Flexible user-guided network layout for biomedical applications. This project will develop techniques for automatic layout of biological network diagrams, allowing users to guide the layout while satisfying any required placement constraints and drawing conventions. As part of the project, these methods will be integrated into several real-world systems biology applications for network browsing and authoring.
Deep correction of DNA sequencing errors by data mining algorithms. This project aims to investigate the many layers of error correction problems in the terabytes of genomic sequence data, and aims to solve these problems by novel data mining algorithms. High-throughput sequencing platforms have generated massive amounts of useful raw data, but also made widespread errors. The new algorithms are capable of correcting errors at deeper layers to further enhance data quality. Expected outcome inclu ....Deep correction of DNA sequencing errors by data mining algorithms. This project aims to investigate the many layers of error correction problems in the terabytes of genomic sequence data, and aims to solve these problems by novel data mining algorithms. High-throughput sequencing platforms have generated massive amounts of useful raw data, but also made widespread errors. The new algorithms are capable of correcting errors at deeper layers to further enhance data quality. Expected outcome includes the knowledge advancement of genomic data industry and interdisciplinary collaboration between biotechnology and data mining. This also provides significant benefit for genomic decisions in forensics and personalised medicine which demand accurate genomic information.Read moreRead less
Efficient data mining methods for evidence-based decision making. This project aims to develop efficient data mining methods for causal predictions. Evidence-based decision making (EBD), such as evidence-based medicine and policy, is always preferable. To support EBD, causal predictions forecast how outcomes change when conditions are manipulated. Progress has been made in theoretical research on causal inference based on observational data, but few methods can automatically mine causal signals ....Efficient data mining methods for evidence-based decision making. This project aims to develop efficient data mining methods for causal predictions. Evidence-based decision making (EBD), such as evidence-based medicine and policy, is always preferable. To support EBD, causal predictions forecast how outcomes change when conditions are manipulated. Progress has been made in theoretical research on causal inference based on observational data, but few methods can automatically mine causal signals from the data and methods for efficient causal predictions based on data are even fewer. This project will apply its methods to biomedical problems. The outcomes could support smart and data-driven evidence based decision making in many areas, such as therapeutics and government policy making.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
Domain-specific visual languages for big data analytics applications. This project aims to invent domain-specific visual languages and support model-driven engineering based infrastructure so domain experts can specify, generate and apply complex data analytics and visualisation techniques. Many domains, including intelligent transport, business intelligence, and population health, need more effective “big data” analytics and visualisation. A challenge is to combine detailed domain knowledge – w ....Domain-specific visual languages for big data analytics applications. This project aims to invent domain-specific visual languages and support model-driven engineering based infrastructure so domain experts can specify, generate and apply complex data analytics and visualisation techniques. Many domains, including intelligent transport, business intelligence, and population health, need more effective “big data” analytics and visualisation. A challenge is to combine detailed domain knowledge – what the data means and what it can be used for – with sophisticated, scalable computational techniques to mine and present information from the huge volumes of raw data. This project is expected to improve productivity and quality of big data analytics and visualisation in critical domains.Read moreRead less
Metamorphic slices and their applications in fault localization. The main purpose of this project is to enhance the quality of software. The expected outcomes include the delivery of new cost-effective methods to debug software, and the extension of current debugging methods to be applicable in wider contexts.
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
Metamorphic Testing: An In-Depth Study to Enhance the Failure-Detection Capability of Software Testing Without an Oracle. Nowadays, software is pervasive and ubiquitous. It plays a significant role in the daily lives of all kinds of people. The Australian software industry has bloomed in recent years. Our research results will improve the cost-effectiveness of software development, thereby upgrading the nation's software productivity and quality. These factors are conducive to the export of soft ....Metamorphic Testing: An In-Depth Study to Enhance the Failure-Detection Capability of Software Testing Without an Oracle. Nowadays, software is pervasive and ubiquitous. It plays a significant role in the daily lives of all kinds of people. The Australian software industry has bloomed in recent years. Our research results will improve the cost-effectiveness of software development, thereby upgrading the nation's software productivity and quality. These factors are conducive to the export of software produced by Australians and helpful in raising our nation's competitive advantage towards the goal of becoming a leading nation in the software industry among Asia-Pacific countries.Read moreRead less
A Comprehensive Testing Methodology for Embedded Software. Embedded systems are a bedrock technology for many high-technology industries. They are used in many safety-critical situations, such as medical devices and car control systems, amongst hundreds of other applications. Unfortunately, current practice still sometimes results in disastrous mistakes remaining undetected, leading to multi-million dollar losses and in some cases even deaths. Improved testing methods for these systems offer ....A Comprehensive Testing Methodology for Embedded Software. Embedded systems are a bedrock technology for many high-technology industries. They are used in many safety-critical situations, such as medical devices and car control systems, amongst hundreds of other applications. Unfortunately, current practice still sometimes results in disastrous mistakes remaining undetected, leading to multi-million dollar losses and in some cases even deaths. Improved testing methods for these systems offer the potential of reducing such catastrophic losses. Improved embedded system testing techniques can offer Australia a competitive advantage in this strategically important industry. We will work to distribute our results to the Australian embedded systems community.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