Australia's Virtual Herbarium

Australia’s Virtual Herbarium (AVH) provides web-based access to a federation of Australia’s 6 million plant specimen records held in major herbaria across the country, and makes them available over the internet to researchers and the public. 

Researchers can select specimens by family, genus, species, the herbarium where they are stored, and when, where and by whom they were collected.

Information is provided about each specimen, including its biological name, associated species and ecological preferences. The specimen information can be provided on the web page either as a table or a map showing the location of the speciments, or it can be obtained as a file in one of a selection of formats.

To facilitate getting the data into the AVH database, administrators can upload data in a variety of industry standard formats.

The data deluge is a major challenge for researchers; how can data from different studies, different research groups, and in different formats be integrated and shared with collaborators and other researchers?

eResearch SA has been working with special interest groups to develop solutions to the data problem. Using advanced information communication technologies, we’re building web-based data repositories for controlled data sharing and public access.

The AVH is a pioneering effort with particular value in displaying information about the geographic distribution of species, enhanced by images, descriptive text and identification tools. This is transforming the use of data that stretches as far back as the earliest days of European settlement.

AusStage Visual Mapping

Jonathan Bollen, Flinders University
Nathan Lambert, eResearch SA Summer Scholarship Receipient
Bradley Williams, eResearch SA Summer Scholarship Receipient

eResearch SA offers summer scholarships to academic high performers with an interest in eResearch. In 2008, eResearch SA awarded scholarships to Nathan Lambert and Bradley Williams to visualise networks of artistic collaboration using AusStage, supervised by Jonathan Bollen, Flinders University.

AusStage is a relational database of performing arts events. It records the relationships between events, venues, organisations, people, and resources. Researchers know, anecdotally, that social networks operate in the field of performing arts. They also know that interactions between artists, as they train, rehearse and work together, have implications for the kinds of artists they become and the kinds of performances they make. AusStage records the history of these networks of contacts and collaborations. Mapping performing arts events lets us see where artists perform and how productions travel. Network visualisation lets us see how performing artists interact.

The scholarship students set out to analyse these networks by visualising data from AusStage in network graphs and geographic maps. Nathan developed new approaches to analysing data in AusStage by using network visualisation to address the question, ‘who works with whom?’ His project explored software applications, data migration, and techniques for visualising AusStage network data relating to the performing arts in South Australia.

Bradley developed methods for integrating AusStage and venue data with geo-coded data from sources such as the Australian Bureau of Statistics, so as to display the results on interactive maps using Google Maps. His tasks were to research how AusStage data and Google Earth could be used together to provide a visualised map of the data, and how this data could be used in an informative way.

Nathan was successful in creating network graphs that displayed how contributors linked other contributors together (in most cases the linking contributors were the directors, playwrights, or designers). His graphs also provided a visual display of the Australian Dance Theatre’s toured work, showing the company’s wide coverage both within Australia and internationally, links between contributors who had participated in an Adelaide Festival or Fringe event, and a graph of all contributors to a South Australian event between 1970 and 1980.

Bradley found that Google Earth was limited in that it displayed historical events on a contemporary map. He was able to overlay historical maps on Google Earth so that venue data from the late 1800s could be displayed on a map from the same time.

The results of both of these scholarships will feed into future developments in AusStage. Perhaps the most exciting thing about these scholarships is that the approaches to data visualisation the students developed were central in attracting $500,000 of National eResearch Architecture Taskforce (NeAT) funding to develop production services based on these prototypes.

Grass microarray database project

Joy Raison, eResearch SA
Dr. Ute Baumann, Australian Centre for Plant Functional Genomics (ACPFG)

Abiotic stresses, such as temperature, water logging, drought, salinity and mineral deficiencies or toxicities are a major cause of yield and quality loss in cereal crops.

To develop varieties with resistance or increased tolerance to such stresses, scientists at the Australian Centre for Plant Functional Genomics (ACPFG) are working to determine which genes are activated or repressed in different varieties under different stress conditions, and the function of these genes in the metabolism of the plants.

Microarray technology has been developed to simultaneously detect the expression levels of thousands of genes in a sample of biological material. Microarray experiments are performed to determine differential gene expression in multiple biological samples.

The biological material could come from any organism, at any developmental stage, be from any tissue of the organism, and have undergone any treatment or stress regime. The design of each experiment will determine the biological material to be used and any treatments that will be applied to it.

To support genomic research, the results of microarray experiments can now be lodged at different web sites and made available to the public.

To take advantage of the information that these publicly available microarray datasets may have in relation to cereals under different abiotic stresses, eResearch SA, in conjunction with the ACPFG, developed a database to store microarray experiment related data on any species in the Poaceae (grass) family.

The aim of the Grass Microarray Database project is to collect, manage, and provide access to ACPFG and public microarray experiment data and related information for grass species in a single format.

Biologists, bioinformaticians and others are expected to access the data. Interfaces will be developed for each of these use groups to access the information they require.

Remote research collaboration using Access Grid

Rebecca Squires, Australian Research Alliance for Children and Youth (ARACY)

Access Grid is an internet-based collaborative communications package. It incorporates video and audio-conference tools, remote interactive control of software, and distributed viewing of content.

