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
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 400Â 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 400Â 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
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
Formalizing Software Design Pattern Concepts and Pattern Specifications using Metamodeling. Software design is currently an ad-hoc process that relies too heavily on each designer's personal experience. Software design patterns capture design know-how and make it reusable by identifying the problem and context in which a family of solutions can be applied. This project will use a formal metamodeling approach to define the concepts underlying software design patterns and hence will create precise ....Formalizing Software Design Pattern Concepts and Pattern Specifications using Metamodeling. Software design is currently an ad-hoc process that relies too heavily on each designer's personal experience. Software design patterns capture design know-how and make it reusable by identifying the problem and context in which a family of solutions can be applied. This project will use a formal metamodeling approach to define the concepts underlying software design patterns and hence will create precise and rigorous pattern specifications. Through this approach, we will incorporate patterns into the Unified Modeling Language (UML), the dominant object-oriented modeling language. Our pattern specifications will assist UML tool developers integrate software design patterns into their tools.Read moreRead less
Enhancing model-driven architecture with support for verification and validation. The proposed project will augment emerging methodologies for applying model-driven architecture to include verification and validation tools and techniques. This will decrease the time and effort required to develop software systems, and lead to better quality systems. It will evaluate and integrate existing verification and validation tools and techniques into the standards currently being developed to facilitate ....Enhancing model-driven architecture with support for verification and validation. The proposed project will augment emerging methodologies for applying model-driven architecture to include verification and validation tools and techniques. This will decrease the time and effort required to develop software systems, and lead to better quality systems. It will evaluate and integrate existing verification and validation tools and techniques into the standards currently being developed to facilitate model-driven architecture. This will strengthen Australia's software-based industries and its prominent role in defining international standards in this area.Read moreRead less
Analysing and Generating Fault-Tolerant Real-Time Systems. Safety-critical real-time systems are being deployed increasingly in diverse areas such as controlling critical infrastructure like transportation (e.g., railway signalling) as well as in defence applications (e.g., fly-by-wire). Such systems must be dependable and hence must be built using fault-tolerant strategies.
This project is researching frontier ICT technologies for analysing, designing and generating fault-tolerant systems, con ....Analysing and Generating Fault-Tolerant Real-Time Systems. Safety-critical real-time systems are being deployed increasingly in diverse areas such as controlling critical infrastructure like transportation (e.g., railway signalling) as well as in defence applications (e.g., fly-by-wire). Such systems must be dependable and hence must be built using fault-tolerant strategies.
This project is researching frontier ICT technologies for analysing, designing and generating fault-tolerant systems, concentrating on their software control components.Read moreRead less
A Grid based platform for multi-scaled biological simulation. Heart disease currently affects over 3.5 million Australians. In 2006 it claimed the lives of almost 46,000 Australians (34% of all deaths). We will develop enabling technology that underpins cardiac disease research, offering potential for new treatments and pharmaceutical therapies. Even a small improvement in this area can translate into significant national benefit. Further, the mathematical techniques and software tools we will d ....A Grid based platform for multi-scaled biological simulation. Heart disease currently affects over 3.5 million Australians. In 2006 it claimed the lives of almost 46,000 Australians (34% of all deaths). We will develop enabling technology that underpins cardiac disease research, offering potential for new treatments and pharmaceutical therapies. Even a small improvement in this area can translate into significant national benefit. Further, the mathematical techniques and software tools we will develop, whilst focused on heart tissue, will have broader applicability, and may underpin advancements in other disciplines. Finally, we expect that the software solutions and infrastructure will have both commercial and strategic value in their own right.Read moreRead less
Verified Emulation of Legacy Mission Computer Systems. Processor obsolescence is a serious maintenance problem for long-lived computer control systems in military aircraft and other critical applications. A promising solution is to interpose an emulator program between the original "legacy" software and a replacement processor. Unfortunately, no techniques exist for accurately verifying that this procedure preserves the original system's functional and timing behaviour. A particular challenge ....Verified Emulation of Legacy Mission Computer Systems. Processor obsolescence is a serious maintenance problem for long-lived computer control systems in military aircraft and other critical applications. A promising solution is to interpose an emulator program between the original "legacy" software and a replacement processor. Unfortunately, no techniques exist for accurately verifying that this procedure preserves the original system's functional and timing behaviour. A particular challenge is that processor emulations involve both legacy code and new subroutines, written in different programming languages. This project will enable verification of safety and mission-critical emulated systems by devising a multilingual modelling and reasoning formalism, based on program refinement theory.Read moreRead less