David P. Bullivant

An Overview of CellML 1.1, a Biological Model Description Language

CellML is an XML-based exchange format developed by the University of Auckland in collaboration with Physiome Sciences, Inc. CellML 1.1 has a component-based architecture allowing a modeller to build complex systems of models that expand and reuse previously published models. CellML Metadata is a format for encoding contextual information for a model. CellML 1.1 can be used in conjunction with CellML Metadata to provide a complete description of the structure and underlying mathematics of biological models. A repository of over 200 electrophysiological, mechanical, signal transduction, and metabolic pathway models is available at www.cellml.org.

A virtual environment and model of the eye for surgical simulation

An anatomically detailed 3-D computer graphic model of the eye and surrounding face within a virtual environment has been implemented for use in a surgical simulator. The simulator forms part of a teleoperated micro-surgical robotic system being developed for eye surgery. The model has been designed to both visually and mechanically simulate features of the human eye by coupling computer graphic realism with finite element analysis. The paper gives an overview of the system with emphasis on the graphical modelling techniques and a computationally efficient framework for representing anatomical details of the eye and for finite element analysis of the mechanical properties. Examples of realistic images coupled to large deformation finite element model of the cornea are presented. These images can be rendered sufficiently fast for the virtual reality application.

Modelling chloride and CO2 chemistry in the wairakei geothermal reservoir

Abstract The chloride and CO 2 chemistry of the Wairakei geothermal field, New Zealand, has been modelled using an extended version of the geothermal simulator TOUGH2. This version of the simulator solves the equations for the transport of reacting chemical species in multi-phase fluids, and is applied here to a detailed, full-scale geothermal reservoir model for the first time. Reactions involving the speciation of CO 2 to H 2 CO 3 and HCO 3 − are included in the model, as is the “Henrys Law” reaction for exsolution of aqueous CO 2 to the vapour phase. Because CO 2 speciation in water is pH dependent, a reaction involving the most important weak acid buffer at Wairakei (H 4 SiO 4 ) has also been included in the model. The chloride is treated as a conservative, non-reacting species that is present only in the liquid phase. Results from the model compare favourably with measured chloride and CO 2 data from Wairakei covering the period 1959–1987.

The CellML 1.1 Specification.

This document specifies CellML 1.1, an XML-based language for describing and exchanging models of cellular and subcellular processes. MathML embedded in CellML documents is used to define the underlying mathematics of models. Models consist of a network of reusable components, each with variables and equations manipulating those variables. Models may import other models to create systems of increasing complexity. Metadata may be embedded in CellML documents using RDF.

A neurobehavioural framework for autonomous animation of virtual human faces

We describe a neurobehavioural modeling and visual computing framework for the integration of realistic interactive computer graphics with neural systems modelling, allowing real-time autonomous facial animation and interactive visualization of the underlying neural network models. The system has been designed to integrate and interconnect a wide range of computational neuroscience models to construct embodied interactive psychobiological models of behaviour. An example application of the framework combines models of the facial motor system, physiologically based emotional systems, and basic neural systems involved in early interactive behaviour and learning and embodies them in a virtual infant rendered with realistic computer graphics. The model reacts in real time to visual and auditory input and its own evolving internal processes as a dynamic system. The live state of the model which generates the resulting facial behaviour can be visualized through graphs and schematics or by exploring the activity mapped to the underlying neuroanatomy.

Open Source Software Infrastructure for Computational Biology and Visualization

The CMISS software package is used in many biological research areas for multiscale computational biology and visualization. Some major components of this suite have recently been released under an open source license, specifically modules for field storage, 3D graphics, mathematical field operators and image processing. Interfaces are being developed to facilitate integration with other applications and the Internet

BL: A Visual Computing Framework for Interactive Neural System Models of Embodied Cognition and Face to Face Social Learning

Our behaviour emerges as the result of many systems interacting at different scales, from low level biology to high level social interaction. Is it possible to create naturalistic explanatory models which can integrate these factors? This paper describes the general approach and design of a framework to create autonomous expressive embodied models of behaviour based on affective and cognitive neuroscience theories.

Embodying models of expressive behaviour and learning with a biomimetic virtual infant

Face to face interaction is vital to social learning, however detailed interactive models which capture the richness and subtlety of human expression do not currently exist. As a step towards this goal, this paper gives an overview of the novel approach we are taking to develop BabyX, an experimental computer generated psychobiological simulation of an infant combining models of the facial motor system and theoretical computational models of basic neural systems involved in interactive behaviour and learning. These models are implemented in a novel modeling language for neural systems designed for animation and embodied through advanced 3D computer graphics models of the face and upper body of an infant. The system analyzes video and audio inputs in real time and generates autonomous animation through neurobehavioural models.

CellML 1.1 for the definition and exchange of biological models

Abstract CellML™ is an exchange fonnat developed by the University of Auckland in collaboration with Physiome Sciences, Inc., for describing the structure and underlying mathematics of biological models. CellML 1.0 has already been used to define electrophysiological, mechanical, signal transduction, and metabolic pathway models. Although CellML 1.0 is sufficient to describe most biological models, the structure is inadequate to support the increasingly complex systems in biology. CellML 1.1 has been developed to extend the component-based architecture of CellML 1.0 to facilitate model expansion and re-use.

Multi-scale and multi-physics visualization

Accurate computational models of physiology require the coupling of different physical processes that occur across a wide range of spatial scales. The interpretation and analysis of the calculated results of these models require the integrated visualization of these multi-scale and multi-physics processes. A number of different strategies for doing this are presented for a model of the heart left ventricle.