It can be used for remote meetings with talking heads, for remote teaching or meetings, as well as one-way or interactive content display, and, with the appropriate applications, interactive research and research discussion with remote control of software and hardware.

The Australian Research Alliance for Children and Youth (ARACY), a national non-profit organisation, makes use of eResearch SA’s videoconference room to hold monthly seminars. ARACY uses Access Grid technology to make the process of information exchange simple, beneficial and cost effective, and believes it is integral in helping to share information across time and distance barriers.

These seminars are used to share research project experiences and outcomes, as well as to disseminate data, and inform members and stakeholders regarding a wide range of issues affecting the wellbeing of children and young people.

ARACY’s member base spans Australia, and includes more than 1000 individuals and organisations. By creating virtual seminars, ARACY enables members and stakeholders to meet face-to-face. As one participant commented, ‘It really overcomes the tyranny of distance. It’s wonderful to be able to ‘virtually’ attend such seminars in my field of research.’

Meetings involve up to 70 participants and feature a shared PowerPoint presentation which is viewed simultaneously in each location, in conventional meeting room conditions. The flexibility of Access Grid technology supports ARACY’s goal to build and support collaborations of researchers, policy makers and practitioners across disciplines, to share knowledge and foster new ways of thinking and working.

eResearch SA’s Access Grid facility allows ARACY to maintain a high level of information exchange and to keep up to date with progress in all the various sectors impacting the wellbeing of children and young people. Access Grid also means members can meet personally without the need for extensive travel. Meetings may be held as often as is felt necessary, and with great freedom in scheduling.

Ocean modelling

 

Associate Professor Jochen Kaempf, Lecturer in Oceanography, Flinders University

In South Australia no issue is more important than water. To ensure drinking water is available in times of severe drought the State Government has invested $228 million in building a seawater desalination plant at Port Stanvac, Adelaide.

Associate Professor Jochen Kaempf, Lecturer in Oceanography, and his research group at Flinders University have been using eResearch SA’s supercomputing facilities for hydrodynamic modelling purposes in a rich variety of applications.

For example, Jochen’s model simulations have enhanced our understanding of the risks that seawater desalination poses to the marine environment.

Using eResearch SA’s high performance computing facilities, Jochen has been able to model the mixing of desalination brine with seawater to measure the impact on the dilution of salinity in sea water, and monitor the risk of marine pollution.

His model’s predictions currently play an important role in assessing the viability of BHP Billiton’s proposal to build a seawater desalination plant in Upper Spencer Gulf as part of the Olympic Dam expansion.

Jochen’s current focus is to develop new methods to quantify marine connectivity in the ocean, which is fundamental to understanding the ways marine systems operate including their response to environmental change. Overall, his research contributes to the implementation of sound, sustainable management of marine resources in Australia.

More information contact:
Assoc. Prof. Jochen Kaempf (email: jochen.kaempf@flinders.edu.au)

Mixed-metal and nano-sized catalytic clusters

Researchers from the School of Chemistry and Physics at the University of Adelaide have been using eResearch SA’s supercomputers to investigate the properties of catalysts that could be used to improve some of the world’s most significant chemical processes.

The development of more efficient catalysts holds huge potential gains for both industry and the environment. Catalysts speed up chemical reactions, significantly reducting capital costs for businesses, improving chemical and energy efficiency, and reducing the impact on the environment.

Around 80% of all current industrial chemical processes use catalysts. The world’s largest and arguably most important catalysed industrial process is the Haber-Bosch process for producing ammonia from N₂ and H₂. It alone consumes a huge 1% of the world's energy supply, meaning the potential gains from the discovery of more efficient catalysts are great.

Recent research effort has focussed on improving catalytic activity through the use of nano-sized metal particles. Nano-sized metal clusters containing 3–40 atoms have been shown to induce catalysed activity at significantly lower temperatures than bigger metallic surfaces. By combining the advantages of mixed-metal catalysts and nano-sized metal clusters, researchers think it may be possible to achieve unprecedented control over the activity, efficiency and selectivity of metallic catalysts.

To produce these improvements, researchers are working to understand the microscopic details of the catalytic process and, in particular, how molecular interactions with mixed-metal clusters change as a function of nanoparticle size and composition. Research currently being carried out using eResearch SA’s facilities addresses this; the goal is to undertake systematic experimental and computational investigations into the chemical and physical properties of mixed-metal clusters and their interactions with several important molecules such as N₂, CO, and CO₂.

One day this might even help researchers solve the holy grail of catalytic processes—how to convert atmospheric CO₂ gas simply and easily into another chemical compound, thus offering the world a clear climate change solution.

Fluid mechanics and turbulence modelling

Researchers from the School of Mathematical Sciences at the University of Adelaide are using eResearch SA's facilities to explore fluid mechanics and undertake sophisticated turbulence modelling.

Turbulence is characterised by unsteady three-dimensional fluid motion over a wide range of spatial and temporal scales. It is a fundamental problem in many fields, including astrophysics, oceanography, meteorology, combustion, aeronautics and engineering.

