Search Results for "simulations" - Page 9
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Showing 583 open source projects for "simulations"
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SAMFF
A Refined Empirical Force Field to Model Protein-SAM Interactions
...Based on AMBER14 and GAFF, we systematically tuned the Lennard-Jones parameters of selected amino acid sidechains and the functional group of SAM with repeated metadynamics and umbrella sampling simulations. The final parameter set has yielded a significant improvement in the free energy values with R = 0.83 and MSE = 0.65 kcal/mol. We applied the refined force field to predict the adsorption orientation of lysozyme on CH3-SAM. For details, please refer to our publication: Bhadra and Siu, "A Refined Empirical Force Field to Model Protein-SAM Interactions Based on AMBER14 and GAFF" (submitted) https://cbbio.online/software/SAMFF/index.html -
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RTC-simulator
Simulation and Control of Processing Plants
...This is a simple interactive simulator including 20 different applications for such aspects as PID and DMC controller tuning, advanced level control, Smith prediction, Kalman filtering, and control strategies for a furnace, a boiler, and a hybrid system. A tutorial gives brief background to the theory and programming of each application, plus a stepwise set of objectives to illustrate the main features. The simulations include a number of the techniques described in Applied Process Control – Essential Methods, and that book’s accompanying volume, Applied Process Control – Efficient Problem Solving. Actually, RTC is not merely a suite of simulations: Each application can be switched from “MODEL” to “PLANT” mode for real-time control of equipment through a somewhat basic interfacing arrangement. ... -
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Virtual Laboratory Environment
A multi-modeling and simulation environment to study complex systems
...VLE is based on the discrete event specification DEVS. and it implements the DSDE formalism (A merge of Dynamic Structure DEVS, DSDEVS, with Parallel DEVS, PDEVS). VLE provides a complete set of C++ libraries, called VFL (VLE Foundation Libraries), to develop DEVS models, to gets results of simulations, to launch simulation on cluster. The models can be developed with the DEVS formalism or with the classical mathematical formalism: Ordinary Differential Equation with Euler, Range-Kutta or QSS integrator, Finite state automaton (FDDEVS, UML State chart, Hybrid Petri net). The VLE environment provides an IDE to develop C++ models, DEVS coupled models. ... -
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TEESer
Tool for Engineering Emergent Selforganizing bEhavioR
Teeser is a java-based integration framework for engineering emergent self-organizing behavior in distributed systems. It contains tools for analysis, tuning, macroscopic probing and simulations of distributed systems. Library of tools can be extended and everybody is encouraged to provide and share its tools with the community. The main idea is to provide application designers ability to seamlessly use tools which are helpful to design self-organizing behavior. Designers can continue to use their domain tools such as favorable simulator and by pluging it into the framework can take advantage of distributed simulations in the grid, various analyzers, optimizers (particle swarm optimization, genetic algorithms, ...). ... -
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Catalyst
An Algorithmic Trading Library for Crypto-Assets in Python
Catalyst is an algorithmic trading library for crypto-assets written in Python, originally developed to let quants and developers design, backtest, and deploy trading strategies in a unified environment. It builds on top of Zipline, extending that ecosystem to support crypto exchanges and high-resolution historical data (daily and minute bars). Users can express strategies in Python, run backtests against historical price data, and analyze performance through built-in metrics and analytics... -
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BNNPT
A powerful method for nonlinear dependence of two continuous variables
...Finally, permutation test was applied to detect the significance of the observed square error. To evaluate the strength of BNNPT compared to seven other methods, we performed extensive simulations to explore the relationship between methods and compared the false positive rates and statistical power using both simulated and real RNA-seq datasets. -
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Simultra
Multiagent simulator of road traffic in Qt/C++ and OpenStreetMap.
Simultra is an open-source, hybrid road traffic simulator designed to handle large roadmaps in real-time. It combines microscopic and mesoscopic simulations into one multiagent hybrid simulator. The large-scale maps are modelled mesoscopically in real-time, and the complex traffic interactions benefit from detailed agent-based microscopic simulations. To resolve the concurrency issues within the maps representation and the meso-micro transitions, Simultra combines an event-based mesoscopic model of the maps with a more detailed physical engine. -
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NeuralSyns
NeuralSyns is a neural simulator for large spiking networks.
