E Science Applications
Characteristics of eScience
- High Performance Computation
- Distributed infrastructure
- Instruments are first class resources
- Lots of data
- Not just bigger fundamentally different
Overview of Message Lab role in eScience
One of the defining features of research conducted in Message Lab is that it is applications driven - that means that we use real applications to push the envelope of the tools and techniques that we develop. One outcome of this is that we have assembled a wide range of applications across different domains, and in many cases performed in collaboration with researchers from across the globe. This page shows a selection of eScience projects that have employed our tools and demonstrates their wide applicability.
The Age July 2006 - Message Lab has Super Powers.
eScience Research Themes
Message Lab's involvement in eScience follows a number of themes or disciplines, namely:
- Chemistry and Physics
- Medical and Life Sciences
- Engineering and Design
- Mathematics
- Economics and Finance
- Environmental Science
- Earth Sciences and Astronomy
Chemistry and Physics
Quantum Chemistry
with Wibke Sudholt, Kim K. Baldridge, University of Zurich
Quantum mechanical computer chemical models give accurate predictions but are computationally impractical for large molecules. Hybrid models use quantum mechanics to describe a small active region, and classical molecular mechanics for the rest. Combining the two methods is difficult. This work investigated the pseudobond approach where a hypothetical capping atom is used to saturate the chemical bonds.
Medical and Life Sciences
Drug Design
with Kim K. Baldridge, University of Zurich
Docking of drugs with cells involves interaction between relevant proteins and ligands. Models of this process use either classical molecular dynamics or quantum mechanics. The latter is more accurate but computationally infeasible with complex organic models.
This project has developed a hybrid algorithm, sufficiently accurate and computationally practical, that computes the binding energy for a given protein-ligand geometry. Nimrod/O was used to optimize that binding energy. The strength of the binding gives a measure of the efficacy of the drug.
Cardiac Modelling
Electrical activity of the heart is a product of that of the component myocyte muscle cells which in turn is produced by the flow of ions through ion channels in the myocyte membranes. More detailed models of ion flow processes are being developed with the ultimate aim of understanding both normal and dysfunctional hearts.
Ion Flux in Cardiac Models
with Andrew McCulloch, Anushka Michailova and Roy Kerchoffs, University of California, San Diego
This project used a new model of rabbit ventricular myocytes, running under Nimrod/O, to determine settings for the metabolic factors that would produce realistic behaviour.
Improved Models of Calcium Ion Dynamics
with Anna Sher, David Gavaghan, Denis Noble, and Penelope Noble, Oxford University
This work aims to improve existing ventricular cell models by replacing their description of Ca2+ dynamics with the local Ca2+ control models. This required that the parameters of the Ca2+ subsystem be re-fitted. Nimrod/O was used to optimise these.
Clinical Radiotherapy
with Mary Chin, Velindra Cancer Centre, U. K. and Jonathon Giddy, Cardiff University U. K.
The use of computer models of radiotherapy predicts the dosage delivered to various parts of the body. In a clinical situation this enables a regime tailored for the needs of each patient, to maximise the dose to a tumour while minimising the dose to healthy tissue.
To achieve the required accuracy such models are computationally demanding. This project used Nimrod to distribute the jobs.
Determination of Protein Structure
with Ashley Buckle, Monash University
Structural biology research places significant demands upon computing and informatics infrastructure. Protein production, crystallization and X-ray data collection require solutions to data management, annotation, target tracking and remote experiment monitoring. Structure elucidation is computationally demanding and requires user-friendly interfaces to high-performance computing resources. We are developing Grid computing approaches, using NIMROD, that aim to automate the structure determination process by allowing hundreds to thousands of candidate models to be tested in parallel, along with parameter sweeps. This infrastructure will be pivotal for accelerating the process of structural discovery.
Engineering and Design
Airofoil Design
with Clive Fletcher, CANCES, University of New South Wales, and Andrew Lewis, Griffith University
Computational fluid mechanics provides a mechanism for assessment of the aerodynamics of engineering designs. This project modelled the airflow around a wing profile to determine how the ratio of lift to drag varies with certain shape parameters. Nimrod/G was used to survey the parameter space and Nimrod/O to determine the shape that gives optimal lift to drag.
Flame Kernel Growth in Turbulent Flows
with Karl Jenkins , Cranfield University, UK
Efficient combustion in an engine requires a high proportion of the fuel to be burnt, which in turn depends on the flow of the fuel/air mixture. Computational models are now capable of predicting the turbulent flows involved
This research built new models of the turbulent flow and propagation of the flame front. Nimrod was used to sweep over values of certain parameters in order to determine optimal efficiency.
