ISB 2017 Tutorial - Multiscale modeling in biomechanics

Tutors: David Nickerson, Soroush Safaei, Duncan Bakke, and Thor Besier, Auckland Bioengineering Institute, University of Auckland, New Zealand.

A long term goal for research in biomechanics is to be able to interpret measurements of biomechanical function from multiple physiological scales, including whole body kinematics and kinetics as well as molecular level function through, for example, blood biomarkers or tissue biopsies. This requires multi-scale modelling to relate the molecular function of muscles and other body organs to the integrated performance of the musculo-skeletal system. In many cases it also requires the models to be as specific to the individual as possible.

The Physiome Project is an international effort to establish an open science framework for biophysically-based multiscale modelling, including the development of standards, tools, and databases. The standards include CellML, SED-ML, and FieldML. The software includes OpenCOR, OpenCMISS, and MAP Client. A database of models is available at the Physiome Model Repository (PMR).

The Physiome Model Repository provides a framework for the storage, curation, discovery, and exchange of data. By using standards suitable to their data, scientists maximise their ability to reuse existing knowledge and enable others to make use of their achievements in novel work. Annotations ensure scientists are able to find existing data and are also able to correctly interpret and apply their own data. These tutorials are designed to help demonstrate and promote practices which will aid attendees in their own work. Attendees are encouraged to raise issues specifically related to their needs with the tutors.

In this tutorial we will demonstrate the use of the Physiome Project framework for interpreting physiological measurements of the musculo-skeletal system and show participants how to use the freely available tools OpenCOR, OpenCMISS and MAP-Client and their associated databases. We will also talk briefly about the future directions of the Physiome Project in relation to the musculo-skeletal system.

The following will guide participants through a series of tasks that will highlight some of the capabilities of the tools and technologies mentioned above, as well as to demonstrate some of the benefits of following standards-based workflows for model development and simulation. We believe will help ensure reproducible and reusable science.

Tutorial:

• Preparation
• Sharing
• Further models to explore
• Glossary
• Tutorial to do list

In addition to the actual tutorial material above, we provide here some further material that is relevant to this tutorial. This includes the PMR user documentation and a tutorial introducing CellML, OpenCOR, and PMR.

• Tutorial on CellML, OpenCOR & the Physiome Model Repository
• Auckland Physiome Repository

A final document that might be useful for those wanting further background reading on the use of bond graphs to guide the creation of CellML models is given here: BG-Composite-2017-07-17.pdf.