Open Source Java Simulation Software

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.

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.

Agent-based multiscale model of cancer proliferation dynamics

The BioSimz project aims to deliver a library (as well as the interface) to conduct large-scale biomolecular simulations at their atomic scales of detail. The initiative idea is to observe the protein crowding in vivo; it now can do much more than that!

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.

An attempt to make a n-body simulator with java

LineageEvolver is a simulation system for molecular evolution. Sequence evolution is simulated using modular processes such as substitutions, gene duplication/death, horizontal gene transfer, and more.

Meredys (MEsoscopic REaction DYnamics Simulator) is a particle based stochastic simulation software designed to model and simulate reaction-diffusion systems. (http://www.ebi.ac.uk/compneur-srv/meredys.html)

Molevolve is a Java library for running a Genetic Algorithm to model the 3-dimensional structures of peptide chains from amino-acid sequences. Client code can specify its own peptide chain model, fitness functions and GA operations. Requires JDK 1.5.

A collection of applets used to demonstrate physics and math principles. The applets include: a ray diagram drawing applet, a collision of disks applet, an electromagnetic field mapper and a 3d hydrogen orbital simulation.

The Self-Organizing Map Maker for Education and Research. Features include 3D-visualization of the training process, various 2D and 3D map topologies, easy extensibility to additional topologies.

Stochastic Pi Machine (SPiM), created by Microsoft, is a programming language for modeling biological processes. Two tools are available from Microsoft for simulation. A web application Visual SPiM, and a destkop application SPiM Player. Both simulation tools require to be run on a Windows platform. Fortunately Microsoft has also released a command line version for Linux and Mac OS based on OCAML however this version will only output a CSV file for the simulation results. SPiM2Eclipse provides a bridge for those running SPiM from the command-line by allowing simulations to be completed by a single click, displaying an embedded plot of the results. Features: -As an Eclipse plugin you have all of the powerful features of Eclipse available to you. -Syntax color highlighting -One-click simulation with plotting For more information on SPiM see the offical project website at: http://research.microsoft.com/en-us/projects/spim/

Synapsodel is an agent-based model of synaptic neurotransmission.

This project and all source code has moved to GitHub, see https://github.com/virtualcell

Esra is a 100% pure java library for the interactive analysis of molecular mechanics data. Mangles your data in your favorite scripting language.

molecular simulation program for anisotropic particle shape and potential

gfit creates an interface between computational models and experimental data and provides tools for their analysis