EEMnz/Assessment-thermal-models

Python codes for Assessment of thermal mode-based kinetic models via stratified cross-validation and TPE optimization

Language: Python - Size: 460 KB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 0 - Forks: 0

AMICI-dev/AMICI

High-performance sensitivity analysis for large ordinary differential equation models

Language: C++ - Size: 211 MB - Last synced at: 3 days ago - Pushed at: 5 days ago - Stars: 125 - Forks: 31

ReactionMechanismGenerator/ARC

ARC - Automatic Rate Calculator

Language: Python - Size: 56 MB - Last synced at: 10 days ago - Pushed at: 10 days ago - Stars: 46 - Forks: 24

ergodicio/adept

Automatic-Differentiation-Enabled Plasma Transport in JAX

Language: Python - Size: 6.04 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 33 - Forks: 6

klamt-lab/COBRA-k

A Python package for "classic" Constraint-Based Reconstruction and Analysis (COBRA) and the new COBRA with kinetics (COBRA-k). Link to documentation:

Language: Python - Size: 201 MB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 6 - Forks: 1

dweindl/rxnrater

steady-state rate equations for enzyme-catalyzed reactions

Language: Python - Size: 75.2 KB - Last synced at: 3 days ago - Pushed at: 21 days ago - Stars: 0 - Forks: 0

PySCeS/pysces

The official PySCeS project source code repository.

Language: Python - Size: 10.5 MB - Last synced at: 4 days ago - Pushed at: about 1 month ago - Stars: 39 - Forks: 11

yundumbledore/PET-TRACER

Posterior estimation of kinetic parameters from dynamic PET data with consistency models

Language: Jupyter Notebook - Size: 130 MB - Last synced at: 27 days ago - Pushed at: 27 days ago - Stars: 2 - Forks: 0

gemshub/GEMSGUI

GEM-Selektor graphical user interface (GEMSGUI)

Language: HTML - Size: 153 MB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 2 - Forks: 2

Isoherranen-Lab/RBP4_TTR_Retinol_Binding_Model

Serum retinol, RBP4, TTR statistical analysis and simulated binding

Language: HTML - Size: 2.13 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0

bowman-lab/enspara

Modeling molecular ensembles with scalable data structures and parallel computing

Language: Python - Size: 9.29 MB - Last synced at: 6 days ago - Pushed at: about 1 month ago - Stars: 36 - Forks: 17

markovmodel/PyEMMA 📦

🚂 Python API for Emma's Markov Model Algorithms 🚂

Language: Python - Size: 10.3 MB - Last synced at: 24 days ago - Pushed at: almost 2 years ago - Stars: 327 - Forks: 124

AbeelLab/jaxkineticmodel

Building, simulating, and training systems biology models using JAX/Diffrax

Language: Jupyter Notebook - Size: 29.8 MB - Last synced at: about 2 months ago - Pushed at: 3 months ago - Stars: 4 - Forks: 0

SystemsBioinformatics/stochpy

StochPy is a versatile stochastic modeling package which is designed for stochastic simulation of molecular control networks

Language: Python - Size: 266 KB - Last synced at: 23 days ago - Pushed at: 3 months ago - Stars: 41 - Forks: 11

itpplasma/GORILLA

GORILLA: Guiding-center ORbit Integration with Local Linearization Approach

Language: Fortran - Size: 40.9 MB - Last synced at: 3 days ago - Pushed at: 2 months ago - Stars: 10 - Forks: 3

gemshub/GEMS3K

Language: C++ - Size: 61.7 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 8 - Forks: 6

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

Language: Jupyter Notebook - Size: 397 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 45 - Forks: 34

Kinetica-jl/Kinetica.jl

Automated chemical reaction networking with long-timescale kinetic simulations in Julia

Language: Julia - Size: 19.2 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 6 - Forks: 0

EnzymeML/enzymeml-specifications

📖 - Formal definition of EnzymeML in various schema languages as well as APIs in various programming languages

Language: Go - Size: 2.02 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 2 - Forks: 1

ovitrac/radigen

Radigen 🧪⚛️: Python-based chemical kernel for simulating oxidation reactions from prompts

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biomass-dev/biomass

A Python Framework for Modeling and Analysis of Signaling Systems

Language: Python - Size: 26 MB - Last synced at: 6 days ago - Pushed at: 3 months ago - Stars: 30 - Forks: 13

kmaeda16/libRCGA

libRCGA is a C library for real-coded genetic algorithms (RCGAs).