NeuralSyns is a neural simulator for large spiking networks. New neuron and synapse dynamics can be added, and complex network models can be easily built using the included tool NetBuilder. OpenGL is used to show the network's architecture and activity. -
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OpenGrowth
OpenGrowth is a program which constructs de novo ligands for proteins.
...OpenGrowthGUI, FOG2.0, and the 3Mer-Screen stand-alone can be found in OpenGrowth_1.0.zip. To prepare new fragments you need BuildingFragments_1.0.1.zip and the scripts for MD simulations are in MD-Scripts_1.0.1.zip. SMoG2016.tar.gz allows to compute a score with the newly developed function (J. Chem. Inf. Mod., http://pubs.acs.org/doi/abs/10.1021/acs.jcim.6b00610). For any questions, please send emails exclusively at opengrowth-discuss@lists.sourceforge.net. -
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SPARTA
Direct Simulation Monte Carlo (DSMC) Simulator
SPARTA is a parallel DSMC code for performing simulations of low-density gases in 2d or 3d. Particles advect through a hierarchical Cartesian grid that overlays the simulation box. The grid is used to group particles by grid cell for purposes of performing collisions and chemistry. Physical objects with triangulated surfaces can be embedded in the grid, creating cut and split grid cells. -
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MIMO OFDM
MATLAB implementation source code accompanying the book MIMO-OFDM
...The repository is structured to match chapters in the book, providing code for topics such as OFDM basics, MIMO channel models, channel estimation, PAPR, spatial multiplexing, diversity techniques, etc. It helps readers replicate examples in the textbook and test MATLAB simulations of wireless communication schemes. Spatial multiplexing and diversity schemes. MIMO channel modeling and simulation. Spatial multiplexing and diversity schemes. -
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As of August 2018 Spheral++ has moved to Github -- please see the current repository at https://github.com/jmikeowen/spheral We are leaving a frozen version here on SourceForge for historical reasons. Spheral++ provides a steerable parallel environment for performing coupled hydrodynamical & gravitational numerical simulations. Hydrodynamics and gravity are modelled using particle based methods (SPH and N-Body).
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NOMAD is a C++ code that implements the MADS algorithm (Mesh Adaptive Direct Search) for difficult blackbox optimization problems. Such problems occur when the functions to optimize are costly computer simulations with no derivatives.
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Vital Sign Simulator
Patient vital sign simulator for medical emergency training purposes
The vital sign simulator simulates a patient monitor and is intended for use in medical emergency training simulations. In combination with a (cheap) cpr-manikin, it offers a low-cost alternative to commercial high-tech patient simulation manikins. It is used with a dual monitor system, one monitor with controls for the operator and one providing the vital signs to the trainees. Heart rate, oxygen saturation, etCO2, respiratory rate, blood pressure and various moving ecg-samples can be set and changed at any time by the operator. ... -
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...Interactive Structure Analysis of Amorphous and Crystalline Systems is a cross-platform software developed to analyze the structural characteristics of three-dimensional models built by computer simulations.
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...Nonlinear Pulse Propagation Solver (NPP) is a program, written in C/C++, that solves NSE in an arbitrary waveguide. It has a user friendly interface, which allows a user to enter the pulse and waveguide parameters and execute simulations. The program can be invoked within MATLAB and any other scripting language. It can export the results in different formats including ASCII text “.txt” and MATLAB “.mat” format. The program can also utilize the power of GPU via CUDA. With a modern gaming card “NVidia GTX TITAN”, a speed increase of a factor of 100 times can be achieved. ...
