Search Results for "kinetics"
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Showing 31 open source projects for "kinetics"
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Catalyst.jl
Chemical reaction network and systems biology interface
... simulation and parameter estimation of mass action ODE models, Chemical Langevin SDE models, stochastic chemical kinetics jump process models, and more. Generated models can be used with solvers throughout the broader SciML ecosystem, including higher-level SciML packages (e.g. for sensitivity analysis, parameter estimation, machine learning applications, etc). -
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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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Nest-o-Patch
Software for analysis of patch-clamp recordings and other wave data
This program was designed mainly for preconditioning and analysis of electrophysiological data, including patch-clamp and 2-electrode voltage clamp recordings. The program includes tools both for basic analysis of whole-cell recordings or analysis of single channel properties. Program can display and analyse long traces incuding many sweeps, series and even groups simultaneously. Current amplitudes or time intervals are easily measured. Single channel conductance, kinetics, NPo, as well... -
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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. -
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Cantera is a suite of object-oriented software tools for problems involving chemical kinetics, thermodynamics, and/or transport processes. It can be used from MATLAB, Python, C++, or Fortran.
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DissoKin
Dissolution Kinetics Software Excel Based
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3D ResNets for Action Recognition
3D ResNets for Action Recognition (CVPR 2018)
We uploaded the pretrained models described in this paper including ResNet-50 pretrained on the combined dataset with Kinetics-700 and Moments in Time. We significantly updated our scripts. If you want to use older versions to reproduce our CVPR2018 paper, you should use the scripts in the CVPR2018 branch. -
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nlabck
Numerical Laboratory on Chemical Kinetics
NLabCK is an open source software tool to simulate numerically the behavior of reacting chemical systems or other dynamical systems (changing over time) provided they can be represented as a set of molecular chemical reactions. -
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Computation of empirical parameters in user-defined non-linear chemical kinetic models. Has a facility to compare 3 empirical models on the same graph to visually judge which model predicts the experimental data better. The empirical models can be input in the GUI as user-defined functions. This tool was written for the publication of "Modelling of Curing Kinetics of Amine Cured Epoxy Resins for Vacuum Assisted Resin Infusion Molding" (The Canadian Journal of Chemical Engineering, 2013), where...
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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. -
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cupSODA
Deterministic simulator of mass-action based models
... kinetics, and then exploiting the numerical integration algorithm, LSODA -
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FAST Simulations
An Open source Analysis and SImulation Toolbox for Fuel Cells
... and developer, David 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. -
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Pyclamp
A Python package used to extract and analyse electrophysiological data
Pyclamp is Python package used to extract and analyse electrophysiological data. A graphical user interface has been developed to allow a user to run the pack- age without requiring any knowledge of Python code. Presently, Pyclamp is designed to perform very specific forms of analysis on evoked synaptic responses: Data analysis (under development) : This is a highly user-interactive en-vironment that can be used to discriminate synaptic events, obtain various measures of their kinetics... -
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Polaris CFD
Aerodynamics simulations based on gas kinetics
Polaris CFD is a complete CFD software suite for Aerodynamics simulations created by Alta Dynamics. It is validated to provided accurate results for both internal and external flow problems. Its viewer is built on ParaView for pre and post processing. -
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Chemical Kinectics Solver
Basic Chemical Kinetics Solver
The project lives on GitHub - please see: https://github.com/DetlevCM/chemical-kinetics-solver -
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SPR MCMC
A windows executable for running the Bayesian inference on SPR data.
A windows executable (C# application) to run the Bayesian inference to estimate the affinity kinetics as well as the active concentration on the SPR (surface plasmon resonance) data. -
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ForStoch
Fortran Stochastic Simulator for Chemical Kinetics
ForStoch is a FORTRAN software suite for Stochastic Simulation of Checimal Kinetics. The stochastic simulation algorithm (SSA), proposed by Gillespie, is a cardinal simulation method for the chemical kinetics. Because the SSA simulates every reaction event, the amount of the computational time is huge when models have many reaction channels and species.This drawback motivates many attempts to improve the efficiency with the accuracy.The ForStoch includes orignial Gillespie SSA and other... -
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NanocalcFX
Open Source Data Evaluation Software
NanocalcFX is a free and open source evaluation software for a simple yet comfortable solution to deal with thousands of transport kinetics measured with a fluorescence microscope or similar kinetics. Data can be imported from CSV or Excel files or using the dedicated image stack analyser (NISA). You can get sample data at the nanocalcFX homepage. Note that nanocalcFX is currently in a beta state. -
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BriPy
A BRIC-seq data analysis package written in Python.
... analysis. -What is BriPy? BriPy package is a BRIC-seq data analysis tool written in Python. It can calculate RNA half-life for each transcript and draw graphs describing the kinetics of RNA decay. In the future, it will provide several useful modules(e.g. calculating RPKM of each transcript from BAM file or ELAND output file). -Prerequisites To use BriPy package, you will need Python and the following extension packages. Python2.7 or higher NumPy SciPy Matplotlib -
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PLASMAKIN: a chemical kinetics package
A library to compute the electron and chemical kinetics on plasmas
PLASMAKIN is a package to handle physical and chemical data used in plasma physics modeling and to compute gas-phase and gas-surface kinetics data: particle production and loss rates, photon emission spectra and energy exchange rates. -
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modelMaGe2.0 is a software application that automatically generates mathematical models in Copasi format (www.Copasi.org) by removing model components from a given master model. Candidate models can automatically be fitted to provided data.
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itermd
Software tools for applications of simulations by iterations.
... for the user: quickly programme his simulation. Requires knowledge of C language. Knowledge of gtk and cairo (for simple graphs) is not necessary. See examples. -sugar fermentation kinetics -parachute drop -cycle of a water tank heated by solar panels -curve of chase For your simulation, simply copy and adapt some lines corresponding explicit examples. -
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ezBioNet is a biological modeling and simulation tool of molecular interaction that occurred in a cell. We aim that this software can be used for collecting biological data and making biological models to simulate it by biological researchers. ezBioNet can build a detailed biological model including signal transduction, enzyme kinetics, expression network, etc. It also support number of numerical analysis method to simulate the biological reaction networks.
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Statistical Thermodynamics Book Codes
Source codes for statistical thermodynamics and stochastic kinetics
The codes for conducting simple molecular simulations are available, as described in the textbook "Statistical Thermodynamics and Stochastic Kinetics. An Introduction for Engineers".