Visual Analytics for Next Generation Sequencing. Next-generation sequencing technologies have brought a revolution in biology and healthcare, while taxing the ability of scientists and clinicians to identify and process relevant data, to make sense of it all and communicate it to others in a concise and meaningful way. This project aims to tackle this problem through fundamentally new approaches to data selection and visualisation at very large scale, actively encoding for insight into underlyin ....Visual Analytics for Next Generation Sequencing. Next-generation sequencing technologies have brought a revolution in biology and healthcare, while taxing the ability of scientists and clinicians to identify and process relevant data, to make sense of it all and communicate it to others in a concise and meaningful way. This project aims to tackle this problem through fundamentally new approaches to data selection and visualisation at very large scale, actively encoding for insight into underlying biological and biomedical processes, bringing sustainable discovery of new relationships and variations within the data. The project aims to support new approaches to medical diagnosis and treatment, and offer crucial lessons to address the broader challenge of understanding large, complex data sets.Read moreRead less
Next-generation genomic resources to tackle parasitic diseases of animals. The revolution in genomics provides unprecedented opportunities to tackle destructive parasitic diseases affecting billions of animals worldwide. Through a synergy of leading-edge technologies and a strong partnership with BGI International, this project aims to deliver major conceptual advances in the understanding of parasitism; an unparalleled skills-base in genomics and bioinformatics; innovative new molecular technol ....Next-generation genomic resources to tackle parasitic diseases of animals. The revolution in genomics provides unprecedented opportunities to tackle destructive parasitic diseases affecting billions of animals worldwide. Through a synergy of leading-edge technologies and a strong partnership with BGI International, this project aims to deliver major conceptual advances in the understanding of parasitism; an unparalleled skills-base in genomics and bioinformatics; innovative new molecular technologies; and new treatments and diagnostic tests as biotechnological outcomes. This leap forward in Australia will substantially enhance the global profile of parasitology research, training and employment opportunities for early career scientists, and improve access to international research funding and networks. Read moreRead less
Searching for near-exact protein models. This project aims to develop novel and efficient heuristic-based algorithms leading to near accurate protein tertiary structure models. Knowledge about protein structures is fundamental to our understanding of living systems. The progress on experimental determination of these structures has been extremely limited and remains an open challenge in molecular biology. Computational prediction of protein structures from sequences is emerging as a promising ap ....Searching for near-exact protein models. This project aims to develop novel and efficient heuristic-based algorithms leading to near accurate protein tertiary structure models. Knowledge about protein structures is fundamental to our understanding of living systems. The progress on experimental determination of these structures has been extremely limited and remains an open challenge in molecular biology. Computational prediction of protein structures from sequences is emerging as a promising approach, but its accuracy is far from satisfactory. The software systems developed in this project will be used in structural identification of target proteins in drug design. This will make drug design process more efficient, saving time and cost, potentially saving lives.Read moreRead less
Statistical Methods for Next Generation Genome-Wide Association Studies. This project aims to develop cutting-edge statistical methods to analyse large genomic datasets and identify genetic variants associated with inter-individual differences in various human traits. Knowledge of trait-associated DNA variants is instrumental in understanding how natural selection has shaped human traits. By integrating genomic data from diverse and underrepresented populations, this project further expects to c ....Statistical Methods for Next Generation Genome-Wide Association Studies. This project aims to develop cutting-edge statistical methods to analyse large genomic datasets and identify genetic variants associated with inter-individual differences in various human traits. Knowledge of trait-associated DNA variants is instrumental in understanding how natural selection has shaped human traits. By integrating genomic data from diverse and underrepresented populations, this project further expects to contribute to the equitable use of genomic technologies in humans, regardless of geographical origins. Expected outcomes of this research include novel analysis methods and software tools, which should broadly and significantly benefit gene discovery in other species, including those of agricultural relevance.Read moreRead less
Reconstructing proteins to explain and engineer biological diversity. The aim of this project is to develop computational methods to construct entirely new proteins. Computational reconstruction of enzymes that have been extinct for over 400 million years has revealed remarkable opportunities for biotechnological innovation. The intended outcomes are to develop bioinformatics methods to broaden the scope of ancestral protein reconstruction to include protein super-families, to establish what spe ....Reconstructing proteins to explain and engineer biological diversity. The aim of this project is to develop computational methods to construct entirely new proteins. Computational reconstruction of enzymes that have been extinct for over 400 million years has revealed remarkable opportunities for biotechnological innovation. The intended outcomes are to develop bioinformatics methods to broaden the scope of ancestral protein reconstruction to include protein super-families, to establish what specific changes led to the evolutionary success of a protein, and to re-run evolution to generate proteins that perform in conditions suitable for industrial and agricultural applications, in particular the production of hydroxylated fatty acids for bioplastics. By examining proteins from many life forms, the project plans to develop a novel bioinformatics strategy to understand their evolution and engineer new proteins for use in production of chemical commodities.Read moreRead less
