SciML/Catalyst.jl

Chemical reaction network and systems biology interface for scientific machine learning (SciML). High performance, GPU-parallelized, and O(1) solvers in open source software.

Language: Julia - Size: 205 MB - Last synced at: about 15 hours ago - Pushed at: about 16 hours ago - Stars: 477 - Forks: 79

SciML/SBMLToolkit.jl

SBML differential equation and chemical reaction model (Gillespie simulations) for Julia's SciML ModelingToolkit

Language: Julia - Size: 2.37 MB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 42 - Forks: 11

xiaomingfu2013/DelaySSAToolkit.jl

DelaySSAToolkit.jl: a tool in Julia for stochastic simulation with delays

Language: Julia - Size: 9.41 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 16 - Forks: 5

SciML/ReactionNetworkImporters.jl

Julia Catalyst.jl importers for various reaction network file formats like BioNetGen and stoichiometry matrices

Language: Julia - Size: 2.51 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 27 - Forks: 9

adityak714/scientific-computations

A collection of projects done individually, and with a peer, in Stochastic and Deterministic Simulations, Least Squares Analysis, and the usage of Singular Value Decomposition for Low-Rank Image Compression, as well as in Pattern Recognition, as part of a master's level course in Scientific Computing at Uppsala University.

Language: Jupyter Notebook - Size: 3.29 MB - Last synced at: 9 days ago - Pushed at: 9 days ago - Stars: 0 - Forks: 0

SciML/FiniteStateProjection.jl

Finite State Projection algorithms for chemical reaction networks

Language: Julia - Size: 464 KB - Last synced at: about 20 hours ago - Pushed at: 6 months ago - Stars: 20 - Forks: 9

mmariani123/ctmc_project

My current main work in progress which will probably branch into a second population genetics paper (solely deterministic here). CTMC malaria life-cycle SSA (stochastic) modelling project with potential CLI or Shiny UI. Mostly MALAB and Rust with some Python3 and C. See my main collaborator's faculty page: Potential employers are free to contact.

Language: Makefile - Size: 91.5 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0

mauricelanghinrichs/memocell

Bayesian inference of stochastic cellular processes with and without memory in Python.

Language: Python - Size: 55.4 MB - Last synced at: 8 days ago - Pushed at: about 1 month ago - Stars: 1 - Forks: 1

darrenjw/smfsb

Documentation, models and code relating to the 3rd edition of the textbook Stochastic Modelling for Systems Biology

Language: AMPL - Size: 62.5 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 32 - Forks: 5

clauswilke/pinetree

🌲 a flexible gene expression simulator with codon-specific translation rates

Language: C++ - Size: 3.25 MB - Last synced at: 3 days ago - Pushed at: 21 days ago - Stars: 11 - Forks: 5

Theophilus-Dwamena/A-three-state-continuous-time-Markov-jump-model

Stochastic simulation of Enzyme kinetics at work

Language: Jupyter Notebook - Size: 612 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0

vsukhor/utils

A collection of some handy utilities

Language: C++ - Size: 513 KB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 0 - Forks: 0

TommasoTarchi/stocco

A new implementation of a well-known stochastic model for carcinogenesis, augmented with competition dynamics and spatial structuring.

Language: Python - Size: 39.4 MB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 0 - Forks: 0

adolgert/CompetingClocks.jl

Simplest simulation to use non-Exponential transitions

Language: Julia - Size: 12 MB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 5 - Forks: 0

augustinas1/MomentClosure.jl

Tools to generate and study moment equations for any chemical reaction network using various moment closure approximations

Language: Julia - Size: 8.5 MB - Last synced at: 6 months ago - Pushed at: 8 months ago - Stars: 44 - Forks: 6

louisreese/CrisprCutSim

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

Language: C++ - Size: 922 KB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0

wcota/dynSIS

Implementation of SIS epidemic model for large and heterogeneous networks using Fortran.

Language: Fortran - Size: 1.51 MB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 9 - Forks: 2

t-silvers/kerr_mean_field_paper_2021 Fork of lkerr34/kerr_mean_field_paper_2021

Language: Mathematica - Size: 107 KB - Last synced at: 12 months ago - Pushed at: 12 months ago - Stars: 0 - Forks: 0

DLab/BBRC

Models for Biochemical and Biophysical Research Communications manuscript

Size: 86.9 KB - Last synced at: about 1 year ago - Pushed at: over 6 years ago - Stars: 0 - Forks: 1

ctogle/mini_gillespiem

Scalable stochastic simulation of chemical networks

Language: Jupyter Notebook - Size: 2.66 MB - Last synced at: about 1 year ago - Pushed at: almost 5 years ago - Stars: 0 - Forks: 0

ADicksonLab/OpenRXN

A free, open-source tool for modeling chemical reaction networks in Python

Language: Python - Size: 46.9 KB - Last synced at: about 1 year ago - Pushed at: over 1 year ago - Stars: 11 - Forks: 2

MrsYuuki/Gillespie_stoch_model

Working with Gillespie algorithm in order to exam Double step gene expression model.

Language: Python - Size: 257 MB - Last synced at: about 1 year ago - Pushed at: about 4 years ago - Stars: 1 - Forks: 1

yannlelorier/Stochastic-processes-network-epidemic

A simulation of the propagation of a virus using the Gillespie algorithm

Language: C++ - Size: 3.37 MB - Last synced at: over 1 year ago - Pushed at: almost 5 years ago - Stars: 0 - Forks: 0

mirnylab/pdSim

Gillespie simulations of advantageous drivers & deleterious passengers in cancer

Language: C - Size: 860 KB - Last synced at: over 1 year ago - Pushed at: about 6 years ago - Stars: 0 - Forks: 0

wangl-cc/EvolutionaryModelingTools.jl

Simulate evolutionary biology models with Gillespie algorithm.

