EnzymeML.jl

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🧬 About

EnzymeML.jl is the Julia implementation of the EnzymeML data format, providing seamless interfaces to popular modeling packages including DifferentialEquations.jl and ModelingToolkit.jl. It enables researchers to easily extract ODE systems, initial conditions, and parameters from EnzymeML documents for advanced biochemical modeling and parameter estimation.

✨ Features

• 🔄 Direct ODE System Creation: Generate ODE systems directly from EnzymeML documents
• 📊 Multi-measurement Support: Handle multiple initial conditions from experimental data
• 🎯 Parameter Extraction: Automatically extract and manage model parameters
• 📈 Visualization Ready: Built-in plotting capabilities for results analysis
• 🌐 EnzymeML Suite Integration: Seamless integration with the EnzymeML Suite GUI
• ⚡ High Performance: Leverages Julia's speed for computational efficiency

📦 Installation

Note: EnzymeML.jl is currently under development and not yet registered in the Julia package registry. You can install it by cloning the repository and adding it to your local Julia package environment.

using Pkg
Pkg.add("EnzymeML")

Or via the Julia REPL package manager:

] add EnzymeML

🚀 Quick Start

Here's a simple example to get you started:

using EnzymeML
using DifferentialEquations
using Plots

# Load an EnzymeML document
enzmldoc = load_enzmldoc("./ode_example.json")

# Create the ODE system directly from the document
sys, vars, params = @system(enzmldoc)

# Extract initial conditions and parameters
u0s = extract_measurements(enzmldoc, vars)
p = extract_parameters(enzmldoc, params)

# Create and solve the ODE problem
tspan = (0.0, 200.0)
prob = ODEProblem(sys, first(u0s), tspan, p)
sol = solve(prob, Tsit5())

# Visualize results
plot(sol)

📚 Examples

Explore comprehensive examples demonstrating different aspects of EnzymeML.jl:

🔬 ODE Systems

Learn how to create and solve ordinary differential equations from EnzymeML documents.

• Load EnzymeML documents
• Create ODE systems from reactions
• Handle multiple initial conditions
• Parameter estimation and updating

⚗️ Reaction Networks

Work with biochemical reaction networks using Catalyst.jl integration.

• Reaction system creation
• Multi-condition solving
• Results visualization
• Document updates

📊 Visualization

Create publication-ready plots from your EnzymeML data.

• Data plotting
• Result visualization
• Export capabilities

🖥️ EnzymeML Suite Integration

Connect with the EnzymeML Suite for GUI-based document management.

• REST API integration
• Document synchronization
• Live parameter updates

🤝 Contributing

We welcome contributions! Please open an issue or pull request.

📄 License

This project is licensed under the MIT License - see the LICENSE file for details.

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Made with ❤️ by the EnzymeML Team