The equations governing turbulent flow have been known for over a century, however there is no known general solution. Instead, computers can be used to obtain approximate solutions. The problem is that in most cases of practical interest, the range of scales is so enormous that the computational problem cannot be solved on even the largest supercomputers. Therefore, simplified models are needed.

The goal of the researchers is to produce tractable models capable of reliably predicting turbulent flows. This involves the use of both state-of-the-art turbulence models and large-scale computational resources.

eResearch SA's supercomputer Corvus is being used to run code for this research project—the scale of the calculations is such that they could not be run on ordinary machines.

The image to the right is a visualisation of a turbulent mixing layer—the flow formed between two streams of different velocity. The image shows the mixed fluid only, coloured according to composition.

Quest for the South Magnetic Pole

Mark Pharoah, South Australian Museum

South Australian Maritime Museum

Dr. Paddy McGee, eResearch SA

During the 1908-1909 expedition to find the location of the South Magnetic Pole, stereographic photography was used to record various aspects of the expedition.

As part of the "Quest for the South Magnetic Pole" exhibition at the South Australian Maritime Museum, some of these stereo images are in display as red/cyan anaglyphs, allowing them to be viewed by groups of people at a time. The processing to convert the digitised copies of the original prints to anaglyph format was undertaken at eRSA, using the following steps:

• cut the left- and right-hand-side images from the digitised original
• clean / repair the images as necessary to reduce the appearance of spots, scratches and other faults
• adjust black and white levels, and gamma to improve the dynamic range of the images
• align the two images to provide a good sense of depth, suitable zero parallax, and acceptable ghosting in the final anaglyph image
• crop to suit a 4:3 landscape aspect ratio whilst maintaining the important sections of the image
• render as a single red/cyan image.

Using the anaglyph format for the displayed stereo images allows for flexibility (works with standard monitors and projectors), simplicity (only one standard projector or monitor is required), and robustness (allowing for touring the exhibition).

        

       

Flinders Ranges in stereo

Tim Baier, VFXgang
Rae Grierson, SA Great

Tim Baier works in the visual effects industry and is committed to the use of stereographic visuals in both an entertaining and intellectually satisfying way.

He has produced a stereo "documentary" covering the Flinders Ranges and the Arkaroola region in particular. A self-funded project, this work brings the geology of the Ranges to life in a way that is not possible via monoscopic (or two-dimensional) imagery.

Using single and paired cameras, the regimes range from macrophotography through to landscape photography from a microlight aircraft, all in stereo. Both single and time-lapse sequences were captured.

The many images thus obtained were developed into a cohesive presentation, in collaboration with Doug Sprigg (Arkaroola Wilderness Sanctuary), Professor Ian Plimer (Professor of Mining Geology at the University of Adelaide) and Dr. Jim Gehling (SA Museum), who all contributed to the accompanying text. The result is a work that describes in detail the unique geology of the Flinders Ranges via stereo imagery and informed comment.

The intent is to provide an audio-visual documentary, with stereo visuals, that can be shown at venues capable of screening stereo images. It is hoped that this project will generate an interest for visually and intellectually stimulating stereographic content that will be accessible to the public.

In association with SA Great, eResearch SA, and the Art Gallery of SA, this project was launched at a breakfast event on December 12th, 2007. The venue was the Radford Auditorium at the Gallery, where a portable (passive polarised) stereo projection rig was set up for the event.

After introductions by Judy Potter (CEO of SA Great), Christopher Menz (Director of AGSA), and Tim Baier, a screening of the work was given.

This event took place during the "A Century in Focus" exhibition at the Gallery, in which a number of antique stereo images were displayed as anaglyphs on computers monitors. The full range of stereo photography was on show, from early examples in that exhibition, to current state-of-the-art imagery at the launch.

As the original imagery for this project was taken at very high resolution (well above HD), the content is suitable for viewing at venues which have sufficiently large projectors to take advantage of the resolution inherent in these images.

A century in focus: Stereo images at the Art Gallery of SA

Julie Robinson, Senior Curator of Prints, Drawings and Photographs, Art Gallery of SA
Maria Zagala, Associate Curator of Prints, Drawings and Photographs, Art Gallery of SA
Dr. Paddy McGee, eResearch SA

A Century in Focus was an exhibition at the Art Gallery of South Australia (9/11/07 – 28/1/08), covering a century of South Australian photography from the 1840s to the 1940s.

Part of the exhibition covered stereo photography taken by George Burnell and H. H. Tilbrook. Burnell's images document a trip along the Murray River in the 1860s, whilst Tilbrook's images are from a few decades later, and were taken in a variety of locations.

A selection of original card-mounted stereo pairs from the Gallery's collection was digitised for conversion to a format suitable for viewing on computer monitors in the exhibition space. Red/cyan anaglyph presentation was selected as the method for most convenient display in this context.

At eResearch SA, the image files were processed as follows:

• The left and right-hand side images were cut from the digitised originals, and saved separately.
• These images pairs were rotated and translated as necessary for good alignment, and to give an acceptable level of ghosting when viewed with anaglyph glasses. Some edge-of-field depth conflict was on occasion necessary in order to achieve this.
• Image pairs were saved as single red/cyan anaglyph images.
• Black, gamma and white levels were adjusted so as to improve the dynamic range of the images.
• Scratches, blemishes, etc, were removed in order to improve the quality of the images, in particular to reduce their presence in either just the right- or left-side image, which can have a significant detrimental effect on stereopsis.

