99 Open source projects that are alternatives of or similar to SBMLToolkit.jl

CellMLToolkit.jl is a Julia library that connects CellML models to the Scientific Julia ecosystem.

The SBML Test Suite is a conformance testing system. It allows developers and users to test the degree and correctness of the SBML support provided in a software package.

Fast uncertainty quantification for scientific machine learning (SciML) and differential equations

GPU-acceleration routines for DifferentialEquations.jl and the broader SciML scientific machine learning ecosystem

Solving differential equations in R using DifferentialEquations.jl and the SciML Scientific Machine Learning ecosystem

Parameter estimation for dynamical models using high-performance computing, batch and mini-batch optimizers, and dynamic load balancing.

Benchmarks for scientific machine learning (SciML) software and differential equation solvers

A library for building differential equations arising from physical problems for physics-informed and scientific machine learning (SciML)

A framework for developing multi-scale arrays for use in scientific machine learning (SciML) simulations

Julia interface to Sundials, including a nonlinear solver (KINSOL), ODE's (CVODE and ARKODE), and DAE's (IDA) in a SciML scientific machine learning enabled manner

Robust, Fast, and Parallel Global Sensitivity Analysis (GSA) in Julia

The SciML Scientific Machine Learning Software Organization Website

Benchmarking, testing, and development tools for differential equations and scientific machine learning (SciML)

Multi-language suite for high-performance solvers of differential equations and scientific machine learning (SciML) components

A library of useful callbacks for hybrid scientific machine learning (SciML) with augmented differential equation solvers

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

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

PyDEns is a framework for solving Ordinary and Partial Differential Equations (ODEs & PDEs) using neural networks

A standalone program that reads files created with the graphical network editor Escher and converts them to files in community standard formats.

Python library for ODE integration via Taylor's method and LLVM

A simple but powerful C++ DAE (Differential Algebraic Equation) solver

A collection of functionality around rooted trees to generate order conditions for Runge-Kutta methods in Julia for differential equations and scientific machine learning (SciML)

An integrated visual environment for metabolic modeling with common methods such as FBA, FVA and Elementary Flux Modes, and advanced features such as thermodynamic methods, extended Minimal Cut Sets, OptKnock, RobustKnock, OptCouple and more!

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

A component of the DiffEq ecosystem for enabling sensitivity analysis for scientific machine learning (SciML). Optimize-then-discretize, discretize-then-optimize, and more for ODEs, SDEs, DDEs, DAEs, etc.

Helicopter Scientific Machine Learning (SciML) Challenge Problem

Fortran Library for numerical INTegration of differential equations

Boundary value problem (BVP) solvers for scientific machine learning (SciML)

C++ library for ODE integration via Taylor's method and LLVM

Universal modeling and simulation of fluid dynamics upon machine learning

Fortran Object-Oriented Differential-equations Integration Environment, FOODIE

Backend for DiffEqOnline, a webapp for scientific machine learning (SciML)

A web application to visualize and edit pathway models

Easy scientific machine learning (SciML) parameter estimation with pre-built loss functions

Owl's Differential Equation Solvers

Wrappers for the SciPy differential equation solvers for the SciML Scientific Machine Learning organization

Latent Differential Equations models in Julia.

ODE system solver made simple. For IVPs (initial value problems).

Advanced Multilanguage Interface to CVODES and IDAS

Bulirsch-Stoer integration of systems of ordinary differential equations in JavaScript

Artifitial Neural Networks for Solving Ordinary and Partial Differential Equations, in this case, Schrodinger's Equation for One Particle in a 1-Dimentional Box

Reachability analysis for closed-loop control systems

EPDE - partial differential equations discovery framework

An integrated software environment for multi-algorithm, multi-timescale, multi-spatial-representation simulation of various cellular phenomena

Repository for B0M36SPJ

Simulate PK-PD models defined as ODE systems

High-performance simulations of the Porous Electrode Theory for Li-ion batteries

A web application to visualize and edit the pathway models represented by SBGN Process Description Notation

Work in Progress to refactor and modernize the ODEPACK Library

This package contains a macro for converting expressions to use muladd calls and fused-multiply-add (FMA) operations for high-performance in the SciML scientific machine learning ecosystem

A python library for metabolic networks sampling and analysis

The official PySCeS project source code repository.

📖 Generation and Applications of Knowledge Graphs in Systems and Networks Biology

Files for my Nonlinear Systems and Controls class.

Workshop in omics integration and systems biology

Designs for new Base array interface primitives, used widely through scientific machine learning (SciML) and other organizations

Differential equations on manifolds

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

A brian2 extension to simulate spiking neural networks on GPUs

Computational Neuroscience Crash Course (CNCC 2019)