Human-Computer Interaction Design for Air Traffic Control
with Andrew Neal, Jacqueline Wicks and Peter Lindsay, ARC Centre for Complex Systems.
This project is developing a new approach to human reliability assessment of human-computer interaction design options with application to air traffic control. Operator Choice Models were developed for conflict detection and resolution tasks using experimental data collected from simulator trials with student subjects. The formal models were further used to explore the effect on performance of different computer-based tools. A parameter sweep was conducted, using the Nimrod tool, to compare predicted operator performance for four different design options on a range of different traffic patterns.
Antenna Modelling
with Andrew Lewis and Seppo Saario, Griffith University
The design of a test rig for a handset antenna incorporated a ceramic bead in order to reduce the distortion of the radiation pattern during testing. The design needed to choose properties of the bead to minimise that distortion. This was calculated using an electromagnetic model of the antenna and rig. As each calculation required over 20 minutes on a high end workstation, Nimrod was used both to explore the design space for the bead properties, and to find optimal settings.
Fatigue Based Design Optimisation
with Rhys Jones, Kumanan Krishnapillaia and Daren Peng, Monash University
Fatigue failure in structures is caused by the growth of cracks when subjected to repeated stresses. The process can now be modelled using finite element analysis to compute the stress field and models predicting the growth of crack tips within that field. Nimrod/G has been used to determine the effect of controlable parameters and Nimrod/O to determine optimal shapes that minimise crack growth.
Mathematics
Mathematicians have for centuries used numerical evidence to suggest hypotheses and sometimes to disprove them. More recently, certain types of theorems have been proved by computer programs.
The Norm of the Generalized Stieltjes Transform
Tom Peachey and Colin Enticott, Message Lab, Monash University
Integral transforms are commonly used in Physics and Engineering. The generalized Stieltjes transform, for example, has been applied in string theory. But the "norm" of this transform (its effect on the "size" of the functions transformed) is a long unsolved mathematical problem.
This project developed software to evaluate the effect of the transform on a particular class of functions. Then the evaluation of the norm becomes an optimization problem on the output. Nimrod/O was used to perform the optimization, running inside a Nimrod/G sweep which varied the relevant parameters.
Economics and Finance
Estimating Complex Production Functions
with Mark Neal, University of Queensland
Production functions are rules that relate economic outputs to the necessary inputs. This work used maximum likelihood methods of estimating the coefficients in these rules. The computations used Shazam econometric software running under Windows. By distributing the task using enFuzion (the commercial version of Nimrod), the computational task was reduced from several weeks to a few days.
Environmental Science
Sensitivity of the Australian Monsoon to Savannah Fire
with Amanda Lynch, Klaus Görgen, Monash University
This project investigates the climatic effects of a change in the fire regime in the savannah lands of northern Australia. Each simulation spanned a 21 year frame; 90 simulations were required, generating a major computational task. This was executed using Nimrod/G.
Climate Modelling with Web Services
with John McGregor and Jack Katzfey, CSIRO Marine and Atmospheric Research, Melbourne.
The task of computing a global climate model at a fine enough resolution to capture local features is computationally huge, and near the limit of current technology. Instead a global model (the Conformal-Cubic Atmospheric Model) simulation is computed with a coarse grid and the results used to drive a simulation having a fine grid over the local region of interest.
For a variety of reasons, the two models may be performed at different geographical locations. This project demonstrated the use of web services to control the workflow. In particular, the GriddLes approach enabled the models to communicate without modification and even allowed the local modelling to begin before the global model was complete.
Earth Sciences and Astronomy
Interactive Inversion in Structural Geology
with Louis Moresi and David May, Monash University, and Dietmar Müller, University of Sydney
Geophysical models of evolution of the earth's crust require specification of various model parameters. This project was concerned with the inverse problem of determining input parameters that produce realistic earth dynamics. This is can be phrased as an optimization problem, minimizing the difference between the model output and realistic evolution. However, assessment of such differences is best achieved by the subjective evaluation of expert observers. For this purpose, Nimrod/O was extend (to Nimrod/OI) to allow interactive assessments of the animations produced by the model.
Meteorite Formation
with Kurt Liffman, CSIRO Materials Science and Engineering, Melbourne
Meteorites are assumed to have formed in the solar nebula during the formation of the solar system. This work investigates the hypothesis that they formed in the innermost regions of the nebula and were then ejected to outer regions. Such a history should have effects on the size sorting of the chondrules and metal grains that compose the meteorite.
This project performed Monte Carlo simulations of this formation process, using Nimrod to distribute the work.
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