Open Source Perl Simulation Software for Windows

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.

The program does nmr product operator calculations for one, two, three and four spins. 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.

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.

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.

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.

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

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.

Structuring & Modelling of Collaterized Debt Obligations (CDOs)

The Collaborative Testing System (CTS) tests parallel software using various implementations of MPI. It works on multiple platforms and supports batch systems including LSF, LCRM and workstations without a batch system. It includes a numerical diff tool.

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 instructions on installing and using the tool. It is advised to use 32-bit version (Eclipse) associated in the "MGSyn supplementary files", as the 64-bit version will by default demand huge memory, which may lead to Java exceptions.

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.

A graphical microcode simulator with a reconfigurable datapath.

Simulator of virtual animals made up of biological neural networks for research in the Computational Neuroscience field.

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

QCS is a quantum computer simulation written by Philipp Jungmann, Torsten Mandel and Maximilian Plenert as a software project under Dr. Michael Winckler (IWR) and Dr. Jian-Wei Pan (PI), University of Heidelberg.

RYUON : many-particle simulation suite

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.

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.

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.

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.

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

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.

A perl/Gtk2 GUI for VNUML (http://www.dit.upm.es/vnuml/). This GUI will let you quick prototype your VNUML topology by graphically placing, linking and editing network elements, reading/writing VNUML files and run your simulation right from the GUI.