The Auckland Bioengineering Institute (ABI) develops and maintains a wide range of software — from lightweight automation tools to major international open‑source platforms. Much of this work contributes to the global Physiome Project, supporting reproducible computational physiology and biomedical research.
If you have a codebase that you believe belongs under the ABI‑Software organisation, please open an issue in the new‑repo‑requests repository. A member of the ABI‑Software team will review your request.
Below are examples of key open‑source projects developed or maintained by ABI researchers and developers.
Where possible, the primary ABI contact for each project is listed in the People section.
Funded by the NIH, the SPARC Portal accelerates autonomic neuroscience research by providing access to digital resources that can be shared, cited, visualised, computed, and used for virtual experimentation.
Discover more:
🔗 SPARC Portal
🔗 Map Viewer
A web platform supporting biomedical research in New Zealand, providing user‑friendly access to research data, project information, and progress monitoring.
Discover more:
🔗 About 12 Labours
Powered by the PMR2 software suite, the Physiome Model Repository hosts CellML models developed worldwide over the past two decades. PMR2 integrates:
- The Zope/Plone CMS
- The Git version control system
Find out more:
🔗 Physiome Model Repository
A Python framework for building toolchains and utilities for working with the JavaScript/Node.js ecosystem from Python.
Learn more:
🔗 Calmjs
A C++ library implementing the CellML specification, with bindings for Python, JavaScript, and Julia. Supports CellML 2.0, upgrades from CellML 1.x, model analysis, and code generation for simulation tools such as CVODE and KINSOL.
Explore more:
🔗 libCellML
A cross‑platform C++ library (with Python bindings) used as the backend for OpenCOR. Released under Apache 2.0.
Check it out:
🔗 libOpenCOR
A reproducible workflow environment with plug‑in tools for mapping and modelling workflows. Forms the basis of the SPARC Scaffold Mapping Tools.
Check it out:
🔗 MAP Client
🔗 Scaffold Mapping Tools
Continuum modelling software including the Zinc library.
Website:
🔗 CMLibs.org
A modelling and visualisation library written in C/C++ with APIs for C, C++, and Python. Used to build interactive graphical interfaces. Cmgui is the legacy visualisation tool built on Zinc.
Source code:
🔗 github.com/cmlibs/zinc
A cross‑platform environment for organising, editing, simulating, and analysing CellML files. Released under GPL v3.0.
Check it out:
🔗 OpenCOR
ZincJS is a WebGL‑based 3D interface library built on three.js.
Scaffoldvuer is a simple web interface for 3D model visualisation using ZincJS.
Discover more:
🔗 ZincJS
🔗 Scaffoldvuer
ABI developers and maintainers and their associated key projects.
| Name | Username | Key Projects |
|---|---|---|
| Alan Garny | agarny | OpenCOR, libOpenCOR, libCellML |
| Alan Wu | alan-wu | ZincJS, Scaffoldvuer, SPARC Portal, 12‑Labours Portal |
| Hugh Sorby | hsorby | libCellML, Mapping Tools, CMLibs |
| Richard Christie | rchristie | CMLibs Zinc Library |
| Tommy Yu | metatoaster | CalmJS, Physiome Model Repository |
To request a new repository under the ABI‑Software organisation, please open an issue here:
🔗 https://github.com/ABI-Software/new-repo-requests/issues/new?template=new-repo-request.yml
A member of the ABI‑Software team will review and process your request.