For the exhibition, the final anaglyphs were assembled into a cycling PowerPoint presentation, and displayed on LCD monitors. Red/cyan anaglyph glasses were available at each monitor for viewing.

The siting of the displays within the exhibition space is in accordance with the progression of the original photography in its historical context. Thus, the display of Burnell's work is early in the exhibition, as he flourished early in the era under consideration; Tilbrook worked later, and that display is positioned accordingly.

Experimentia: An Inter-Arts project

Director/Choreographer: Amanda Phillips
Composer: Alexander Waite Mitchell
Software Design: Jonathon Mah, Damian West
Performers: Gala Moody, Lisa Griffiths, Deon Hastie
Live Technology Performance: Alex Mitchell & Damian West
Filming: Alex Waite Mitchell, Damian West & Amanda Phillips

3xperimentia is a series of investigations at the interface of 3D stereoscopics and the visual and performing arts that has resulted from a successful arts-business partnership between eResearch SA and the team of interarts collaborators headed by Amanda Phillips and Alexander Waite Mitchell. 

3xperimentia is an ongoing public art and performance project that will evolve over time. Since 2007, this research has resulted in several outcomes including rendered versions of film and dance film creation, computer generated imagery and the development of custom software that facilitates live cinema and interactive installation versions of the work.

The flagship production 3xperimentia: Live Cut, Australia’s first 3D-stereo live edit performance, grew from this significant partnership. 3xperimentia: Live Cut, is a performed 3D stereoscopic cinema work fusing contemporary dance, computer generated imagery and real-time interactive effects.

Collaborating across performance and technology and continuing the artistic repertoire of Amanda Phillips and Alexander Waite Mitchell, the 3xperimentia creative team includes visual programming by Jonathon Mah and pre-filmed dance footage of stellar Australian performers Gala Moody, Lisa Griffiths & Deon Hastie.

3xperimentia: Live Cut was named ‘Best of The Fringe’ in The Advertiser for the 2009 Adelaide Fringe, and the production received a 2009 Ruby Award for Innovation; the Rubies are South Australia’s premier arts and cultural awards. This recognition confirms the value of the in-house research that the team conducts at eResearch SA through the use of the Visualisation Laboratory, camera systems and visualisation consultancy. 

Noted at the 2008 World Dance Alliance Global Summit as a ‘work with a high level of social and artistic currency,’ 3xperimentia integrates and develops both technology and performance.

The work is potently live as the dual un-rendered video streams are triggered through touch activation, operator manipulation and audio-reactive environments.

The continuing support of eResearch SA is vital to the research that this team of collaborators is conducting, and is an exciting example of a South Australian cross-industry partnership.

3D visualisation of protein modelling

Associate Professor Maria Hrmova, Australian Centre for Plant Functional Genomics

Protein modelling provides techniques whereby the three-dimensional structure and biological function of protein molecules can be identified.

Associate Professor Maria Hrmova from the Australian Centre for Plant Functional Genomics and the University of Adelaide researches the structures of agriculturally significant grass proteins for research into improving crop resistance to abiotic stresses such as temperature, drought, and salinity.

Results from X-ray crystallography studies of the proteins are processed using eResearch SA supercomputers. This processing allows the atomic structure of the proteins to be modelled.

Other software is used to display these models, so that they may be studied and interpreted visually. A stereo three-dimensional visualisation workstation, with specifications developed by eResearch SA, allows researchers to perceive the protein model in three-dimensional space; that is, as a natural, solid body, the shape and structures of which may be seen and interpreted intuitively by visual means.

The addition of the extra dimension of depth when it is perceived directly by stereopsis, rather than only indirectly by other clues such as occlusion or shading, greatly improves the ability to interpret structure and relationships within complex shapes.

Stereo visualisation makes it possible to precisely interpret the electron density map with respect to structural features such as backbone or ligands and how these features relate to each other. Interactions between these and other components, such as those between protein and DNA, or protein and carbohydrate, can then be modelled to help determine the precise biological role of the protein in the organism.

The eResearch SA visualisation workstation is supplied as a complete, integrated and ready-to-go system. For 3D display use, it incorporates a workstation graphics card, high-end cathod ray tube monitor, infra-red emitter with shutter glasses, and is pre-installed with Linux and appropriate open-source visualisation software.

Interactive stereo visualisation of modelled molecular structures

Dr. Grant Booker, School of Molecular and Biomedical Science, University Of Adelaide

Using molecular visualisation software such as Chimera, eResearch SA's VisLab and the SAVRC allow researchers to view molecules with full stereoscopic vision. This allows their three-dimensional structures to be interpreted much more readily than is the case with non-stereo imagery. This is particularly important when the interaction between molecules is of concern, since this is related to how closely the different molecules' surfaces can come into contact.

The ability to see directly this level of contact allows researchers to classify and rank molecular models very rapidly, thus greatly enhancing the efficiency of the molecular modelling process.

