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Catalyst: Fast and flexible modeling of reaction networks
Torkel E Loman1,2, Yingbo Ma3, Vasily Ilin4
1Sainsbury Laboratory, University of Cambridge, Cambridge, United Kingdom.
Plos Computational Biology
|October 18, 2023
Summary
Catalyst.jl is a new Julia library for simulating chemical reaction networks (CRNs) up to 100x faster than existing tools. It offers a flexible, high-performance platform for modeling, analysis, and code generation in Julia.
Area of Science:
- Computational chemistry
- Chemical kinetics modeling
- Scientific software development
Background:
- Chemical reaction networks (CRNs) are fundamental to many scientific domains.
- Accurate and efficient simulation of CRNs is crucial for advancing research.
- Existing tools often face limitations in performance and flexibility.
Purpose of the Study:
- Introduce Catalyst.jl, a Julia library for CRN modeling and simulation.
- Provide a flexible and high-performance solution for diverse CRN representations.
- Enable a streamlined pipeline for CRN specification, analysis, and code generation.
Main Methods:
- Developed Catalyst.jl as a Julia-native domain-specific language and intermediate representation.
- Implemented support for stochastic chemical kinetics, chemical Langevin equations, and reaction rate equations.
- Leveraged ModelingToolkit.jl and Symbolics.jl for symbolic analysis and code compilation.
- Conducted comprehensive benchmarks comparing Catalyst.jl performance against other tools.
Main Results:
- Catalyst.jl achieves simulation runtimes one to two orders of magnitude faster than popular alternatives.
- The library offers a flexible and feature-rich environment for CRN modeling.
- Demonstrated broad extensibility and composability with other Julia libraries.
Conclusions:
- Catalyst.jl provides a significant advancement in high-performance CRN simulation.
- Its Julia-native approach facilitates symbolic manipulation and optimized code generation.
- The library is poised to enhance research across various scientific disciplines through its efficiency and flexibility.
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