Open Source Perl Simulation Software - Page 2

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

NX is a program for nonadiabatic molecular dynamics in the electronic excited states. It is based on the surface hooping approach.

Project moved to https://github.com/ivandeex/optikus

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

Plotamber is a Perl script for an easy and automated plotting of properties derived from molecular dynamics or minimization calculations done with Amber, NAMD or Charmm.

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.

SimRecommender is a modular perl framework to simulate and test attacks on recommender systems. It uses a plug-in architecture to integrate different attacks and recommender algorithms.The development was supported by NSF award IIS-0812042 (see README).

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.

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.

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.

Virtop is a software providing solution for simulating computer networks with scenarios on a single machine. It is mainly intended for education purposes like organizing practice classes in computer networks in the universities.

Collection of utilities based on two basics classes: Matematica and VarData. Matematica) performs math operations on vectors and matrices for smoothing, interpolation, convolution, image processing... VarData) manipulate a structure of points connected by links. Addraw) openGL engine. ElPoly) analyze mechanical properties of polymer and membrane like structures. Addyn) perform molecular dynamics and Monte Carlo simulations and has a solver for 4th oder PDE. Avvis) perform all the operation of Matematica on different sets of data visualized on a Qt graphical interface. DrImage) image manipulation on the Matematica filters. The program is intended to use as less as possible external libs (optional: openGL, gsl, fftw, cgal, png, tiff, boost, MPI, Qt...).

gen_names populates customer/invoice tables with random (but realistic looking) data. The data has been gathered from various sources including census and local council web sites. It is supposed to be used to road test various DBMS solutions.

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.

PharmML is a markup for pharmacometrics markup language documented at http://pharmml.org/. This project provides a converter between the conventional mathematical infix notation and the math markup used by PharmML. The online version has been disabled. Please download for offline use.

Magnetostatic finite differences simulation tool based on GNU Octave and a Perl/Tk user interface.

Seqsee is a program that extends integer pattern sequences in a human like way.

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.

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