From Dr. Booker: "We have been using the VisLab to review protein structures that have been determined either locally or with colleagues from interstate and overseas. The ability to discuss the details of the three-dimensional structures with others helps to make sense of the molecular mechanisms associated with the functions of these proteins.

"Using the Vis Lab, we review the results of molecular docking experiments. We screen a target protein structure with the 3D coordinates of structures of up to 500,000 organic compounds using Dock 5.0 from the UCSF. A consensus-scoring algorithm is then used to select candidate structures that may act as ligands for the target. As a group, we are able to decide which of the top 50 candidates meet a range of criteria such as how well the shape of the molecule complements the binding site.

"We then purchase those compounds that meet our criteria for testing in biochemical or biological assays. Using this process we have been able to find high-affinity enzyme inhibitors.

"We have also been using SAVRC for Biochemistry III tutorials in order better to explain the intricacies of protein structure to students."

Visualisation of quantum chromodynamics

Professor Derek Leinweber, Discipline of Physics, University of Adelaide

Quantum chromodynamics (QCD) is a theory used to describe the interactions of quarks and gluons, fundamental sub-atomic particles which comprise more-familiar particles such as protons and neutrons.

Converting the mathematics of QCD theory into computer code, researchers are able to model the behaviour of these fundamental fields and particles. Such simulations are run on powerful supercomputers, such as those operated by eResearch SA, where their high computational speed and data-handling ability allow the vast number of calculations required to be performed in reasonable time frames.

Visualisation packages, such as Advanced Visual Systems (AVS) Express, are used to convert the large amount of data which are generated by such simulations into images. In many cases, various parameters of the model are calculated on a regular (x,y,z) grid, and AVS Express will be used to display these data as a three-dimensional plot.

Such graphical representation allows the researcher to see the variation in the data values across the simulated space in a simple and intuitively understood way. If the data are generated for different values of time, the evolution of these quantum-scaled fields and particles may be shown in a way that greatly assists their understanding.

Furthermore, with the appropriate display hardware (such as eResearch SA's VisLab, SAVRC, or desktop visualisation workstations), the images can viewed in real-time in stereo. As in many other fields of study, such stereoscopic viewing allows one much more readily to interpret complex three-dimensional structure than does monoscopic viewing. Indeed, the use of general visualisation software such as AVS Express, coupled with stereoscopic display, is of benefit to many areas of research.

Some of Professor Leinweber's animation work (see here for several examples), produced using AVS Express, was used in Professor Frank Wilczek's 2004 Nobel Prize Lecture.

South Australian Museum: Icthyosaur modelling project

Dr Ben Kear, SA Museum and School of Environmental and Earth Sciences, University of Adelaide

The South Australian Museum enjoys a globally significant collection of palaeontology specimens including unique and well-preserved fossil remains of ichthyosaurs, marine reptiles from the Mesozoic period.

In collaboration with Dr Ben Kear, a vertebrate palaeontologist from the SA Museum and the University of Adelaide, and Ben Hill, a student from the University of South Australia, eResearch SA provided advanced computing and visualisation support for a project to reconstruct the head of one such ichthyosaur.

With Dr Kear's advice, Ben Hill created a three-part computer model of the skull of an ichthyosaur. The model is as anatomically accurate as possible, including the size and position of the muscles controlling the jaw, the position of the eye and possible location and shape of the "nose".

The base of the model is a scan of a well-preserved ichthyosaur skull; on this were built several major muscles (from scars left on the skull) and then the external surface of the ichthyosaur.

The skull was scanned at the Queen Elizabeth Hospital. The DICOM images were then converted to .stl format (using Osirix) and imported into Rhino for the reconstruction and eventual animation using Quicktime Pro.

A number of marine fossils have been found in areas of Australia that are now well inland; studies of the geological history of Australia show that it once had a major inland sea.

 

 

 

 

 

Impossible images project

Professor Chris Mortenson, Discipline of Philosophy, School of Humanities, University of Adelaide

The term 'impossible images' refers to images depicting objects which cannot exist in normal 3-D Euclidean space.

Impossible images have a long history, stretching back to the walls of Pompeii. However, the major work was done in the twentieth century, beginning with Oscar Reutersvaard 1934, then following him some twenty years later by M.C.Escher and Roger Penrose, then later many others including Bruno Ernst.

Work has tended to focus on producing new sorts of images, while little work has been done on their mathematical description. However, the most fruitful approach to the latter would seem to be to define geometrical objects existing in an inconsistent 3-D space, with projections to the 2-D images.

This project aims to investigate impossible images on several levels.

1. to continue the work of producing new sorts of images
2. to classify those already found: so far, it seems that four main types have been discovered
3. to animate these images
4. to apply the techniques of stereoscopic images and virtual reality to produce 3-D effects
5. to provide mathematical descriptions of the inconsistent 3-D spaces, utilising the techniques of inconsistent mathematics.

For an example of the animation work being done, watch 'Escher Meets Ernst', by Peter Quigley, Chris Mortensen and Steve Leishman.

