kinetic-modeling

There are 1 repository under kinetic-modeling topic.

markovmodel / PyEMMA
🚂 Python API for Emma's Markov Model Algorithms 🚂
python hidden-markov-model molecular-dynamics analysis markov-state-model tica time-series hmm bayesian-methods markov-model mbar kinetic-modeling umbrella-sampling molecular-modeling
Language:Python 305
AMICI
AMICI-dev / AMICI
Advanced Multilanguage Interface to CVODES and IDAS
differentialequations sensitivities simulation adjoint-sensitivities forward-sensitivities sbml systemsbiology cvode python kinetic-modeling mechanistic-models sensitivity-analysis cvodes idas pysb petab ode parameter-estimation hacktoberfest modeling
Language:Jupyter Notebook 107
ReactionMechanismGenerator / ARC
ARC - Automatic Rate Calculator
thermodynamics kinetic-modeling automation quantum-chemistry arc reactions rate-coefficients
Language:Python 42
SystemsBioinformatics / stochpy
StochPy is a versatile stochastic modeling package which is designed for stochastic simulation of molecular control networks
stochastic-simulation-algorithm kinetic-modeling systems-biology python bioinformatics console-application
Language:Python 39
hyperpolarized-mri-toolbox
LarsonLab / hyperpolarized-mri-toolbox
The goal of this toolbox is to provide open-source research-level and prototyping software tools for hyperpolarized MRI experiments. It is currently based on MATLAB/Octave code, and includes code for designing radiofrequency (RF) pulses, imaging gradients, data reconstruction, and data analysis. doi: 10.5281/zenodo.1198915
mri rf-pulses kinetic-modeling hyperpolarized-mri-experiments mri-acquisition mri-signals
Language:Jupyter Notebook 38
BioSystemsUM / MEWpy
Metabolic Engineering Workbench
strain optimization kinetic-modeling microbial-communities modeling omics-data-integration python simulation
Language:Python 35
PySCeS / pysces
The official PySCeS project source code repository.
kinetic-modeling python simulation mca sbml console-application steady-state bioinformatics
Language:Python 34
bowman-lab / enspara
Modeling molecular ensembles with scalable data structures and parallel computing
biophysics clustering protein-structure markov-state-model kinetic-modeling molecular-dynamics python molecular-modeling
Language:Python 33
JBEI / KineticLearning
Learning Kinetic Models from Time Series Proteomics and Metabolomics Data
machine-learning kinetic-modeling synbio
Language:Jupyter Notebook 28
biomass
biomass-dev / biomass
A Python Framework for Modeling and Analysis of Signaling Systems
python systems-biology computational-biology simulation kinetic-modeling parameter-estimation ode biochemical-networks dynamical-systems ordinary-differential-equations systems-biology-simulation modeling optimization network-analysis
Language:Python 24
bio-phys / PyDHAMed
Dynamic Histogram Analysis To Determine Free Energies and Rates from Biased Simulations
md-simulations science python free-energy free-energies kinetics kinetic-modeling molecular-dynamics
Language:Jupyter Notebook 19
ergodicio / adept
Automatic-Differentiation-Enabled Plasma Transport in JAX
automatic-differentiation boltzmann-equation computational-fluid-dynamics fluid-mechanics kinetic-modeling machine-learning plasma-physics
Language:Python 18
pasmopy
pasmopy / pasmopy
Patient-Specific Modeling in Python
systems-biology cancer personalized-medicine kinetic-modeling patient-specific-modeling python computational-biology systems-biology-simulation precision-medicine precision-oncology in-silico-clinical-trial biochemical-networks digital-twin
Language:Python 17
rinku-mishra / xoopic
XOOPIC is a two-dimensional 3-velocity particle-in-cell simulator. It can handle electrostatic and electromagnetic models, has a large variety of boundary conditions, supports multiple gasses and gas chemistry, and is easily reconfigurable via an input file.
particle-in-cell kinetic-modeling plasma-physics
Language:C++ 17
LLNL / EQ3_6
EQ3/6, a Software Package for Geochemical Modeling
kinetic-modeling thermodynamic-calculations geochemical-modeling
10
KarrLab / wc_rules
Rule-based modeling for whole-cell models.