RNA structure prediction by deep learning and evolution-derived restraints. This project addresses the long-standing structure-folding problem of Ribonucleic acids (RNA) whose solution is essential for elucidating the roles of noncoding RNAs in living organisms. The proposed approach will detect hidden homologous sequences and enhance evolutionary covariation signals by developing new algorithms for search and smarter neural networks for deep learning. The project expects to generate new tools ....RNA structure prediction by deep learning and evolution-derived restraints. This project addresses the long-standing structure-folding problem of Ribonucleic acids (RNA) whose solution is essential for elucidating the roles of noncoding RNAs in living organisms. The proposed approach will detect hidden homologous sequences and enhance evolutionary covariation signals by developing new algorithms for search and smarter neural networks for deep learning. The project expects to generate new tools for structure-based probing of RNA evolutional and functional mechanisms. The outcomes should provide significant benefits by high-accuracy computational modelling of RNA structures that are difficult and costly to solve by current structural biology techniques but important for enabling biotech and clinical applications.Read moreRead less
Elucidating the genetics of attention deficit hyperactivity disorder by integrating pathway and prediction analyses. Attention deficit hyperactivity disorder (ADHD) is the most common psychiatric disorder in children; while treatments are available they are ineffective for many patients. This project will develop methods for predicting genetic effects at the level of the biological mechanism to assist in identifying new drug targets and behavioural interventions.
Cost-effective use of assertions in the verification and validation of distributed and real-time systems. The project will reinforce Australia as a world leader in empirical software engineering and software verification and validation research, thus building on Australia's strengths in ICT research and innovation. Through the involvement of a local software verification and validation company and through industrial case studies, this project will also improve the software verification and valid ....Cost-effective use of assertions in the verification and validation of distributed and real-time systems. The project will reinforce Australia as a world leader in empirical software engineering and software verification and validation research, thus building on Australia's strengths in ICT research and innovation. Through the involvement of a local software verification and validation company and through industrial case studies, this project will also improve the software verification and validation capabilities of local industry, allow them to save software development costs, and improve the quality of the software produced.Read moreRead less
Practical Tools and Techniques for the Testing of Concurrent Software Components. This project will develop tools and techniques for the practical, systematic testing of concurrent software components. Testing is a major means for ensuring that software performs as expected, but testing concurrent software is poorly understood even though the majority of complex, computer-based systems are concurrent in nature. The complexities arising from the non-deterministic nature of such software means tha ....Practical Tools and Techniques for the Testing of Concurrent Software Components. This project will develop tools and techniques for the practical, systematic testing of concurrent software components. Testing is a major means for ensuring that software performs as expected, but testing concurrent software is poorly understood even though the majority of complex, computer-based systems are concurrent in nature. The complexities arising from the non-deterministic nature of such software means that testing tools and techniques used for simpler, sequential software are inadequate. The outcomes of this project will consist of practical techniques for the effective testing of concurrent software components in general and tools for the testing of Java components in particular.Read moreRead less
Effective software process improvement in a large-scale defence contracting environment. Most organisations struggle to consistently develop high-quality software on schedule and within budget. Continuing changes in technologies and customer expectations complicate this challenge. Software process improvement frameworks aim to guide organisations towards best practice. This project will assess practical experience with individual software process improvement frameworks in a large-scale defence c ....Effective software process improvement in a large-scale defence contracting environment. Most organisations struggle to consistently develop high-quality software on schedule and within budget. Continuing changes in technologies and customer expectations complicate this challenge. Software process improvement frameworks aim to guide organisations towards best practice. This project will assess practical experience with individual software process improvement frameworks in a large-scale defence contracting environment, with the goal of developing an effective strategy for integrating them. The outcomes will include documented experience with specific process improvement frameworks and a strategy for an overall framework that combines them.Read moreRead less