For more information, see Inconsistent Images.

eResearch SA's role in this project was the provision of stereo stills and video of real-life scenes which were edited in an attempt to convert real objects to impossible objects within the real-world framework, as well as advising on convenient viewing methods for such stereo content.

eResearch SA can advise on, and assist with, the capture, processing and display of stereographic stills and video imagery. We also have experience processing archival stereograms for display with contemporary equipment.

 

 

 

Bragg about Adelaide

Mark Pharoah, SA Museum

Craig Hill / Dr. Paddy McGee (eResearch SA)

When a beam of X-rays is passed through a regular, crystalline substance, the X-rays are diffracted, and will form a pattern on a suitable recording surface. The actual structure of the crystalline substance may be determined by the correct interpretation of this diffraction pattern. The discovery of this technique was of extreme importance in the many fields of research which involve chemical and molecular structure.

William Henry Bragg and his son William Lawrence Bragg won a Nobel Prize in 1915 for their definitive work in X-ray crystallography. In 1886, W.H. was appointed the Elder Chair of Mathematics and Experimental Physics at the University of Adelaide, and in 1908, W. L. graduated from the same institution with a B.A. with First-Class Honours in Mathematics.

As part of an exhibition at the State Museum of South Australia, eResearch SA developed a short presentation that covered the Braggs' use of X-ray diffraction in crystallography, its relevance to the deduction of the structure of DNA, and future prospects for crystallography in Australia.

This involved the creation of stereo computer-generated animations to represent X-ray diffraction by salt crystals and the crystalline form of DNA, and the processing of archival stereographic images for display in our VisLab. Scripting and presentation were done by eResearch SA staff.

As part of the opening of the Bragg exhibition, a presentation of the show was attended by the Premier Mike Rann, the Hon. Dr. Jane Lomax-Smith, and Professor Baroness Susan Greenfield (SA Thinker-in-Residence at the time).

This show ran once daily on week-days, for six weeks during August–September 2005, and was held in the eResearch SA VisLab.

 

 

 

 

'Harmony of the Spheres' concerts

Syntony vocal ensemble

Dr. Paddy McGee (eResearch SA)

Computer-generated animations developed by eResearch SA were used as a visual backdrop for concerts presented by Adelaide-based vocal group Syntony.

The animations consisted of a tour of our solar system, visiting all the major planets, including (as it was at that time) Pluto. Presentation was monoscopic, as a portable stereoscopic projection rig was not available, and most importantly, the visuals were intended as an accompaniment to the music, and not the other way around.

Rendering software was used to generate the imagery, with the virtual camera path set so as to display the main aesthetic qualities of the various planets.The animations were not timed to the pieces performed; during performance, a filler animation of a starry background was used between planet fly-bys, and was run until it was felt that the next fly-by should begin.

The two concerts were held in the Art Gallery of SA Auditorium, and at Veritas Winery in the Barossa Valley, in September and October 2004.

Flinders Medical Devices and Technologies

Professor Karen Reynolds, Flinders University

Many medical procedures rely on correct manipulation of both medical and surgical tools and anatomical structures. Flinders Medical Devices and Technologies is developing realistic medical and surgical simulations using computing (virtual reality) technologies. Haptics (or the sense of touch) is an important element of these simulations.

Haptics is a emerging area, and the more researchers do, the more the realisation emerges that it really is very early days in this field. Using eResearch SA's haptics workbench, the team at Flinders have been continuing to develop real-time applications, concentrating on the physics of simulations (methods for collision detection, deformation and so on) which is fundamental to the quality of the haptics.

The team is currently working on an endotracheal intubation simulator to teach doctors how to perform effective airway management. The haptics workbench uses a mirror to co-locate the virtual environment with the haptic environment. This is important in medical simulation because the user's hand needs to be where they see it in the scene.

Biotechnology sector

Biotechnology is a strategic area for South Australia, which hosts many world-class bioscience research groups in medical, agricultural and environmental bioscience with a wide range of applications including diagnosis and treatment of disease, wine chemistry, plant and livestock breeding, aquaculture, pest management, and water quality.

One of the crucial requirements for biotechnology is access to leading-edge bioinformatics capability enabling storage, querying and processing of biological data sets. This includes support for computationally intensive tasks such as searching and analysis of gene and protein data, protein modelling studies, drug design, and molecular dynamics simulations.

Biological data is increasing rapidly in size and complexity, which is driving the uptake of advanced high performance computing and grid computing technologies in bioscience. The Department of Plant Science at the Waite Institute and the recently established Australian Centre for Plant Functional Genomics study the physiology, molecular biology and genetic makeup of plants, with particular focus on the improvement of commercially important food crops such as wheat and barley.

The Centre has made signficiant contributions to support eResearch SA's high performance computing facilities, which are used for a variety of applications including gene and protein sequence analysis.

Bioinformatics

In the field of bioinformatics, the combination of computer science, information technology and the life sciences has been producing extraordinary results. Complex biological systems have begun to yield their secrets to the superior analytical and processing power of eResearch methods and technologies.

At eResearch SA, we’re working with bioinformatics researchers to develop new approaches for analysing patterns of ‘repeats’ in genetic code. Our bioinformatics specialists work closely with academic researchers to discover patterns in repeated code, annotate them, and classify them into groups.

