java. GEP is, like genetic algorithms, a branch of evolutionary computing. The framework separates the process of evolution from the process of interpretation of the chromosome, allowing the use of various schemes. For example, graphs may be used as terminals and graph operations as operators in the chromosome instead of the usual double precision numbers. It implements mutation, transposition, and recombination. Options and rates are easily configured through an XML file. A mechanism to load fitness cases in bulk is also provided.