Open Source Java Simulation Software for BSD

4-Dimensional Cell Simulator (4DiCeS) is a framework on hybrid (stochastic and deterministic) modeling and simulation of (whole) cell environments in 4D. The framework may incorporate any reaction and diffusion algorithms applicable in a 4D grid layout.

Basic life is an application that desires to simulate basic life based on some basic chemistry/physics rules. This environment provides particles that can bond, vibrate, react, etc. in order to create basic cells

Extended Bioaccumulation Framework (ExBAF) is a tool for assessing bioaccumulation in foodwebs. Supports several bioaccumulation models and provides tools for analysis and visualization.

Grid-Enabled Molecular Simulation Repository (GEMS)

JPhysChem - a mathematical modeling toolbox designed to provide an abstract layer and a comprehensive graphical front-end for general model building and specific modeling and data processing in the field of mass spectrometry and physical chemistry.

MoSGrid focuses on the configuration and provision of Grid services for molecular simulations and annotation of the results with metadata and their provision for data mining and knowledge generation. It is based on Liferay technology togethe with gUSE.

PUPIL (Program for User Package Interface and Linking), is a software environment that allows developers to link quickly and efficiently together multiple pieces of software in a fully automated multi-scale simulation. More specifically, it supports QM/MM MD simulations where the user might choose among any of the different MD engines and QM engines, which are connected to PUPIL as external programs through a tiny specific interface. One of the main advantages here is that the user can use most of the functionalities that may have those external programs interfaced without the necessity to be reimplemented again on independent interfaces. In fact, this simulation interface concentrates all the common code involved in the coupling terms of the QM/MM approach.

The Gecko Hamaker open-source software project is a full implementation of the fully retarded Lifshitz formulations for isotropic and anisotropic plane-plane and cylinder-cylinder interactions with intervening interlayer materials, planar systems of up to 99 layers, and graded interfaces for the modeling of grain boundaries or other continuously changing systems, accompanied by a database of material optical properties spectra. The machine-readable optical property database is available for download and as a web service and makes available the full spectral optical properties of over 150 materials from both ab initio calculations and experimental measurements.