Search Results for "cell simulation"
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Showing 74 open source projects for "cell simulation"
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Deploy Red Hat Ansible Automation Platform on Microsoft Azure for a strategic automation solution that allows you to orchestrate, govern and operationalize your Azure environment.
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... coordinates and unit cell parameters, and further edit and modify them as required. (3) Format conversion: ATOMKIT software supports the conversion of structure file formats required by various common material simulation software. (4) Visualization: ATOMKIT offers powerful visualization capabilities that allow users to intuitively observe and analyze crystal structures.
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Beampath
Beam dynamics simulations in linear accelerators and beamlines
BEAMPATH is a 2D and 3D code for simulation of space charge dominated beam dynamics in linear particle accelerators and beam transport. The program is used for particle-in-cell simulation of axial-symmetric, quadrupole-symmetric and z-uniform beams in a channel containing RF gaps, radio-frequency quadrupoles, multipole lenses, solenoids, bending magnets, accelerating waveguides. Detailed description of model can be found in Y.K.Batygin, “Particle-in-cell code BEAMPATH for beam dynamics... -
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NeuroML is an XML-based description language for defining and exchanging neuronal cell, network and modeling data including reconstructions of cell anatomy, membrane physiology, electrophysiological data, network connectivity, and model specification
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GroIMP
Growth-grammar related Interactive Modelling Platform
... can interactively select the rules to be applied. GroIMP provides classes that can be used in modelling: Turtle commands, further geometrical classes like bicubic surfaces, the class Cell which has been used in the Game Of Life implementation, and so on. The outcome of a model is visualised within GroIMP. In the visual representation of the model output, users can i -
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The Development System for Auditory Modelling (DSAM) is a computational library designed specifically for producing simulations of the auditory system. It brings together many established auditory models within a flexible programming platform.
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life plus
life plus is based on Conway's game of life... but with much more.
life plus is python based, but runs at a reasonable speed for enjoyment. The number of neighbors determines a cell's color in next generation. Very interesting growth patterns can be created with tiny centered seeds or randomly. Conway's Game of Life is easily implemented (see suggestions). With multiple generations (up to 6 different sets of rules), the number of various other possible ecosystems are practically infinite. And it all looks neat! (lifeplus linux app added, see files) Some... -
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DESC Pro
Discrete event simulation for solar cell production
The aim of the DESC Pro program is to try to capture the dynamics of modern solar cell production lines using discrete event simulation techniques. All process and transportation events within the whole line can in principle be included in the simulations, which gives the advantage that dynamic aspects such as planned maintenance and random micro-stops can easily be taken into account. -
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PMCGPU
Parallel simulators for Membrane Computing on the GPU
Membrane Computing is a new research area (within Natural Computing) that aims to provide computing devices abstracted from the functioning and structure of living cells. These devices are called P systems. The objective of this project (PMCGPU) is to bring together all the researchers working on the development of parallel simulators for P systems, specially those using the GPU (e.g. CUDA, OpenCL, etc). Other parallel platforms are also welcome (multicore and manycore, FPGAs,... -
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The openFuelCell project is a forum to develop open source computational fluid dynamics (CFD) software to model fuel cells. Fuel cells http://en.wikipedia.org/wiki/Fuel_cell are devices that convert hydrogen and oxygen to water and electricity, and are promising renewable energy conversion devices. Computational fluid dynamics tools are used to size and rate fuel cell systems. OpenFoam is an open source CFD toolbox, available for downloading at http://www.openfoam.com/, written in C...
