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: 208 MB - Last synced at: 3 days ago - Pushed at: 8 days ago - Stars: 487 - Forks: 80

VishvasRanjan/Learning-Chemical-Reaction-Networks-CRNs

This repository contains the work that was conducted under the joint supervision of Dr. Behera and Prof. Sbalzarini at the Sbalzarini Lab, Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG) and the Center for Systems Biology Dresden (CSBD).

Language: Jupyter Notebook - Size: 10.2 MB - Last synced at: 13 days ago - Pushed at: 13 days ago - Stars: 0 - Forks: 0

clauswilke/pinetree

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

Language: C++ - Size: 3.25 MB - Last synced at: about 24 hours ago - Pushed at: 3 months ago - Stars: 12 - Forks: 5

augustinas1/MomentClosure.jl

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

Language: Julia - Size: 8.67 MB - Last synced at: about 6 hours ago - Pushed at: 27 days ago - Stars: 45 - Forks: 6

twallema/pySODM

Simulating and Optimising Dynamical Models in Python 3

Language: Python - Size: 16.1 MB - Last synced at: 15 days ago - Pushed at: about 2 months ago - Stars: 10 - Forks: 2

adolgert/CompetingClocks.jl

Simplest simulation to use non-Exponential transitions

Language: Julia - Size: 12.7 MB - Last synced at: 26 days ago - Pushed at: about 2 months ago - Stars: 5 - Forks: 0

SciML/SBMLToolkit.jl

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

Language: Julia - Size: 2.6 MB - Last synced at: 4 days ago - Pushed at: 2 months ago - Stars: 43 - Forks: 11

SciML/ReactionNetworkImporters.jl

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

Language: Julia - Size: 2.78 MB - Last synced at: 4 days ago - Pushed at: about 1 month ago - Stars: 28 - Forks: 9

SciML/FiniteStateProjection.jl

Finite State Projection algorithms for chemical reaction networks

Language: Julia - Size: 471 KB - Last synced at: 8 days ago - Pushed at: 2 months ago - Stars: 20 - Forks: 9

xiaomingfu2013/DelaySSAToolkit.jl

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

Language: Julia - Size: 9.41 MB - Last synced at: 7 days ago - Pushed at: 2 months ago - Stars: 16 - Forks: 5

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: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0

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: 3 months ago - Pushed at: 3 months 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: 4 days ago - Pushed at: 4 months 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: 63.5 KB - Last synced at: 8 days ago - Pushed at: 5 months ago - Stars: 32 - 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: 6 months ago - Pushed at: 6 months ago - Stars: 0 - Forks: 0

vsukhor/utils

A collection of some handy utilities

Language: C++ - Size: 513 KB - Last synced at: 11 months ago - Pushed at: 11 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: about 1 year ago - Pushed at: about 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: about 1 year ago - Pushed at: about 1 year 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: 10 months ago - Pushed at: 10 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: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

DLab/BBRC

Models for Biochemical and Biophysical Research Communications manuscript

Size: 86.9 KB - Last synced at: over 1 year ago - Pushed at: almost 7 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: over 1 year ago - Pushed at: about 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: over 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: about 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: over 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: 11 days ago - Pushed at: almost 3 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: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

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: almost 2 years 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: about 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: over 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: almost 2 years ago - Pushed at: over 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: almost 2 years ago - Pushed at: almost 2 years 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: almost 2 years ago - Pushed at: almost 4 years ago - Stars: 0 - Forks: 0

SergioPachonDotor/ToyMaker

Language: Python - Size: 217 KB - Last synced at: about 8 hours ago - Pushed at: almost 2 years ago - Stars: 2 - Forks: 0

shehio/Computational-Biology

Language: Jupyter Notebook - Size: 21.6 MB - Last synced at: 8 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: about 2 years ago - Pushed at: about 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: 8 months ago - Pushed at: 8 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: over 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: 7 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: over 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: almost 6 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: 7 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: over 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: almost 2 years ago - Pushed at: almost 7 years ago - Stars: 1 - Forks: 0

j-lazo/population_models

Language: Python - Size: 1.09 MB - Last synced at: over 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: over 2 years ago - Pushed at: almost 8 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: about 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: over 2 years ago - Pushed at: over 7 years ago - Stars: 1 - Forks: 1