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.
BALLView is an extensible viewer for bio-molecular structures. It provides all standard models and offers rich functionality for molecular modeling and simulation, including molecular mechanics methods (AMBER, CHARMM, and MMFF94 force fields), continuum electrostatics methods employing a Finite-Difference Poisson Boltzmann solver, secondary structure calculation, molecular editing and docking. Since BALLView is based on BALL (the Biochemical ALgorithms Library), it is easily extensible on the level of C++ code. In addition, it provides a Python interface with Integrated Development Environment features to allow interactive rapid prototyping.
Libecc is a C++ elliptic curve cryptography library that supports fixed-size keys for maximum speed. The goal of this project is to become the first free Open Source library providing the means to generate safe elliptic curves, and to provide an important source of information for anyone with general interest in ECC.
Cell Electrophysiology Simulation Environment is a framework to perform electrophysiological simulations. It can, for example, simulate cardiac myocyte electrical activity. It is useful for simulations of action potentials, individual ionic currents, and changes in ionic concentrations.
The Chemistry Development Kit (CDK) is a library of Java classes for chemo-, bioinformatics, computational chemistry, and chemometrics. It provides important algorithms like substructure search, SMILES, Gasteiger charges, QSAR descriptor calculation, 3D structure generation, 2D layout and rendering, many IO formats, atom typing, and more.
Chump is a table-driven assembler and dissembler with a very fast new architecture input format. Both the assembler and disassembler are created using a single description. It comes with descriptions for ARM, MIPS, Stump, and 6809. It is intended for use as a library compiled with other programs to allow line assembly and disassembly.