We’re working with local scientists to scrutinise the bovine and equine genomes (among others) and learn more about which patterns occur together and which don’t. From this process, researchers are uncovering previously unknown repeat patterns in a variety of genomes.

The meaning and implications of repeated fragments has long been a subject of debate for genetic researchers. Strings of ‘repeated’ DNA comprise the bulk of the human genome but we know very little about what they do and how the segments relate to each other.

Understanding how and why these repeats function might one day help uncover some of the mysteries of evolution, explain different traits in populations of the same species, or reveal the workings of ‘repeat disorders’ in humans, such as Huntington’s Disease and Fragile X Syndrome.

Chemistry

The use of high performance computing in chemistry plays an important role in determining molecular structure and function, and the energetics and rates of chemical reactions. eResearch SA has a variety of computational tools available to enable chemists to apply the most appropriate theoretical modelling approach to the molecular systems of interest.

The design of advanced materials and molecular assemblies with novel physical and chemical properties represents a critical component in the development of emerging technologies. Molecular recognition is a specific non-covalent molecular attraction. Researchers are using eResearch SA's resources to explore a range of molecular recognition phenomena, including the molecular topologies of metal ion activated molecular receptors and light or pH controlled molecular devices. The figure shown here illustrates the structures of two aromatic anion receptors.

Another project concerns the oxidation chemistry of silylene (SiH₂), which is important in semiconductor manufacture and the photonics and aerospace industries.

 

 

 

 

 

Computer science

Researchers in the Distributed and High Performance Computing (DHPC) group work closely with eResearch SA in the procurement, installation, benchmarking and testing of supercomputing facilities. The DHPC group also uses eResearch SA facilities for research projects in parallel and grid computing.

Recent work has developed improved tools that allow highly accurate measurements of the communications performance of parallel computers. This has many applications, including the testing and optimisation of communications networks, protocols and algorithms. Results from these tools are also used in related work that has developed more accurate techniques for modelling and analysing the performance of parallel programs.

The DHPC group has been working on grid computing for several years. This research addresses the problem of effectively utilising multiple distributed computing resources for complex applications, particularly those involving the access and processing of data from large distributed data archives, such as image data from satellites or aerial surveys.

 

 

 

 

 

Fluid dynamics

Research mathematicians and engineers have a major impact on a wide variety of fundamental industrial, geophysical and engineering problems, encompassing applications such as:

• fluid flow through permeable media (petroleum engineering and water resource and salinity management)
• clean combustion technologies (reducing greenhouse emissions)
• drag reduction and noise control (automobile, ship and submarine design)

All these applications require techniques from computational fluid dynamics combined with very powerful computers to produce reliably accurate solutions to the nonlinear equations governing fluid flow.

Access to eResearch SA facilities allows Australian researchers in computational fluid dynamics to remain competitive with US, European and Japanese researchers at the forefront of these fields. It also provides an attraction to international collaborators. eResearch SA facilities also support new initiatives in modelling the dynamics of plasmas in the space environment.

Numerical modelling of ocean waves

A scientist at the US National Weather Service/NOAA studying the contribution of ocean swell to the global wave climate began his research in Adelaide on eResearch SA computers. Dr Jose Henrique Alva is using numerical modelling to study ocean wave heights, which is important in areas such as oceanographic and meteorological studies, ship routing, engineering design and recreational activities.

Figure 1 (below left) shows the yearly average significant height of waves generated at high latitudes of the South Atlantic Ocean for 2001. Figure 2 (below right) shows the monthly mean significant height of waves generated at high latitudes of the South Indian Ocean during December 2001. Both figures show how far waves generated with-in a given ocean basin can penetrate into other oceans as swell, carrying significant amounts of energy over very long distances over the Earth. This information will be used to generate the first study of how global swell affects ocean wave conditions.

 

 

 

Dr Alves has collaborated on this project with Professor Ian Young (University of Adelaide), Dr Hendrik Tolman (NWS/NOAA) and Mr Fabricio Branco (University of Sao Paulo, Brazil).

Computation of flow over a long circular cylinder

Flow over long circular cylinders occurs commonly in engineering projects. A prime example is towed array sonar, where a cylindrical tube containing a series of hydrophones is towed behind a ship or submarine. The sounds detected by the hydrophobes can be processed to obtain information such as the bearing of neighbouring vessels or the possible locations of oil reserves. The turbulent flow of water over the surface of the sonar interferes with the detection of weak acoustic signals. Detailed study of such flows will be expected to lead to improved sonar designs and processing techniques. The figure shows a snapshot of the time varying flow speed near a stationary cylinder in axial flow, computed using a parallel program developed by Milton Woods, a doctoral student in mechanical engineering.

Physics

The Standard Model of the universe is founded on quantum field theories in which the forces between the constituents of matter are mediated by the exchange of particles. Of particular interest is quantum chromodynamics (QCD), the theory proposed to describe the strong nuclear force, one of four fundamental forces of nature. The only way to reveal the properties of this fundamental theory is to numerically simulate the theory on a space-time lattice with millions of sites, which requires the use of high performance parallel supercomputers.

