Software development

The Bioengineering Software Development Group (BSDG) is staffed by professional software developers and researchers contributing to a range of open source projects grouped under the Physiome project, with strong collaboration with other Auckland Bioengineering Institute members and overseas researchers.

The software developed by the group is also used both by the ABI and by international collaborators. This work has a significant research component and has resulted in numerous publications in recognised research journals.

The Physiome Project of the International Union of Physiological Sciences is a worldwide public domain effort to provide a computational framework for understanding human and other eukaryotic physiology. It aims to develop integrative models at all levels of biological organisation, from genes to the whole organism via gene regulatory networks, protein pathways, integrative cell function, and tissue and whole organ structure/function relations.

Related information

• Visit the IUPS Physiome Project website
• Read about the ABI Physiome Research Group

CellML is an XML-based language designed to specify, store, and exchange models of biological systems. It is used to describe the components, and the mathematical relationships between components, of biological models.

Related information

• Visit the CellML website for more information on this project
• Find out about the CellML Research Group

FieldML is typically used for the representation of 3D models, incorporating information relevant to a bioengineering context, such as information within the volume describing tissue structure, distribution of proteins and other biochemical compounds, anatomical and other biological annotation. These fields can be used to represent the dynamic geometry and solution fields of computational models at multiple scales, from cells and tissues to organs and organisms.

Related information

• Visit the FieldML page for more information on this project

OpenCMISS is a comprehensive software system for multi-physics and multi-scale bioengineering simulation. It is based on the original CMISS system, developed by the ABI over decades. OpenCMISS uses modern software development tools, and the system architecture supports both shared memory parallel processing and distributed memory parallel processing. Models and solutions are represented using FieldML. OpenCMISS is provided as a software library that can be embedded in a wide range of other software systems.

Related information

• Visit the OpenCMISS website for more information on this project

Cmgui is a software system primarily for visualisation of 3D bioengineering models , including the main types of models that FieldML represents, such as the simulation result fields from CMISS and OpenCMISS. Cmgui has advanced functions for the definition of computed fields, and custom visualisations. Cmgui is provided as both a stand-alone desktop application and a software library that that can be embedded in a wide range of other software systems. Zinc is an add-on for Firefox which allows cmgui visualisations to be embedded in web pages.

Related information

• Visit the cmgui page for more information on this project
• Download the Zinc add-on for Firefox

The Physiome Model Repository (PMR2) is an open source software system which can be used to provide a web accessible model repository for Physiome models. The PMR2 runs the CellML repository, where a web view is available for each model in the repository. It can be used for combined Physiome models that use multiple model representations such as CellML and FieldML.

Related information

• Visit the PMR2 page for more information on this project
• Explore the CellML repository

The Cardiac Atlas Project (CAP) seeks to establish a structural and functional atlas of the heart. The Bioengineering Software Development Group has developed the CAP database, which houses a few thousand cardiac magnetic resonance images (MRIs), and associated dynamic geometrical models of cardiac structure that have been fitted to the MRI data.

Related information

• Visit the Cardiac Atlas web site for more information on this project

The research component of the Bioengineering Software Development Group projects includes postgraduate study opportunities for students interested in applying advanced techniques from software engineering or computer science to problems in bioengineering software development. This is a new and emerging field, with opportunities for research into:

• Advanced multi-scale visualisation (and use of technologies such as OpenGL, WebGL and distributed visualisation software architecture)
• Symbolic representation of mathematical models
• Approaches to Physiome scale model databases and image databases
• Application of new techniques in multi-scale multi-physics bioengineering simulation such as the use of GPGPUs, HPC systems and parallelisation of numerical algorithms
• Other related bioengineering software development areas.

If you are interested in any of these opportunities, please contact Randall Britten, r.britten@auckland.ac.nz.