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chemfiles
Modern library for chemistry file reading and writing
Chemfiles is a modern and high-quality library for reading and writing trajectory files created by computational chemistry simulations program. These trajectories contains atomic positions, velocities, names, topology and sometimes more. Running simulations produce enormous amounts of data, which has to be post-processed to extract physical information about the simulated system. Chemfiles provides an interface to access this information which is - unified: the same code will work with all the supported formats; - simple: the interface is easy to use and extensively documented. ... -
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PixelFlow
A Processing/Java library for high performance GPU-Computing (GLSL)
PixelFlow is a Processing library focused on advanced graphics and visual effects, offering an extensive suite of GPU-based tools for visual artists, researchers, and creative coders. It enables real-time simulation and rendering of complex effects such as fluid dynamics, reaction-diffusion systems, soft shadows, and more, all powered by GLSL shaders. Its modular structure allows for chaining and composing various visual effects easily, making it ideal for installations, performances, and... -
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OpenRTDynamics
A framework for implementing real-time control systems
- - - T H I S P R O J E C T M O V E D T O G I T H U B - - - A framework for the implementation of advanced real-time control systems which uses signal/block-based schematics (like Simulink) extended by several features like state machines and online-exchangeable sub-simulations. Besides, this framework properly handles multiple threads, their communication, allows to synchronise control systems to external events (e.g. variable timers or incoming network packages) and provides many other nice features. Because of a high-level schematic-description language -- in form of provided Scilab commands -- only a minimal implementation-effort (no error-prone C-programming) is required. -
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IPS Framework
A simple Python framework for loosely-coupled multiphysics simulations
...One of the novel features of the IPS framework is its ability to support parallelism at multiple levels: components can launch individual parallel tasks, and also launch multiple tasks concurrently. The framework can execute multiple components concurrently, and even multiple simulations, all within the same pool of compute nodes. -
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River Simulations and Python
Management of river simulations with Python
The scripts and example projects are supplement of the paper "Integration of Python and HEC-RAS for automation of river flow and transport simulations". The paper is prepared by Tomasz Dysarz. Name of software: HEC-RAS and Python Developer: Tomasz Dysarz Mail address: Poznan University of Life Sciences, Department of Hydraulic and Sanitary Engineering, ul. Piatkowska 94A, 60-649 Poznan, POLAND E-mail address: tdysarz@gmail.com Hardware required: PC that supports Python Software required: Python 2.7.x, HEC-RAS 5.0.3 Programming language: Python 2.7.x -
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LIGGGHTS-PUBLIC
Official release of the LIGGGHTS DEM software by DCS Computing
...It is used to model granular materials, powders, bulk solids, and industrial particle-flow systems. The project originated from the LIGGGHTS ecosystem and has been used in combination with CFDEM coupling workflows for particle-fluid simulations. It helps users study mechanical contact, particle motion, collision behavior, packing, flow, and equipment-scale granular processes. The software is especially relevant for engineering applications where macroscopic behavior emerges from many particle-level interactions. Its main value is providing a DEM simulation engine for researchers and engineers who need detailed particle-scale modeling in open-source workflows. -
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MEMBPLUGIN
MEMBPLUGIN: studying membrane complexity in VMD
MEMBPLUGIN is a membrane analysis tool for molecular-dynamics simulations. It is a collection of visual and command-line tools that can be run within the Visual Molecular Dynamics (VMD) environment to analyze biomolecular simulations of lipid bilayers. -
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Acoustic Research Tool (ART)
Acoustic Simulation Library for Frequency and Time Domain Simulations.
ART is a flexible simulation framework for wind instruments. It includes a growing library of modelling elements. So far bore discontinuities, branches, tone holes, cylindrical and conical tubes, Bessel horns and bent tubes are available for frequency domain modelling. In the time domain generic bidirectional propagation elements, scattering elements, fractional delays, convolution with reflection functions and general z-domain networks are available and can be described using MuParserX... -
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Iphigenie
A fast and versatile molecular dynamics program
The molecular mechanics (MM) program Iphigenie provides a broad range of molecular dynamics (MD) methods and technologies, including polarizable force fields (PMM), the HADES reaction field, and QM/(P)MM hybrid simulations.
