Showing 19 open source projects for "reaction"

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  • 1
    OpenFOAM

    OpenFOAM

    The Open Source CFD Toolbox

    OpenFOAM - The Open Source CFD Toolbox. OpenFOAM is a generic, programmable software tool for Computational Fluid Dynamics (CFD). For more information, see: - Main Website: https://openfoam.org - C++ Source Documentation: https://cpp.openfoam.org - Issue (Bug) Tracking: https://bugs.openfoam.org - User Guide: https://cfd.direct/openfoam/user-guide
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    Downloads: 2,469 This Week
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  • 2

    ADE_3D_FEM

    A 3D ADE FEM solver including a manual and a basic preprocessor

    A 3D Advection-Diffusion Equation Finite Element Method solver including a user's manual and a basic pre-proccessor.
    Downloads: 0 This Week
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  • 3
    PeMSyn

    PeMSyn

    Matlab/Scilab-FEMM based GUI to Assist the Design of Permanent Magnet

    ... for PC during the design process - Winding Wizard Assistant - Performance Simulator (FEMM Based) --- No-Load and On-Load parameters assessment considering armature reaction and saturation effects --- Torque Curve Capability assessment --- Parallel Processing (Matlab only) TUTORIAL included! https://www.youtube.com/channel/UCP2N1ELg1SAqlA8VCkSWRlw https://dx.doi.org/10.18618/REP.2020.2.0009 http://dx.doi.org/10.1109/COBEP/SPEC44138.2019.9065650 geyverson@ieee.org
    Downloads: 0 This Week
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  • 4

    diauxic growth model ensemble

    An ensemble of models showing diauxic growth behavior

    ... be categorized according to regulatory, stoichiometric, and physiological constraints and differ from each other on only a single aspect. We distinguish four groups of models: (1) flux balance models that only define reaction kinetics for substrate uptake and by-product excretion, (2) kinetic models without and (3) kinetic models with regulation on the metabolic and/or genetic level, and (4) resource allocation models.
    Downloads: 2 This Week
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  • 5
    STochastic Engine for Pathway Simulation
    Stochastic simulator for signaling pathways occuring in biological cells. Handles reaction-diffusion processes in 3D tetrahedral meshes. Please check our new repository: https://github.com/CNS-OIST/STEPS
    Downloads: 0 This Week
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  • 6

    cupSODA

    Deterministic simulator of mass-action based models

    cupSODA is a simulator of biological systems that exploits the remarkable memory bandwidth and computational capability of GPUs. cupSODA allows to efficiently execute in parallel large numbers of simulations, which are usually required to investigate the emergent dynamics of a given biological system under different conditions. cupSODA works by automatically deriving the system of ordinary differential equations from a reaction-based mechanistic model, defined according to the mass-action...
    Downloads: 0 This Week
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  • 7
    pybrn is a Python package for the analysis of biochemical reaction networks. It provides basic model handling capabilities, import from SBML, analysis of conservation relations, steady state computation and model simulation.
    Downloads: 0 This Week
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  • 8
    FAST Simulations

    FAST Simulations

    An Open source Analysis and SImulation Toolbox for Fuel Cells

    ... B. Harvey. Features of FAST-fc include transport of gases and liquids, multi-step reaction kinetics, transient and steady state operation for performance and durability, and scalable dimensionality from 1D - 3D domains. Future development work is on-going in FAST-fc and our strategic development schedule includes membrane degradation, improved liquid water transport models through the application of pore networks, and extension to stack-level simulation.
    Downloads: 0 This Week
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  • 9

    FERN: Fast Explicit Reaction Networks

    Quickly and explicitly solving sets of differential equations.

    FERN is a CUDA program that implements new methods for solving large sets of stiff differential equations using explicit integration methods. For the theory behind the program (due to Mike Guidry), see http://arxiv.org/abs/1112.4778 .
    Downloads: 0 This Week
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  • 10
    Glycosylation Microviewer

    Glycosylation Microviewer

    An application create, simulate and adjust N-linked glycosylation.

    ... is used to adjust the kinetic parameters of Michaelis-Menten equations in glycosylation reaction network. A dynamic plot is supplied to show the value of mole amout and mole fraction of various glycoform. Thanks to Alexey Balakin and Alessandro Presta. Alexey Balakin supply mathgl(https://sourceforge.net/projects/mathgl) that make the implementation of dynamic plot in this application easily. Alessandro Presta supply fga(https://sourceforge.net/projects/fga) that provide a powerful use of GA.
    Downloads: 0 This Week
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  • 11

    RSSA

    Rejection-based stochastic simulation algorithm (RSSA)

    Rejection-based stochastic simulation algorithm (RSSA) is an efficient exact algorithm for doing stochastic simulation of biochemical reaction systems. RSSA improves over state of the art of stochastic simulations by avoiding and collapsing as much the number of propensity updates.
    Downloads: 0 This Week
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  • 12

    SPSens

    Stochastic parameter sensitivity analysis for chemical networks

    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...
    Downloads: 0 This Week
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  • 13
    Building controls often have a PID Loop (Proportional Integral Derivative). Adjust PI&D terms in realtime and visually see what the reaction to the system will be. This is a real-time simulator with speed adjustment. Software requires the old MS Java Machine to run. Interested in an updated desktop version? Please drop me a note in the forum or my blog: http://right-handed-monkey.blogspot.com/
    Downloads: 4 This Week
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  • 14
    A high-performance simulation package for sampling the chemical and reaction-diffusion master equations. Primarily intended for running stochastic simulations of microbial cells.
    Downloads: 0 This Week
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  • 15
    The SBML ODE Solver is a command-line tool and programming library (ISO/ANSI C) for construction and numerical integration of an ODE system, derived from an SBML based description of a biochemical reaction network. Development has moved to https://github.com/raim/SBML_odeSolver . Please download the latest version from there!
    Downloads: 1 This Week
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  • 16
    A matlab/octave based reaction transport model describing microbially mediated isotope fractionation processes in porous media.
    Downloads: 0 This Week
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  • 17
    Moleculizer is a tool for simulating and generating biochemical reaction networks that are specified through a set of rules for protein-protein interactions.
    Downloads: 0 This Week
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  • 18
    Meredys (MEsoscopic REaction DYnamics Simulator) is a particle based stochastic simulation software designed to model and simulate reaction-diffusion systems. (http://www.ebi.ac.uk/compneur-srv/meredys.html)
    Downloads: 0 This Week
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  • 19
    4-Dimensional Cell Simulator (4DiCeS) is a framework on hybrid (stochastic and deterministic) modeling and simulation of (whole) cell environments in 4D. The framework may incorporate any reaction and diffusion algorithms applicable in a 4D grid layout.
    Downloads: 0 This Week
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