Search Results for "simulations" - Page 10
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Showing 583 open source projects for "simulations"
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Capsule Cell Tracker
A user-friendly GUI for cell tracking and force estimation.
...In present work we develop an interpolation formula for drag forces on capsule shaped cells near walls that can be used as a simple and accurate substitute for the complex computational fluid dynamic simulations otherwise required to determine fluid-cell interactions. Please refer to our home page or contact us for more information http://www.physics.umu.se/english/research/biological-physics/the-biophysics-and-biophotonics-group/ The software is related to the paper: 'A drag force interpolation model for capsule-shaped cells in fluid flows near a surface' Krister Wiklund, Hanqing Zhang, Tim Stangner, Bhupender Singh, Esther Bullitt, Magnus Andersson* Department of Physics, Umeå University, 901 87 Umeå, Sweden -
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CORU
Network Monitoring tool using java, ssh and snmp
Academic project to implement a distributed monitoring tool linking SNMP (netsnmp) and java (through JNI) to manage gathered data (DB2) and report generation (RRDB). An attempt to use JPCAP to feef NS-2 simulations was made at a very basic stage. -
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SoAx
Structure of Arrays of multiple types
...It has been designed to handle list-like sets of particles (similar to struct {int id; double[3] pos; float[3] vel;};) in the context of high-performance numerical simulations. It can be applied to many other problems. Please check the sample file main.cpp to see examples of code that you can write with SoAx. -
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AmberAnalysis
Command-line tools for analyzing Amber Molecular Dynamics simulations.
A suite of command-line tools for analyzing chemically relevant features of an Amber Molecular Dynamics simulation. Can detect the position of a planar interface between two substances and plot density relative to that interface for atoms of an arbitrary type, name, charge, or residue. Orientation of three-atom residues (such as water) may be calculated and plotted. Uses parallel processing to detect hydrogen bonds, and can produce a bonding profile. Output files can be displayed as graphs... -
MongoDB Atlas runs apps anywhereMongoDB Atlas gives you the freedom to build and run modern applications anywhere—across AWS, Azure, and Google Cloud. With global availability in over 115 regions, Atlas lets you deploy close to your users, meet compliance needs, and scale with confidence across any geography.
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...New project page: https://github.com/yesint/pteros New documentation page: https://yesint.github.io/pteros/ Pteros is the C++ library for custom molecular modeling and simulations codes designed for researchers, not for C++ gurus. Provides facilities for PDB, XTC and TRR files IO, powerful selections, geometry transformations, RMSD fitting and alignment, etc.
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open-dis
Open-DIS implements the IEEE DIS protocol in multiple languages.
An open source implementation of the Distributed Interactive Simulation (IEEE-1278) standard in C++, C-Sharp, Objective-C, Java, Javascript and XML. Example applications including sending and receiving native DIS traffic, X-Plane plugin, and WebSocket/Javascript/WebGL applications. See the individual code directories for each package of interest. This project is inactive and has migrated to a GitHub project at https://github.com/open-dis -
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MimicrEE (Mimicing Experimental Evolution) is a tool for forward simulations of entire genomes. It basically allowes to simulate adaptation from standing genetic variation, thus no 'de novo' mutations are supported. It has been tested with 8,000 individulas having 2,000,000 million SNPs. Documentation: https://sourceforge.net/p/mimicree/wiki/Main/
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MED-FOES
An Agent-Based Simulation of Invasive Pest Insects
...Thus the objective of this software is to estimate the time to local extirpation based on known ranges of developmental, survivorship and reproductive parameters, as well as assumed ranges of an eradication pressure parameter. For a complete analysis and estimate of time to extirpation one would execute a large number of individual simulations evenly distributed over parameter space to estimate the time at which an arbitrary percentage of the simulations show extirpation. -
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BioFVM
3-D diffusion solver for biological problems
...BioFVM was first published in: A. Ghaffarizadeh, S.H. Friedman, and P. Macklin. BioFVM: an efficient, parallelized diffusive transport solver for 3-D biological simulations. Bioinformatics 32(8): 1156-8, 2016. DOI: 10.1093/bioinformatics/btv730 method paper: http://dx.doi.org/10.1093/bioinformatics/btv730 -
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This is a MATLAB model of an end-to-end chain compliant to the DVB-T2 standard (ETSI EN 302 755 available from www.etsi.org). It was originally developed within the DVB consortium (www.dvb.org) by AICIA, BBC, Pace, Panasonic and SIDSA.
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sync-player
Small music player, able to play simulations up to 3 streams of lyrics
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Spark is a physical simulation system. The primary purpose of this system is to provide a *generic* simulator for different kinds of simulations. In these simulations, agents can participate as external processes.
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Phaistos is a framework for all-atom Monte Carlo simulations of proteins. It incorporates several advanced probabilistic models of protein structure for conformational sampling, efficient move-algorithms and the OPLS and PROFASI forcefields.
