2. Introduction to (ODE) Modelling Best PracticesΒΆ
In this series of tutorials we demonstrate some modelling practices that we recommend you follow when developing any mathematical model. The key principles are modularity, reuse, and reproducibility - we demonstrate those here using the tool OpenCOR and the CellML and SED-ML exchange formats, but the principles are valid across the spectrum of computational physiology.
- 2.1. Tutorial on CellML, OpenCOR & the Physiome Model Repository
- 2.1.1. Background to the VPH-Physiome project
- 2.1.2. Install and Launch OpenCOR
- 2.1.3. Create and run a simple CellML model: editing and simulation
- 2.1.4. Open an existing CellML file from a local directory or the Physiome Model Repository
- 2.1.5. A simple first order ODE
- 2.1.6. The Lorenz attractor
- 2.1.7. A model of ion channel gating and current: Introducing CellML units
- 2.1.8. A model of the potassium channel: Introducing CellML components and connections
- 2.1.9. A model of the sodium channel: Introducing CellML encapsulation and interfaces
- 2.1.10. A model of the nerve action potential: Introducing CellML imports
- 2.1.11. A model of the cardiac action potential: Importing units and parameters
- 2.1.12. Model annotation
- 2.1.13. The Physiome Model Repository and the link to bioinformatics
- 2.1.14. SED-ML, functional curation and Web Lab
- 2.1.15. Speed comparisons with MATLAB
- 2.1.16. Future developments
- 2.1.17. References