CellML Tutorials

This section contains a set of tutorials and documents that describe how to use CellML and its associated software. These documents are written to be independent, but it would help to start at the top of this list and work down.

CellML (www.cellml.org) is a model encoding standard that is used to ensure model reproducibility. OpenCOR (www.opencor.ws) is a simulation package written by Alan Garny that is designed for authoring and running CellML models. It is freely available for Windows, Mac and some Linux platforms. The Physiome Model Repository (PMR, https://models.physiomeproject.org) is a repository of CellML and FieldML models, together with associated data, that can be accessed from OpenCOR. This talk will be based on a tutorial that covers the use of CellML, OpenCOR and PMR (see www.cellml.org/getting-started/tutorials).

VPH tools tutorial at EMBC 2013

This tutorial introduces the Physiome Model Repository, OpenCOR, and the MAP framework.

OpenCOR features demonstration

This tutorial introduces the simulation and graphing features of OpenCOR, and outlines some of the other completed or planned functions of the software.

Introduction to modelling with CellML using OpenCell

By following this tutorial you will learn how to create a simple, functional CellML model from scratch using a CellML editing and simulation environment called OpenCell, and how to display the results of simulating this model on a graph.

This tutorial is also available as a YouTube video.

Introduction to modelling with CellML using COR

This tutorial helps you get started with CellML by guiding you through the process of building a model with COR, then using the model you have created to introduce the various parts that make up a CellML file. Modular modelling using CellML 1.1 is also discussed.

Translating a mathematical model into CellML

This tutorial describes the multi-step process of translating a model into CellML. This process typically involves the identification of a model in a published paper, followed by its translation into CellML, simulation, and curation, and ends with the model being uploaded into the CellML Model Repository.

Running simulations and sessions with OpenCell

A OpenCell session is a configuration file that allows a user to set up the interface to display a set of simulation results in a particular way. Sessions are particularly useful for demonstration purposes such as getting a model to automatically reproduce.

Curating models in the CellML Model Repository

An outline of theory underlining CellML model curation and the steps we undertake to get a model into a working condition.

Modular modelling with CellML 1.1

This tutorial discusses how CellML 1.1 can be used to create modular models.

Using generated C code for CellML models

This document contains instructions on how to run the C code that is generated by PMR2, OpenCell, or the CellML API C Code Generation Service (CCGS).

CellML and model repository tutorials

These materials have been prepared for conference workshops or hands-on tutorials, and are provided as .zip files. These archives include PDF documentation and the model files required to complete the tutorials.

Introduction to CellML and modular 1.1 modelling (PKPD models)

Introduction to CellML and modular 1.1 modelling (electrophysiology models)

PMR2 tutorial