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Hole-drilling Eccentricity
Eccentricity correction for the hole drilling strain gauge method
...The depths where the strains are measured in the ASTM E837-13 are taken as reference and specific functions are proposed to use the method without the need of performance finite element model simulations in each new problem. -
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The QuAd library contains MATLAB codes for generating verilog codes of any configuration of QuAd. It also contains functional MATLAB model of QuAd that can be used for simulations at higher abstraction levels. The library also includes PMF and Error Estimation code for QuAd configurations. This open-source library is developed to facilitate comparisons, and to facilitate research and development in AC at higher abstraction levels. In case of usage, please refer to our publication: M. A. Hanif, R. Hafiz, O. ...
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SVCEval-RA
An Evaluation Framework for Adaptive Scalable Video Streaming
...Our approach uses feedback information about the available bandwidth to allow the video source to select the most suitable combination of SVC layers for the transmission of the video sequence. The proposed solution has been integrated into the network simulator NS-2 in order to support realistic network simulations. -
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MuPIF
Multi-Physics Integration Framework (MuPIF)
Multi-Physics Integration Framework (MuPIF) is an integration framework, that will facilitate the implementation of multi-physic and multi-level simulations, built from independently developed components. The principal role of the framework is to steer individual components (applications) and to provide high-level data-exchange services. Each application should implement an interface that allows to steer application and execute data requests. The design supports various coupling strategies, discretization techniques, and also the distributed applications. ... -
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E2F1Map
Logic based simulations of E2F1 regulatory core for disease signatures
We provide comprehensive molecular interaction map of E2F1 transcription factor in tumor progression and metastasis. We provide various scripts, boolean based models to identify molecular signatures for predicting EMT phenotype in bladder and breast cancer model. -
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JBioFramework
Growing suite of proteomics simulations for educational purposes
JBioFramework (JBF) is a set of two different chemical separations simulations (2D Electrophoresis and Mass Spectrometry) that are frequently used in chemistry, biochemistry and proteomics research. It is written in the Java programming language and will run on any and all systems that have the JVM installed. As we continue to develop the software over the coming months/years and attempt to quantify the success of our efforts with testing and reviews, user input is very important. ... -
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Fragment-based Peptide Docking
Fragment-based Peptide Docking
A fortran based fragmentizing-docking-remerging program for long peptides (10-16 amino acids) docking simulations. This program is compiled by intel fortran at OpenSUSE 64-bits. Designed for 4GPU servers. NOTE: AMBER software packages, AMBER Tools and pmemd.cuda must be normally installed to fully operate this program. However you can still sample massive initial structures (500k~2m peptide conformations) without AMBER. Reference: http://pubs.rsc.org/en/content/articlelanding/2017/cp/c6cp07136h Supporter: JM Liao, tiomiya@hotmail.com -
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TransportCR
Tool for Numerical Simulations of Cosmic Rays Propagation
TransportCR is the tool for numerical simulation of cosmic rays propagation based on solution of transport equations. -
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MRiLab
A Numerical MRI Simulation Platform
...The main MRiLab simulation platform combined with those toolboxes can be applied to customize various virtual MR experiments which can serve as a prior stage for prototyping and testing new MR technique and application. If you find MRiLab useful for your work, please cite this paper: Fast Realistic MRI Simulations Based on Generalized Multi-Pool Exchange Tissue Model. IEEE Transactions on Medical Imaging. 2016. doi: 10.1109/TMI.2016.2620961 -
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TrajectorEE
Trajectories of Loci during Experimental Evolution
Visualizes trajectories of loci during experimental evolution using forward simulations -
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Cambridge Rocketry Simulator
Simulate high power rocket flights with splash down plots
This software allows you perform six degree of freedom simulations of High Power Rocket (HPR) and model rocket flights. Parachute descent is also simulated. 3D flight trajectories are produced as well as detailed tabular flight data. Running in Monte Carlo mode allows generates multiple possible flight paths and splash down plots, indicating the probability of landing in an area. Peer-reviewed publication in the Journal of Open Research Software (JORS) http://doi.org/10.5334/jors.137 "Cambridge Rocketry Simulator – A Stochastic Six-Degrees-of-Freedom Rocket Flight Simulator" -
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SIGVerse
Simulator for Human-Robot Interaction, used in the RoboCup@Home
...Since the mechanisms of such real-life intelligent systems are so complex, such as the physical interactions between agents and their environment and the social interactions between agents, comprehension and knowledge in many peripheral fields such as cognitive science, developmental psychology, brain science, evolutionary biology, and robotics. Therefore, we have been developing a simulator environment called SIGVerse, which is a simulator that combines dynamics, perception, and communication simulations for synthetic approaches to research into the genesis of social intelligence. In this paper, we introduce SIGVerse, its example application and perspectives.
