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Mar 17, 2022 - Python
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kinetic-modeling
Here are 37 public repositories matching this topic...
python
markov-model
hmm
time-series
analysis
molecular-dynamics
bayesian-methods
tica
hidden-markov-model
markov-state-model
umbrella-sampling
mbar
kinetic-modeling
molecular-modeling
Open
Lint petab models
StochPy is a versatile stochastic modeling package which is designed for stochastic simulation of molecular control networks
python
bioinformatics
systems-biology
console-application
stochastic-simulation-algorithm
kinetic-modeling
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Jul 12, 2021 - Python
alongd
commented
Jun 28, 2021
Is your feature request related to a problem? Please describe.
When running many species / reaction in ARC, it is often helpful to trace the history of a single species or TS. The current log file is too large to do that conveniently.
Describe the solution you'd like
Create a log file in the output folder of each species / TS with the relevant data.
Modeling molecular ensembles with scalable data structures and parallel computing
python
clustering
protein-structure
molecular-dynamics
markov-state-model
biophysics
kinetic-modeling
molecular-modeling
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Feb 16, 2022 - Python
Learning Kinetic Models from Time Series Proteomics and Metabolomics Data
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Jan 21, 2022 - Jupyter Notebook
The official PySCeS project source code repository.
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Feb 24, 2022 - Python
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
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Apr 8, 2022 - Jupyter Notebook
A Python Framework for Modeling and Analysis of Signaling Systems
python
simulation
optimization
modeling
systems-biology
computational-biology
ode
dynamical-systems
parameter-estimation
ordinary-differential-equations
network-analysis
kinetic-modeling
systems-biology-simulation
biochemical-networks
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Apr 8, 2022 - Python
Dynamic Histogram Analysis To Determine Free Energies and Rates from Biased Simulations
python
science
molecular-dynamics
kinetics
free-energy
free-energies
kinetic-modeling
md-simulations
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Mar 13, 2018 - Jupyter Notebook
Patient-Specific Modeling in Python
python
cancer
systems-biology
computational-biology
precision-medicine
kinetic-modeling
personalized-medicine
digital-twin
precision-oncology
systems-biology-simulation
biochemical-networks
in-silico-clinical-trial
patient-specific-modeling
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Apr 6, 2022 - Python
Rule-based modeling for whole-cell models.
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Apr 6, 2022 - Python
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.
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Jun 2, 2021 - C++
IsoSim: stoichiometric, kinetic and isotopic modeling of metabolic systems
synthetic-biology
systems-biology
dynamical-systems
metabolic-models
kinetic-modeling
metabolic-flux-analysis
13c-mfa
stoichiometric-modeling
13c-fluxomics
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Sep 12, 2019 - R
Kinetic modeling of glucose and acetate metabolisms in E. coli
systems-biology
regulation
dynamical-systems
metabolism
metabolomics
dynamical-modeling
escherichia-coli
metabolic-models
metabolic-network
copasi
kinetic-modeling
fluxomics
metabolic-flux-analysis
isotope-labeling-experiments
13c-fluxomics
metabolic-control
acetate-overflow
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Mar 17, 2021 - Component Pascal
automatized generation of optimized Gillespie algorithm
dependency-graph
data-structures
binary-search-tree
nonlinear-dynamics
temporal-data
kinetic-modeling
reduction-strategies
gillespie-algorithm
pathway-models
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Aug 18, 2018 - Fortran
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May 22, 2020 - Python
X11-based Object-Oriented Particle-In-Cell Code
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Mar 11, 2021 - C++
matlab
thermodynamics
protein-protein-interaction
kinetic-modeling
entropy-production
dissipation
futile-cycle
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Jan 15, 2018 - MATLAB
Electromagnetic wave propagation with 1D-FDTD in the modeled plasma by Maxwellian and Druyvesteyn electron distribution function
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Feb 2, 2022 - MATLAB
Perform identifiability analysis in small kinetic models for experimental design using steady state fluxes and concentrations.
parameter-estimation
metabolic-models
experimental-design
kinetic-modeling
fluxomics
metabolomics-data
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Jun 6, 2019 - Jupyter Notebook
1st order ODE numerical solver
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Oct 6, 2020 - Python
Code for Model-based Design of Bistable Cell Factories for Metabolic Engineering
dynamics
regulation
bifurcation
metabolic-models
metabolic-network
metabolic-engineering
kinetic-modeling
model-based-design
bistable
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Nov 4, 2017 - MATLAB
Julia interface to BioMASS, tailored to parameter estimation in systems biology models
simulation
julia
modeling
systems-biology
computational-biology
dynamical-systems
differential-equations
parameter-estimation
bifurcation
kinetic-modeling
systems-biology-simulation
biochemical-networks
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Mar 24, 2022 - Julia
Model Predictive Control Project for Self-Driving Car ND using C++
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Sep 6, 2017 - C++
libRCGA is a C library for real-coded genetic algorithms (RCGAs).
synthetic-biology
genetic-algorithm
systems-biology
evolutionary-algorithms
parameter-estimation
kinetic-modeling
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Sep 14, 2018 - C
Code for analysis of single cell signaling network kinetics from flow cytometry (CyTOF) datasets
flux
kinetics
simulated-annealing
signaling-pathways
signaling-networks
single-cell
cytof
mass-cytometry
kinetic-modeling
single-cell-analysis
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Mar 17, 2018 - Fortran
Aa free expandable Python package for building and analysing dynamic mathematical models of biological systems.
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May 18, 2021
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CLI already lints, but programmatic interface doesn't lint by default. Model linting should definitely be performed when import fails to avoid having to reimplement validation checks in amici and provide helpful error messages.