Open Source Linux Simulation Software - Page 17

SPICE is a 2D in space, 3D in velocity Particle-In-Cell code intended to simulate plasma-wall interaction.

SPSens is a complete software package written in C that estimates parameter sensitivities for stochastic models of chemical and biochemical reaction networks using Monte Carlo (MC) stochastic simulations. It is possible to estimate sensitivities with respect to system parameters using the following algorithms: finite difference methods (crude monte carlo, common reaction path, coupled finite differences); likelihood ratio methods; and regularized pathwise derivatives. Additionally the package includes basic stochastic simulation algorithms. The package includes several example networks which can be easily modified for other networks. Serial and parallel MPI implementations can be built and called from the command line. The serial implementation of the package can also be called from Matlab via the MEX interface with limited functionality. It supports many user specified options, including the use of antithetic sampling that can be used in some cases to increase efficiency.

Shared-Memory Parallel Smoothed Particle Hydrodynamics (SPH) code for large-scale cosmological simulations.

SLFCFD stands for San Le's Free Computational Fluid Dynamics. It is a package of scientific software and graphical user interfaces for use in computational fluid dynamics. It is written in ANSI C and distributed under the terms of the GNU license.

The Simple Interface for Global Optimization Algorithms allows the specification of arbitrary search/optimization problems, solving of these problems, and the specification and implementation of optimization algorithms like evolutionary algorithms.

Simox has moved to gitlab. Please update your URLs: https://gitlab.com/Simox/simox A platform-independent robot simulation, motion and grasp planning toolbox consisting of three modules: VirtualRobot to simulate and visualize robots, Saba the sampling-based motion planning library and GraspStudio for grasp planning.

Step is an interactive physical simulation program for education. StepCore is a physical simulation library on which Step is based. Please refer to http://edu.kde.org/step for more details.

SuSim stands for Sukhoi Simulator. It is a multipatform flight simulator developed to implement the most simplistic but realistic flight dynamic simulations possible, targeted in the first place to mimic the behaviour of the Su-27 Flanker.

SystemDynamics is a graphical Java application for modeling, visualization and execution of System Dynamics models.

This site hosts the source code for C++ version of the Broker for SBW, NOM module, advanced simulation suite, analysis applications and model editors.

TEACUP automates many aspects of running TCP performance experiments in a specially-constructed physical testbed. TEACUP enables repeatable testing of different TCP algorithms over a range of emulated network path conditions, bottleneck rate limits and bottleneck queuing disciplines. TEACUP utilises a text-based configuration file to define experiments as combinations of parameters specifying desired network path and end host conditions. When multiple values are provided (e.g. for TCP congestion control algorithm), an experiment is made up of multiple tests. For each experiment and test, TEACUP collects a range of data, such as tcpdump files of traffic seen or TCP stack information (e.g. using Web10G). TEACUP also collects a variety of metadata from the end hosts and bottleneck router, such as the actual OS/kernel version(s) used. TEACUP also provides some simple tools for analysing the results of experiments, such as plotting a flow's experienced RTT over time.

Tissue Modeling Tool (TMT) is a Matlab-based open source project aiming to share constitutive modeling code and algorithms within the tissue biomechanics community. It is meant to be modular, fast, and easily extensible.

That project aims at studying the impact of IT systems interactions on traveller demand and airline revenues. Passenger demand is generated (Monte Carlo) and injected into simulated CRS and airline IT systems. Differential analysis is then performed on various changes compared to a bottom line scenario.

A Cellular Automaton simulator written in java (swing).

The Virtual Geoscience Workbench for discontinuous systems is a computer software environment for modelling. We have made the combined Finite-Discrete Element Method (FEMDEM) the core of our solids technology.

Ve3D is a VRML/Open Inventor model viewer. It's an scene composition program since it has tools to manipulate and hide models. It supports active stereo display.

Calculation of radiation view factors by adaptive integration. A cross-platform port of the public-domain code by George Walton.

VirtualVEX is an open-source simulator platform for the VEX robotics design system. It features full competition simulation, with automatic scoring and timing and multiple robot designs to choose from. VirtualVEX is also programmable: users can write and upload code using the bundled VVDevelop IDE, which has one-click deployment and testing support. VirtualVEX also supports dual-pad joysticks similar to those used by the actual VEX platform, allowing users to get realistic driving practice. The software is free and is distributed under the GPL v.3

UPDATE: LATEST VERSION AT http://git.durrantlab.com//jdurrant/wisp Allostery can occur by way of subtle cooperation among protein residues (e.g., amino acids) even in the absence of large conformational shifts. Dynamical network analysis has been used to model this cooperation, helping to computationally explain how binding to an allosteric site can impact the behavior of a primary site often many angstroms away. Traditionally, computational efforts have focused on the most optimal path of correlated motions leading from the allosteric to the primary active site. We present a program called Weighted Implementation of Suboptimal Paths (WISP) capable of rapidly identifying additional suboptimal pathways that may also play important roles in the transmission of allosteric signals. Aside from providing signal redundancy, suboptimal paths traverse residues that, if disrupted through pharmacological or mutational means, could modulate the allosteric regulation of important drug targets.

WebChip allows programmers of all abilities to literally look inside a highly-simplified virtual machine and understand what's going on.

This project aims to provide the wireless support in OverSim to simulate the P2P protocol over Mobile AdHoc Network or Wireless Mesh Network. Our project include the INETMANET-2.0 open source library to facilitate wireless characteristics.

XinCNC is a free software for Computer Numerical Control (CNC).

Ytk is a Tcl/Tk program which adds menus, buttons and features to the basic command line driven Yorick program and language. It also enables usage of all Tcl/Tk widgets and functions including buttons, sliders, checkboxes, and other typical TK widgets to

cogli2 (formerly known as cogli1) is a simple tool to visualise configurations of coarse-grained simulations. It is straightforward to use and it has a few features that make it very handy to produce publication-ready figures. It supports its own file format but implementing additional parsers is fairly easy. As of now it is not well documented, but this is something we will improve upon in the near future.