Language: C - Size: 37.1 KB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0

paulwilhelmvlasov/NumericalFlowIteration

The Numerical Flow Iteration to numerically solve the Vlasov equation

Language: C - Size: 20.8 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 3 - Forks: 0

pasmopy/pasmopy

Patient-Specific Modeling in Python

Language: Python - Size: 5.09 MB - Last synced at: 3 days ago - Pushed at: 3 months ago - Stars: 18 - Forks: 7

USEPA/Inorganic_Chloramine_-Formation_and_Decay_Application

Chloramine Formation and Decay (CFD) Source Code

Language: R - Size: 2.97 MB - Last synced at: 2 months ago - Pushed at: 9 months ago - Stars: 1 - Forks: 3

USEPA/Chlorine_Breakpoint_Curve_Simulator

Chlorine Breakpoint Curve Simulator (CBCS) Source Code

Language: R - Size: 2.99 MB - Last synced at: 2 months ago - Pushed at: 9 months ago - Stars: 3 - Forks: 3

LLNL/EQ3_6

EQ3/6, a Software Package for Geochemical Modeling

Size: 43 MB - Last synced at: 5 months ago - Pushed at: about 3 years ago - Stars: 14 - Forks: 1

Alocaspi/Polymers-Kinetic-Mechanisms

Condensed-phase polymer degradation CHEMKIN format kinetic mechanisms.

Language: Liquid - Size: 11.3 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 6 - Forks: 1

tintin554/multilayerpy

A package to build, run and optimise a kinetic multi-layer model for aerosol particles and films

Language: Python - Size: 4.47 MB - Last synced at: 2 months ago - Pushed at: 8 months ago - Stars: 8 - Forks: 1

ShayanDodge/1D-FDTD-Plane-Wave-Plasma-MATLAB

This repository contains a MATLAB implementation of the 1D Finite Difference Time Domain (FDTD) method for simulating the propagation of plane electromagnetic waves in a plasma medium.

Language: MATLAB - Size: 17.7 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 7 - Forks: 1

KarrLab/wc_rules

Rule-based modeling for whole-cell models.

Language: Python - Size: 1.41 MB - Last synced at: 3 days ago - Pushed at: over 3 years ago - Stars: 10 - Forks: 3

muravyevV/thinks

Applications for analysis of thermal analysis data (DSC, TGA etc) and extraction of the reaction kinetics

Language: R - Size: 2.31 MB - Last synced at: 5 months ago - Pushed at: about 2 years ago - Stars: 1 - Forks: 1

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

Language: MATLAB - Size: 57.6 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 3 - Forks: 2

Shimaa/Ignition_Model

Machine Learning Regression Models for Kinetic Properities to predict Ignition Delay Time (IDT)

Language: Python - Size: 9.77 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

louisreese/CrisprCutSim

Stochastic simulation of CRISPR nucleases cleaving a pool of DNA or RNA

Language: C++ - Size: 922 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

dweth/mcsnac

Code for analysis of single cell signaling network kinetics from flow cytometry (CyTOF) datasets

Language: Fortran - Size: 183 KB - Last synced at: over 1 year ago - Pushed at: over 7 years ago - Stars: 1 - Forks: 0

kmaeda16/RCGAToolbox

RCGAToolbox is a MATLAB toolbox for parameter estimation of kinetic models.

Language: MATLAB - Size: 57.1 MB - Last synced at: about 1 year ago - Pushed at: over 1 year ago - Stars: 3 - Forks: 1

chinghao0703/ThermoTransport

Language: Matlab - Size: 16 MB - Last synced at: over 1 year ago - Pushed at: over 7 years ago - Stars: 1 - Forks: 0

BioSystemsUM/MEWpy

Metabolic Engineering Workbench

Language: Python - Size: 28.6 MB - Last synced at: over 1 year ago - Pushed at: about 2 years ago - Stars: 34 - Forks: 11

JBEI/KineticLearning

Learning Kinetic Models from Time Series Proteomics and Metabolomics Data

Language: Jupyter Notebook - Size: 6.45 MB - Last synced at: over 1 year ago - Pushed at: about 3 years ago - Stars: 28 - Forks: 17

srgathmann/ProgrammableOER

Code accompanying "Dynamic Promotion of the Oxygen Evolution Reaction via Programmable Metal Oxides" by S. R. Gathmann, et al. (ChemRxiv 2024)

Language: Jupyter Notebook - Size: 342 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 1

surajsept/cyanoRBA

A coarse-grained biochemical resource allocation model of phototrophic growth.

Language: Python - Size: 3.46 MB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 0

Ggypa/PET-pc_kinetic_modeling

A simple project for the development of kinetic models for the heterogenous reaction of glycolysis of PET-pc.