It was once thought that the vacuum of space was empty, however we now understand it to be permeated with quark and gluon field fluctuations described by QCD. In fact, scientists believe it requires an enormous amount of energy to clear these fields from the vacuum. Flux tubes of QCD fields form between quarks and confine them within particles such as protons and neutrons, making it impossible to isolate a single quark.

Recent breakthroughs in simulation techniques combined with eResearch SA's world-class supercomputing resources will enable South Australian physicists to determine the predictions of QCD and reveal the manner in which the fundamental forces  of nature give rise to the world around us.

Archimedes Consulting Pty Ltd

Archimedes Consulting Pty Ltd specialises in advanced processing and analysis of the Earth's magnetic and gravity fields with a view to aiding petroleum and mineral exploration. The internationally recognised form provides world-class processing and interpretation of high-resolution aeromagnetic field data. Deep crustal studies are undertaken with the specific interest of denining exploration targets for minerals explorers. The approach taken by Archimedes Consulting to interpretation is unique in that the methods provide results that are competitive with deep reflection seismic methods.

'In our processing of high-resolution aeromagnetic data, it is essential to use powerful multiprocessor computers,' says Dr Irena Kivior, Managing Director of Archimedes Consulting. 'Processing very large data sets requires intense computing and without access to eResearch SA machines it would be considerably more difficult to generate an output for petroleum exploration companies which is competitive with seismic data.' The resulting high-value information can save millions of dollars for petroleum exploration companies.

The link between Archimedes Consulting and eResearch SA was forged while Dr Kivior was working at the University of Adelaide and using University supercomputers in her research. When she formed Archimedes Consulting several years ago, the company became a commercial user of the facilities. The firm continues to use the supercomputing facility for research work with the National Centre of Petroleum Geology and Geophysics.

The techniques used by Archimedes Consulting to analyse data after the initial interpretation involved two principle methods: energy spectral analysis (ESA on grid date) and automatic curve matching (ACM on profile data).

Special processing, analysis and interpretation of aeromagnetic data for hydrocarbon exploration has been undertaken over many sedimentary basins including:

• in Australia, the North West shelf basins, Exmouth Sub-basin, the Barrow/Dampier Sub-basin, Amadeus Basin, Perth Basin and Bowen Basin
• in Egypt, the Gulf of Suez and the Red Sea
• in Saudi Arabia, the Eastern Province Basin, and
• petroleum provinces in the United Arab Emirates.

Proen Design Australia Pty Ltd: Engineering and design

Proen Design Australia is a leading product design and engineering consultancy based in Adelaide, South Australia. Proen combines extensive product design experience with highly sophisticated, state-of-the-art technology to provide product development services from concept design through to manufacture for Australian and international clients.

Proen clients come from a wide range of industries including consumer goods such as water purifiers and EFTPOS terminals, appliances including dishwashers and cooktops, automotive components like alloy wheels and truck chassis, and defence. The engineering analysis performed for clients in these industries places extremely high demands on computing resources, and Proen meets these by using facilities offered by eResearch SA.

Using eResearch SA's advanced supercomputing facilities, Proen can dramatically increase the scale and speed of its models to provide world-class solutions. The availability of these resources is a significant competitive advantage for Proen as the company works to grow its business in a global marketplace.

"With these facilities available to us, we have confidence that we can take on a job of any size," says George Campbell, Proen's director of computer-aided engineering services.

Proen's association with eResearch SA began several years ago in a South Australian university entrepreneurial initiative in which several Proen principals took part. They established an engineering business under the scheme and were able to take advantage of the computing facilities available to them.

Specialists within Proen are equipped to undertake a wide range of product research tasks, and the company's capabilities are further enhanced by strong links with educational institutions. Its research services include innovation and IP generation, technology transfer, market research, and applied research such as acoustic modelling and computational fluid dynamics.

United Water: Distributed systems and environmental technology

Established in 1996, United Water is the largest private water company operating in Australia and New Zealand, providing comprehensive water and wastewater services to more than 1 million people.

In Adelaide, South Australia, United Water is responsible for the management, maintenance and operation of six water treatment plants, four wastewater treatment plants, 130 storage tanks and 300 pumping stations, plus a 15,000km pipe network.

United Water also undertakes extensive research and development activities in both Australia and New Zealand to improve water and wastewater quality. United Water is a key node in the international research and development network of parent companies Thames Water and Vivendi Water. The company's research and development team is based in Adelaide.

UWI R&D is committed to exploring the application of high performance computing to enhance ongoing investigations into water distribution systems (optimisation of capital works programs as well as operations), reservoir modelling (pathogen fates and nutrient cycles), environmental biology (algal population modelling), computational fluid dynamics (water and wastewater treatment process design), and other areas of water resource and intrastructure management.

This committment is represented by a financial contribution to eResearch SA. Research and development is an essential component of United Water's success. The company conducts research internally to ensure that it is constantly innovative for its parent companies, Thames Water and Vivendi Environment, in the areas of water/biosolids reuse and management of algae and as contract researchers for a range of clients.

UWI partners include universities, cooperative research centres, government agencies, local councils, the Centre for Groundwater Studies, Thames Water, Vivendi Environment, other private utilities and the Australian Water Quality Centre. United Water's clients include local councils, state governments, private owners of systems and consultants.