APBS is a software package for the numerical solution of the Poisson-Boltzmann equation (PBE), one of the most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media. Continuum electrostatics plays an important role in several areas of biomolecular simulation, including simulation of diffusional processes to determine ligand-protein and protein-protein binding kinetics, implicit solvent molecular dynamics of biomolecules, solvation and binding energy calculations to determine ligand-protein and protein-protein equilibrium binding constants and aid in rational drug design, and biomolecular titration studies.
gfit analyzes data using models. gfit lets the user create a model for virtually any type of system using a minimal amount of computer code. It is particularly useful for studying various systems in biophysics, biochemistry, and cell biology. The interface for gfit models specifies relationships between input and output variables in a rule-based fashion. It provides flexibility and allows the user to reuse same models for many related problems.
Evolving Games for Unnatural Intelligence is a Java package for unsupervised machine learning based on Evolutionary Game Theory on directed graphs. It is able to segment data without any previuos information on the number of segments. It has no GUI, but implements generalizations of the original method proposed by Li, Chen, He and Jiang in the arxiv paper "A Novel Clustering Algorithm Based Upon Games on Evolving Network", published on 30 Dec 2008.
ODE is a high performance library for simulating rigid body dynamics. It is fully featured, stable, mature, and platform independent with an easy-to-use C/C++ API. It has advanced joint types and integrated collision detection with friction. ODE is useful for simulating vehicles, objects in virtual reality environments, and virtual creatures. It is currently used in many computer games, 3D authoring tools, and simulation tools.
jHepWork (jWork) is an environment for scientific computation, data analysis, and data visualization for scientists, engineers, and students. The program is fully multi-platform (written in Java). Programs can be written in the Java, Jython/Python, and BeanShell scripting languages. Matlab/Octave is supported for symbolic calculations. The program can be used to display data and functions in D and 3D. It comes with a friendly IDE and a code assist.
Madagascar is a software package for multidimensional data analysis and reproducible computational experiments. Its mission is to provide a convenient and powerful environment and a convenient technology transfer tool for researchers working with digital image and data processing in geophysics and related fields. Technology developed using the Madagascar project management system is transferred in the form of recorded processing histories, which become "computational recipes" to be verified, exchanged, and modified by users of the system.