Language: MATLAB - Size: 288 KB - Last synced at: over 1 year ago - Pushed at: almost 2 years ago - Stars: 3 - Forks: 0

TsingelisK/NTUA-Robotics-II

💭 NTUA ECE Robotics II

Language: Python - Size: 1.91 MB - Last synced at: over 1 year ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 0

LMSE/kbistable

Code for Model-based Design of Bistable Cell Factories for Metabolic Engineering

Language: Matlab - Size: 93.3 MB - Last synced at: about 2 years ago - Pushed at: almost 8 years ago - Stars: 0 - Forks: 0

bio-phys/PyDHAMed

Dynamic Histogram Analysis To Determine Free Energies and Rates from Biased Simulations

Language: Jupyter Notebook - Size: 3.36 MB - Last synced at: over 1 year ago - Pushed at: over 7 years ago - Stars: 19 - Forks: 7

ruslankotl/rk-inator

1st order ODE numerical solver

Language: Python - Size: 641 KB - Last synced at: about 2 years ago - Pushed at: almost 5 years ago - Stars: 0 - Forks: 0

MetaSys-LISBP/glucose_acetate_interplay Fork of pierremillard/glucose_acetate_interplay

Supplementary information of Millard et al. 2023

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mbabar09/PNP_kinetics

Solve steady state Poisson-Nernst-Planck equation coupled with high-dimensional rate models for generating high throughput voltammograms.

Language: Python - Size: 12.7 MB - Last synced at: over 1 year ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 0

MetaSys-LISBP/IsoSim Fork of pierremillard/KIEs

IsoSim: stoichiometric, kinetic and isotopic modeling of metabolic systems

Language: R - Size: 221 KB - Last synced at: about 1 year ago - Pushed at: almost 6 years ago - Stars: 6 - Forks: 3

cchandre/VM15D

Hamiltonian fluid reduction of the 1.5D Vlasov-Maxwell equations

Language: Mathematica - Size: 2.12 MB - Last synced at: about 1 month ago - Pushed at: almost 3 years ago - Stars: 1 - Forks: 0

biomass-dev/BioMASS.jl

Julia interface to BioMASS

Language: Julia - Size: 1.66 MB - Last synced at: 3 days ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 2

MetaSys-LISBP/acetate_regulation

Kinetic modeling of glucose and acetate metabolisms in E. coli

Language: Component Pascal - Size: 21.6 MB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 5 - Forks: 2

VlachosGroup/DescriptorMap

Automatic descriptor selection and volcano curve generation

Language: Python - Size: 5.55 MB - Last synced at: over 2 years ago - Pushed at: over 2 years ago - Stars: 2 - Forks: 1

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.

Language: C++ - Size: 49.7 MB - Last synced at: over 2 years ago - Pushed at: over 4 years ago - Stars: 10 - Forks: 0

pierremillard/glucose_acetate_interplay

Supplementary information of Millard et al. 2022

Language: Component Pascal - Size: 241 KB - Last synced at: over 2 years ago - Pushed at: almost 3 years ago - Stars: 0 - Forks: 1

joschwrzr/High-Res-Incubation_modelFit

Applying three different model approaches to an incuabtion data-set

Language: R - Size: 85 KB - Last synced at: over 1 year ago - Pushed at: about 3 years ago - Stars: 0 - Forks: 0

sayanadhikari/xoopic

X11-based Object-Oriented Particle-In-Cell Code

Language: C++ - Size: 52.9 MB - Last synced at: over 2 years ago - Pushed at: over 4 years ago - Stars: 1 - Forks: 0

sedaradoykova/BIOL0044_protometabolism_modelling

Code and reading materials related to my BIOL0044 MSci Investigative Project at the Lane Origins lab.

Language: HTML - Size: 145 MB - Last synced at: 9 months ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0

QTB-HHU/modelbase

Aa free expandable Python package for building and analysing dynamic mathematical models of biological systems.

Size: 1.83 MB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 2

shyamsrinivasan/ident

Perform identifiability analysis in small kinetic models for experimental design using steady state fluxes and concentrations.

Language: Jupyter Notebook - Size: 281 MB - Last synced at: over 2 years ago - Pushed at: over 6 years ago - Stars: 1 - Forks: 2

qvhaelen/typhon

automatized generation of optimized Gillespie algorithm

Language: Fortran - Size: 3.91 MB - Last synced at: about 2 years ago - Pushed at: about 7 years ago - Stars: 1 - Forks: 0

mkoehnke/CarND-MPC-Project

Model Predictive Control Project for Self-Driving Car ND using C++

Language: C++ - Size: 22 MB - Last synced at: over 2 years ago - Pushed at: about 8 years ago - Stars: 0 - Forks: 0