Open Source Perl Simulation Software

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.

Neurospaces is a development center for tools in computational neuroscience. See http://www.neurospaces.org/

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.

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.

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.

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

Filu is aimed to support your stock trading. Some of its features are: Market Scanner, Indicator scripting, TA-Lib support, Postgres driven FIs and indicators, Trading scripting, Backtester with optimizer functionality

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.

RYUON : many-particle simulation suite

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.

A graphical microcode simulator with a reconfigurable datapath.

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.

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.

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.

Perl scripts used in the paper "Index-free de novo assembly and deconvolution of mixed mitochondrial genomes" by McComish BJ, Hills SFK, Biggs P and Penny D (2010) Genome Biology and Evolution 2:410-424.

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.

BRMABench is a system of benchmark per comparison. This benchmark makes diverse routines of test in one determined time, the final time expense is always the same and what it determines score it is the amount of interactions in this same time.

CDNsim is a GNU/LINUX simulation tool for CDNs, written in C++ (core) and python (GUI wizard). It models: redirection policies, cache policies, TCP/IP, batch simulations, statistics extraction and more. CDNsim is uses the OMNet++ library

Structuring & Modelling of Collaterized Debt Obligations (CDOs)

this code include automation for installing Cadence614 with Calibre2011 all you need to do is to install Centos 6.5 32bit on your machine http://archive.kernel.org/centos-vault/6.5/isos/i386/CentOS-6.5-i386-LiveCD.iso and the scripts will do the rest

Capsim(r) C Text Mode Kernel(TMK),DSP and communication blocks, topologies, libraries and tools for the development of high performance block diagram digital signal processing and communications systems,built in interpreter for scripting.SystemC support.

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.