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Molecular Dynamics Studio
Molecular Dynamics Cell Construction
... the initial MD cell. Modifications to PACKMOL allow the atom type data to be passed through to the MSI2LMP software. MSI2LMP creates a LAMMPS input file based on class I or class II force fields. MSI2LMP was modified to use numerically coded force field data generated by NanoEngineer-1. The MMP file format was extended and integrated into all three software applications. http://www.nanoengineer-1.net http://www.ime.unicamp.br/~martinez/packmol/ http://lammps.sandia.gov/ -
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Advanced Vehicle Simulator
Advanced vehicle simulator
This project holds the latest releases for canonical versions of the ADVISOR® Software and "Advanced Vehicle Simulator". ADVISOR is a MATLAB/Simulink based simulation program for rapid analysis of the performance and fuel economy of light and heavy-duty vehicles with conventional (gasoline/diesel), hybrid-electric, full-electric, and fuel cell powertrains. New features are developed under the title "Advanced Vehicle Simulator". Periodically, stable versions of Advanced Vehicle Simulator... -
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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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Virtual Cell
Former home of the Virtual Cell platform (VCell), see http://vcell.org
This project and all source code has moved to GitHub, see https://github.com/virtualcell -
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experix laboratory control system
instrument control, data acquisition display and analysis
... pipes. Interfaces accessible via commands and scripts: file i/o modelled on stdio and stdlib; usb control and bulk transfers; socket operations; webcam; graphics via framebuffer. Applications (not all available yet for download) include: cell poker (like an atomic force microscope); tissue mechanical tester; fluorescence photobleaching; alternating laser excitation fluorescence; fluorescence intensity distribution analysis; iverilog simulation analysis. -
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PC1Dmod
PC1Dmod is an updated version of the solar cell simulator PC1D
PC1Dmod is an updated version of the popular solar cell simulation tool PC1D: https://sourceforge.net/projects/pc1d/ PC1Dmod extends PC1D by (i) including Fermi–Dirac statistics, which can be relevant in regions of high doping, and (ii) adding advanced c-Si models for Auger recombination, band-gap narrowing, carrier mobility, band structure and more. On this page you can now download the executables with all necessary extra files and documentation (now set as the default download... -
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MultiCellDS
MultiCellular Data Standards Project
... of digital cell lines and peer-reviewed simulation and experimental data. A novel part of MultiCellDS is the digital cell line: a digital analogue of experimental cell lines that will help to collect biophysical cell line measurements coming from many research groups and make them readily accessible to an ecosystem of compatible computational models. You can learn more about digital cell lines and other core ideas on this page. We are currently preparing a draft of the upcoming MultiCellDS 1.0. -
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SMeagol
Simulated single molecule microscopy.
SMeagol is a software suite for simulation of live cell single molecule microscopy, mainly aimed at single particle tracking applications. The code uses a combination of Matlab and compiled C++ executables, and runs on linux, windows and mac. Installation instructions, system requirements, and many more details can be found in the manual. If you use SMeagol for in your research, please cite Lindén, M., V. Ćurić, A. Boucharin, D. Fange, and J. Elf. Simulated single molecule microscopy... -
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FAST Simulations
An Open source Analysis and SImulation Toolbox for Fuel Cells
FAST is an Analysis and Simulation Toolbox (FAST) for Fuel Cells (FC) FAST-FC is the doctorate work of David B. Harvey and was developed with support from the U.S. DOE, Ballard, and Queen's University. Derivative works of FAST-FC include FC-APOLLO which is a forked branch of this project intended to capture the code state at the exit of the funded DOE project. FAST-FC is the open and active community branch. FAST-FC is developed and maintained by the original creator... -
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LivMach Framework
A virtual organism simulation framework written in C++
This is a C++ code to simulate life processes and responses to external stimulii in multicellular organisms by replicating the data flow in an actual organism using a straightforward approach. It can simulate both stimulus response and life processes(like respiration,excretion etc.) at the same time using multi-threading techniques. Digital DNA simulation- translation and transcription of DNA template to RNA is now supported. Users can also simulate cells and tissues using inbuilt classes. -
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OPar
OPen ARchitecture PARallel PARticle code
NOTICE: The current version of OPar is hosted on GitHub https://github.com/holgerschmitz/Opar This repository on Sourceforge is no longer maintained! OPar is an open architecture Particle-In-Cell (PIC) code for plasma simulations. The code is based on the Schnek framework. -
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Pixel Empires
A cellular automation simulation governed by probability.
This cellular automation simulation uses probability to control the growth and decay of different cells. This simulation uses cells of 6 different colors each of which is initially given one cell to be placed in a random location on the grid. 3 rules govern the evolution of this system: First, each cell will randomly select an empty cell around it or itself. If an empty cell is selected, a new cell will be formed in it. If the cell selects itself, it will not expand. In the next... -
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SCNVSim
SCNVSim, a tool to simulate somatic CNV and Strucuture Variants
SCNVSim is a Bioinformaitcs tool developed in Java programming language for the simulation of somatic copy number variations and structure variations in cancer genome studies. The tool is capable of simulating features related to tumor samples including tumor purity, aneuploidy and heterogeneity other than common types of SV and CNV. SCNVSim generates the genomes of a cancer cell population with detailed information of copy number status, loss of heterogeneity, and structure variation break... -
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Migration of cells in a social context
Model of the migration of 3T3 fibroblast cells in social context
Code updated. There were a few errors in the physical model of the concentration field of secreted chemokine surrounding each cell, together with a few coding errors. All have been corrected, the model refitted, and all simulations presented in the paper repeated. Results from this corrected model are on par with the published results. See pdf file for details. -
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O2 pathway and ROS generation model
Multi-scale Modeling of Skeletal Muscle ROS Generation
The production of reactive oxygen species (ROS) from the inner mitochondrial membrane is one of many fundamental processes governing the balance between health and disease. It is well known that ROS are necessary signaling molecules in gene expression, yet when expressed at high levels, ROS may cause oxidative stress and cell damage. Both hypoxia and hyperoxia may alter ROS production by changing mitochondrial PO2 (PmO2). This graphical user interface facilitates to parameterize and simulate...