Auckland Bioengineering Institute


Software Development

The Auckland Bioengineering Institute develops several software tools and frameworks to support its research activities.

ABI Software Group


Our software group is composed of professional software developers who contribute to a range of open source projects grouped under the Physiome Project, with strong collaboration with other ABI members and overseas researchers.

While developments are focused on core infrastructural software projects such as OpenCMISS and PMR2, members of the software group are eager to assist Institute members make use of the wide range of software tools and computational methods being developed at the ABI.

The Software Group consists of:

Portrait of

Richard Christie
Software Developer
Email: r.christie@auckland.ac.nz

Portrait of

Alan Wu
Software Developer
Email: alan.wu@auckland.ac.nz

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Noel Zeng
Web Developer/Administrator
Email: noel.zeng@auckland.ac.nz

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Hugh Sorby
Software Developer
Email: h.sorby@auckland.ac.nz

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Tommy Yu
Software Developer
Email: tommy.yu@auckland.ac.nz

OpenCMISS


OpenCMISS is a set of libraries and applications which provide the foundation for developing computational modelling and visualisation software, particularly targeting bioengineering.

OpenCMISS-Iron 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. Iron 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. Iron is provided as a software library that can be embedded in a wide range of other software systems.

OpenCMISS-Zinc (‘Zinc’) is a cross-platform software library for building complete modelling and visualisation applications, from rich model representation to high quality OpenGL graphics rendering.

For more information on this project, visit the OpenCMISS website.
 

Cmgui


Cmgui is a visualisation application built upon the OpenCMISS-Zinc library (see above.) It can be used for  visualisation of 3D bioengineering models, including the main types of models that FieldML represents, such as the simulation result fields from CMISS and Iron. Cmgui has advanced functions for the definition of computed fields, and custom visualisations.

For more information on Cmgui, visit the Cmgui webpage.

 

PMR2


The PMR2 software system is used to provide a web accessible model repository for Physiome models. It is an open source project. PMR2 powers the Physiome model 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.

For more information on this project, visit the PMR2 webpage.
 

Cardiac Atlas Project


The Cardiac Atlas Project (CAP) seeks to establish a structural and functional atlas of the heart. The ABI Software Laboratory 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.

For more information on this project, visit the Cardiac Atlas website.

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