cell-biology kinetic-modeling rule-based-modeling systems-biology whole-cell-modeling
Language:Python 9
itpplasma / GORILLA
GORILLA: Guiding-center ORbit Integration with Local Linearization Approach
fusion-reactor hamiltonian-systems kinetic-modeling numerical-integration numerical-methods plasma-physics simulation stellarator tokamak guiding-center
Language:Fortran 8
tintin554 / multilayerpy
A package to build, run and optimise a kinetic multi-layer model for aerosol particles and films
aerosols kinetic-modeling atmospheric-science atmospheric-chemistry
Language:Python 8
gemshub / GEMS3K
gibbs-energy-minimization thermodynamic-calculations geochemical-modeling chemical-equilibrium-calculations gem-selektor metastability kinetic-modeling reactive-transport-simulations
Language:C++ 7
Plane_Wave_Plasma_1D_FDTD
ShayanDodge / Plane_Wave_Plasma_1D_FDTD
Electromagnetic wave propagation with 1D-FDTD in the modeled plasma by Maxwellian and Druyvesteyn electron distribution function
plasma-physics kinetic-modeling fdtd 1d maxwellian electron-distribution-function
Language:MATLAB 7
MetaSys-LISBP / IsoSim
IsoSim: stoichiometric, kinetic and isotopic modeling of metabolic systems
13c-mfa metabolic-models metabolic-flux-analysis dynamical-systems systems-biology synthetic-biology kinetic-modeling stoichiometric-modeling 13c-fluxomics
Language:R 6
MetaSys-LISBP / acetate_regulation
Kinetic modeling of glucose and acetate metabolisms in E. coli
systems-biology metabolic-models metabolic-flux-analysis isotope-labeling-experiments 13c-fluxomics metabolomics escherichia-coli fluxomics dynamical-systems dynamical-modeling kinetic-modeling regulation metabolic-control copasi acetate-overflow metabolism metabolic-network
Language:Component Pascal 5
Alocaspi / Polymers-Kinetic-Mechanisms
Condensed-phase polymer degradation CHEMKIN format kinetic mechanisms.
chemistry kinetic-modeling plastics polymers pyrolysis reactions
Language:Liquid 3
klamt-lab / GDP-Fucose_OptMet2023_Paper
Contains all relevant data of the 2023 GDP-Fucose paper.
kinetic-modeling model-based-optimization cell-free-production enzyme-cascade gdp-fucose nucleotide-sugar parameter-uncertainty
Language:Component Pascal 3
kmaeda16 / RCGAToolbox
RCGAToolbox is a MATLAB toolbox for parameter estimation of kinetic models.
systems-biology synthetic-biology kinetic-modeling parameter-estimation matlab genetic-algorithm gui sbml petab ode ordinary-differential-equations evolutionary-algorithm
Language:MATLAB 3
lpaggetta / PET-pc_kinetic_modeling
A simple project for the development of kinetic models for the heterogenous reaction of glycolysis of PET-pc.
chemical-engineering genetic-algorithm mathematical-modelling matlab physical-chemistry polymer regression-models kinetic-modeling
Language:MATLAB 3
shyamsrinivasan / ident
Perform identifiability analysis in small kinetic models for experimental design using steady state fluxes and concentrations.
kinetic-modeling parameter-estimation metabolic-models experimental-design fluxomics metabolomics-data
Language:Jupyter Notebook 3
DescriptorMap
VlachosGroup / DescriptorMap
Automatic descriptor selection and volcano curve generation
kinetic-modeling volcano-plot
Language:Python 3
Xenozite / Thermokinetics-Toolset
A set of half automated MATLAB scripts for performing analysis of thermal data (TGA, DSC) and obtaining a kinetic triplet for every reaction stage
alim dsc dtg friedman kas kinetic-modeling ofw solid-state-chemistry tga thermal-analysis kinetic-compensation-effect master-plots vyazovkin
Language:MATLAB 3
gemshub / GEMSGUI
gibbs-energy-minimization thermodynamic-properties geochemical-modeling chemical-equilibrium-calculations chemical-thermodynamics gems3k metastability kinetic-modeling reactive-transport-simulations
Language:HTML 2
Kinetica-jl / Kinetica.jl
Automated chemical reaction networking with long-timescale kinetic simulations in Julia
chemical-kinetics chemical-reactions julia-package kinetic-modeling reaction-network
Language:Julia 2
llvdrhau / Alquimia_Co-culture_ISPR_Optimisation-
Kinetic model and optimization of co-culture bioreactor with in-situ product removal
bioreactor kinetic-modeling multi-objective-optimization uncertainty matlab
Language:MATLAB 2
sayanadhikari / xoopic
X11-based Object-Oriented Particle-In-Cell Code
particle-in-cell kinetic-modeling plasma-physics
Language:C++ 2
cchandre / VM15D
Hamiltonian fluid reduction of the 1.5D Vlasov-Maxwell equations
hamiltonian plasma-physics mathematica matlab numpy scipy python3 vlasov-equation vlasov-solver fluid-simulation fluid-solver kinetic-modeling
Language:Mathematica 1
muravyevV / thinks
Applications for analysis of thermal analysis data (DSC, TGA etc) and extraction of the reaction kinetics
calorimetry kinetic-modeling thermal-analysis thermogravimetry
Language:R 1
ANN_Reforming_Modeling
MuRE-group / ANN_Reforming_Modeling
Official GitHub repository of the paper "Improving the robustness of the hydrocarbon steam reforming kinetic models based on artificial neural networks", developed by MuRE at KAUST (Saudi Arabia).
kinetic-modeling artificial-neural-networks model-discrimination
Language:Python 1