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MCX is a GPU-accelerated, general-purpose, physically-accurate and feature-rich 3-D light transport simulator. It is one of the fastest simulators because it can use tens of thousands of GPU threads to simulate photons in parallel.

Mendel’s Accountant is a biologically realistic, forward-time, parallel, numerical simulation program which models genetic change within a population, as affected by mutation and selection.

...Receiver phase cycling is possible in conjunction with pulse phase cycling to simulate coherence pathway selection. An extensive manual and help files are included. Currently running under Linux and Windows.

Tahoe is a research-oriented platform for the development of numerical methods and models for the simulation of complex material behavior.

MGSyn (Model, Game, Synthesis) is an open-source tool which integrates game-based synthesis into model-driven development for industrial control and automation. It is served for research and educational purposes. MGSyn has been originally developed by Department of Informatics (Unit 6), TU München and fortiss GmbH and is now maintained by fortiss GmbH. The software is released under the GNU General Public License Version 3.0 (GPLv3). Please download the tutorial for step-by-step...

Collaborative infrastructure for Collaborative Product Development (manufacturing) within Extended and Virtual Enterprise.

Elastic network models (ENMs) have been shown to generate the dominant functional equilibrium motions of biomolecules quickly and efficiently. MAVEN simplifies ENM generation, allows for diverse models to be used, and facilitates useful analyses.

SunlightLB is an open-source 3d lattice Boltzmann code which can be used to solve a variety of hydrodynamics problems, including passive scalar transport problems.

SunlightCBM is a suite of perl scripts for constraint-based modelling and flux-balance analysis in metabolic networks.

A rule-based modelling framework for allosteric proteins and biochemical networks.

Synthetic Biology Software Suite (SynBioSS) is composed of a wiki for biochemical kinetic constants, a graphical interface for simulating synthetic biological pathways, and a simulator that runs on either a desktop or supercomputer.

breve is a free, open-source 3D multi-agent simulation package designed for simulating decentralized systems and artificial life.

A way to use XFOIL for airfoil analysis with MATLAB. Utilizes Perl to provide a pty to interface with XFOIL and to parse results to send back to MATLAB. "MatPerlXFOIL: Half MATLAB, Half Perl. Half XFOIL. EXELSIOR!"

The SNP ratio test can assess significance of enrichment of significant associations in genome-wide association studies. Tests can be applied to pathways such as KEGG/GO, or user-defined pathways to test specific hypotheses. See link below for more.

ALC (Automated Layer Construction) is a computer program that highly simplifies the building of reduced modular models of signaling systems, according to the layer-based approach.

A MUD "totally" written in Perl. It runs an engine which relies on a extensible Perl MudLib and interprets user-programmable scripts in a fashion that reminds the old-time LPC MUD, but now everything is in Perl. It uses Perl v.5.10.0 and SQLite 3.3.7.

Given a reference sequence, simhtsd will create a large set of short nucleotide reads, simulating the output from today's high-throughput DNA sequencers, such as the Illumina Genome Analyzer II.

A collection of modeling tools for system comprehension. Includes 1) DEMOS2K - a semantically justified version of DEMOS 2) SAVANT - a tool for evaluating system availability 3) GOLDSTAR - an arbitrary reward calculation system.

Algorithm::MatchingModel is a perl library for running match simulations and statistics for two-sided matching problems. It includes classes for a preference factory, algorithm plug-ins, and gathering statistics between rounds.

Structuring & Modelling of Collaterized Debt Obligations (CDOs)

Simulates and visualizes swarming algorithms with limited communication. Also provides an interface to animate particle motion by playback (with pause, fastforward, and rewind) of path information from files. Can output EPS figures and avi frames.

RYUON : many-particle simulation suite

STOCHSIM is a stochastic simulator for biochemical reactions. The particles are represented as individual software objects which react according to probabilities derived from concentrations and rate constants. Simple spatial structures can be built.

A graphical microcode simulator with a reconfigurable datapath.