Open Source Simulation Software - Page 8

This python package aims to help people set up and analyze molecular dynamics simulations in aqueous-organic solvent mixtures. See D. Alvarez-Garcia et al. Journal of Medicinal Chemistry, 2014.

syfluid is a funny toy as well as a real simulation. It simulates a fluid or a gas in a very colorful, graphic and sometimes psychodelic way. In realtime! Drag while your right mouse button is pressed to "draw" the fluid/density field. Drag while your left mouse button is pressed to make the whole thing move, i.e. to "draw" the "forces" that you're adding to the fluid/density field. Press "r" to clear the screen and "m" to open the menu. Press "1" .. "8" to switch color presets. SPACE to pause. "s" to save a png or jpg. syfluid is written in C++ using OpenGL. Even though it is heavily performance optimized and using OpenGL Shading Language (GLSL), it is a performance hog. Use "f" to show the FPS. If they are lower than 30, then reduce the quality parameter that you find in the menu from 200 to e.g. 100. For very fast graphic cards, try 400 and above. This fluid simulation is based on on Jos Stam's paper: http://www.dgp.toronto.edu/people/stam/reality/Research/pdf/GDC03.pdf

Ani2D provides portable libraries for each step in the numerical solution of systems of PDEs with variable tensorial coefficients: (1) unstructured adaptive mesh generation, (2) metric-based mesh adaptation, (3) finite element discretization and interpolation, (4) algebraic solvers.

Java implementation of Fuzzy Cognitive Maps (FCM). Implementation aims to be: small (and fast), simple to use, flexible enough to be used as a basis for other projects / libraries.

A Java client for the Player/Stage robot platform.

The TRANSIMS Studio application is an integrated development environment for the TRansportation ANalysis and SIMulation System (TRANSIMS). Components include a run time environment to execute TRANSIMS in parallel, as well as a full featured GUI.

jQuantum is a Java program to simulate a quantum computer, to design quantum circuits, and to visualize the execution of quantum algorithms. Another main purpose, however, is to create images in your head, and thereby - understanding.

ALgorithms for Embedding VIrtual Networks Software to evaluate Virtual Network Embedding Algorithms.

Blueprint XAS is a Matlab-based suite designed for the processing and analysis of near-edge x-ray absorption spectroscopy (XAS) data. The suite is designed primarily to assist users in exploring reasonable fit solutions while minimizing user bias.

OpenCell is a user interface for working with CellML models. Features: * Integrate models made up of ODEs. * Supports CellML 1.0 and 1.1, allowing you to build complex models using imports. * Plot and edit graphs. * And more ...

EPx is a "modified version of EnergyPlus v. 7 or 8", a fork of the open-source building energy simulation engine developed by the US Department of Energy. This project also contains the canonical open-source releases of the unmodified EnergyPlus source code.

EcoMod is an OpenGL application for 3D modelling, simulation and visualization of ecosystems. Trees are modelled and used within simulation to render the emerging natural phenomena of spontaneous afforestation process. Multidisciplinary.

We experiment with Evolution of Artifical Neural Networks, combining the two fields of Evolutionary Computation and ANNs. Our methods are applied to a variety of interesting problems. To learn more, click on "Home Page", "Mail", or "Files".

GFtbox is a Matlab package for simulating biological growth of leaves, petals, and similar organs.

JAS-mine is a Java platform that aims at providing a unique simulation tool for discrete-event simulations, including agent-based and microsimulation models. With the aim to develop large-scale, data-driven models, the main architectural choice of JAS-mine is to use whenever possible standard, open-source tools already available in the software development community. It has built-in utilities for communicating with an underlying relational database. In addition, the platform provides standard tools which are frequently used both in agent-based modelling and dynamic microsimulations, like design of experiments (DOE), run-time monitoring and visualization with plots and graphs (GUI), I/O communication and statistical analysis. JAS-mine source code can be found on GitHub, with the core repository at: https://github.com/jasmineRepo/JAS-mine-core and the GUI repository at: https://github.com/jasmineRepo/JAS-mine-gui

JMathLib is used to evaluate complex mathematical expressions and display the results graphically. It can be used either interactively or to interpret script files (m-files). It is a clone of Matlab, Octave, FreeMat, Scilab but written 100% in java.

µic is a modelling engine for simulations of microstructural development. It takes localied behaviours as input from the user and integrates the global behaviour, with the calculation of all interactions as required by the application.

NCE Calculation Framework is a library of routines, models and data applicable to chemical and process engineering calculations, written in Java. -- NEW -- www.chesolver.com *ONLINE CALCULATORS*. A set of solvers to perform calculations consistently on any device, from smart-phone to desktop. The project includes the following ready to use software all based on the same core library: * Online Calculators at www.chesolver.com * Extensions for Libreoffice/Openoffice Calc spreadsheet: - NCE: https://extensions.libreoffice.org/extensions/nce - NCE-Units: https://extensions.libreoffice.org/extensions/nce-units Check out also our video channel: https://www.youtube.com/channel/UCt2EGdw33k2u19PnZAi8YJA

OpenVLAB is an open source integrated framework for the numerical simulation of fluid flows (CFD) based on the resolution of Navier-Stokes equations. It is designed for analysis, design & optimization on airfoils, wings, wind-turbine, and much more..

A simulation environment intended to study and analyze SCADA systems security.

# Satellite Power Analysis Tool (SPAT) The tool was originally created to aid during the Satellite Power System design process, however it has evolved to a Satellite Missoin design tool. The user defines the mission and the Satellite design paramenters and, the tool will output: - Power analysis - Battery charge/discharge analysis - Link budget - Ground track coverage - Ground station visibility SPAT has been developed in MATLAB and MCR (Matlab runtime) is required. SPAT is pre-compiled and currently available for MacOS and Windows email: aitorvs(AT)gmail.com

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

Tellurium (te.) is a Python environment supporting Spyder2 IDE and Jupyter Notebook aimed for large-scale systems and synthetic biology simulation. It combines a number of existing libraries, including libSBML, libRoadRunner (including libStruct), libAntimony, and is extensible via tePlugins. In addition other tools kits such as matplotlib and NumPy are used to provide additional analysis and plotting support.

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

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.