Language: Julia - Size: 2.06 MB - Last synced at: 3 days ago - Pushed at: over 2 years ago - Stars: 7 - Forks: 0

EDS-Bioinformatics-Laboratory/GillespieExamples

Antoine van Kampen: Examples of the Gillespie algorithm

Size: 19.5 KB - Last synced at: about 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

twallema/pySODM

Simulating and Optimising Dynamical Models in Python 3

Language: Python - Size: 11.7 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 8 - Forks: 1

wcota/dynSIS-networkx

Networkx implementation of the SIS epidemic model for large and heterogeneous networks

Language: Python - Size: 28.3 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 14 - Forks: 4

Gdemaude/Gillespie

Numba accelerated implementation of Gillespie's algorithm for simulating stochastic processes

Language: Python - Size: 108 KB - Last synced at: over 1 year ago - Pushed at: almost 4 years ago - Stars: 2 - Forks: 0

durs125/BioResearch

Delay Gillespie Degrade and Fire with variable delay

Language: Python - Size: 463 MB - Last synced at: over 1 year ago - Pushed at: about 4 years ago - Stars: 0 - Forks: 1

locuoco/stochastic-chemical-kinetics

Stochastic chemical kinetics using Gillespie algorithm and chemical master equation, application to enzyme kinetics

Language: C++ - Size: 4.7 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

jacons/Chemical-Reactions-Simulator

Stochastic Simulator of Chemical Reactions

Language: Python - Size: 234 KB - Last synced at: over 1 year ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 0

wcota/dynSIS-py

Implementation of SIS epidemic model for large and heterogeneous networks

Language: Python - Size: 32.2 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 4

voduchuy/KrylovFspSsa

Fortran implementation of the Krylov-FSP-SSA algorithm for solving the Chemical Master Equation.

Language: Fortran - Size: 71.3 KB - Last synced at: over 1 year ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0

SergioPachonDotor/ToyMaker

Language: Python - Size: 217 KB - Last synced at: about 1 month ago - Pushed at: almost 2 years ago - Stars: 2 - Forks: 0

shehio/Computational-Biology

Language: Jupyter Notebook - Size: 21.6 MB - Last synced at: 6 months ago - Pushed at: over 5 years ago - Stars: 6 - Forks: 1

juliorodrigues07/computational_modeling

Computational modeling practical exercises.

Language: Python - Size: 2.61 MB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 0

lillux/gillespie_ssa

Implementation of Gillespie Stochastic Simulation Algorithm

Language: Jupyter Notebook - Size: 495 KB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 0 - Forks: 0

TomMakesThings/Gillespie-mRNA-Simulator

An mRNA reaction scheme simulator using the Doob-Gillespie algorithm in R

Language: HTML - Size: 15.8 MB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 1 - Forks: 0

PhyBi/miRNA-negative-feedback

This repository contains code for simulatuing 'miRNA-mediated negative feedback loop' model, given in the manuscript 'Effects of miRNA-mediated negative feedback on gene expression', using Gillespie algorithm

Language: Fortran - Size: 17.6 KB - Last synced at: 5 months ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

syedtaz/vermillion

Fastest stochastic simulator in the West.

Language: Rust - Size: 174 KB - Last synced at: about 2 years ago - Pushed at: almost 3 years ago - Stars: 0 - Forks: 0

edbonneville/gillespie-shiny

Shiny app simulating stochastic epidemics with Gillespie's direct method.

Language: R - Size: 166 KB - Last synced at: almost 2 years ago - Pushed at: over 5 years ago - Stars: 2 - 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: 5 months ago - Pushed at: about 3 years ago - Stars: 0 - Forks: 0

snsinfu/cxx-distr

Efficient discrete random distribution for C++. The implementation uses array-based sum tree to allow fast sampling and updates of weighted events.

Language: C++ - Size: 146 KB - Last synced at: about 2 years ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 0

qvhaelen/typhon

automatized generation of optimized Gillespie algorithm

Language: Fortran - Size: 3.91 MB - Last synced at: over 1 year ago - Pushed at: over 6 years ago - Stars: 1 - Forks: 0

j-lazo/population_models

Language: Python - Size: 1.09 MB - Last synced at: about 2 years ago - Pushed at: about 6 years ago - Stars: 0 - Forks: 0

nsdumont/Spatial-Epidemics-Dynamics-and-Synchronization Fork of 4MB3-ModelStudents/Project

Final Project for a Mathematical Biology course

Language: TeX - Size: 50.2 MB - Last synced at: about 2 years ago - Pushed at: over 7 years ago - Stars: 0 - Forks: 1

marvinboe/reTASEP

Implementation of TASEP with reinitiation and particles of arbitrary size.

Language: C++ - Size: 15.6 KB - Last synced at: almost 2 years ago - Pushed at: about 9 years ago - Stars: 0 - Forks: 3

KeepFloyding/numericalMethodsMat

A Matlab library of numerical methods for solving differential equations stochastically and continuously .

Language: Matlab - Size: 132 KB - Last synced at: about 2 years ago - Pushed at: over 7 years ago - Stars: 1 - Forks: 1