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
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
Viewable Measures for Component-Based Software Engineering. Software costs over US$300 billion per year worldwide with around 70% of large projects failing to complete in time. Reliable estimation of development effort is a great challenge in Software Engineering. This project aims to develop a reliable multi-dimensional software size measure and an effort estimation model for a new method of development called component based software engineering. We will validate our results theoretically and ....Viewable Measures for Component-Based Software Engineering. Software costs over US$300 billion per year worldwide with around 70% of large projects failing to complete in time. Reliable estimation of development effort is a great challenge in Software Engineering. This project aims to develop a reliable multi-dimensional software size measure and an effort estimation model for a new method of development called component based software engineering. We will validate our results theoretically and test it against empirical data from software industry. We will provide novel visualization techniques to comprehend measurements of large systems. The outcomes will help software projects better estimate deadlines and budgets thus reducing costs significantly.Read moreRead less
Ownership-based Alias Analysis for Securing Unsafe Rust Programs. This project aims to develop an ownership-based alias analysis as a complement to Rust's ownership type system for improving Rust's memory safety. This project, therefore, expects to deliver an alias analysis foundation that can provide stronger memory safety guarantees than the state-of-the-art in detecting memory-safety violations and security vulnerabilities in real-world Rust programs that use unsafe language features. The exp ....Ownership-based Alias Analysis for Securing Unsafe Rust Programs. This project aims to develop an ownership-based alias analysis as a complement to Rust's ownership type system for improving Rust's memory safety. This project, therefore, expects to deliver an alias analysis foundation that can provide stronger memory safety guarantees than the state-of-the-art in detecting memory-safety violations and security vulnerabilities in real-world Rust programs that use unsafe language features. The expected outcomes are a deployable ownership-based alias analysis in the Rust compiler and an industrial-strength open-source framework. These outcomes are expected to provide significant benefits in improving software quality and security in Rust, an emerging language that offers both performance and safety.Read moreRead less
A framework for modelling feature variability and dependencies in software product lines. In most Australian software development organisations software products are developed individually rather than product line based. This project will promote the awareness of product line based software development and provide a frontier technology, the effective feature modelling approaches, to help Australian software industry transform from the single product based development to the product line based de ....A framework for modelling feature variability and dependencies in software product lines. In most Australian software development organisations software products are developed individually rather than product line based. This project will promote the awareness of product line based software development and provide a frontier technology, the effective feature modelling approaches, to help Australian software industry transform from the single product based development to the product line based development to achieve significant improvement on the productivity and the quality of the software development. This improvement will dramatically reduce the cost of software products and alleviate the pressure of skill shortage that currently threatens Australian economy.Read moreRead less
How novel ribosomal RNA gene repeat variants drive cellular function. The hundreds of ribosomal RNA gene repeat copies are a remarkable part of our genomes, as they encode the machinery responsible for all cellular protein synthesis and shape the structure of the nucleus. However, due to their high degree of sequence similarity, they still have not been assembled into the human genome reference. This project will resolve this impasse and furthermore uncover the functional impacts of a newly iden ....How novel ribosomal RNA gene repeat variants drive cellular function. The hundreds of ribosomal RNA gene repeat copies are a remarkable part of our genomes, as they encode the machinery responsible for all cellular protein synthesis and shape the structure of the nucleus. However, due to their high degree of sequence similarity, they still have not been assembled into the human genome reference. This project will resolve this impasse and furthermore uncover the functional impacts of a newly identified molecular diversity in the ribosomal RNA gene repeats. Outcomes include new paradigms for how the ribosomal RNA gene repeats drive protein synthesis and genome structure, and a blueprint to develop novel genomics applications for human health, biotechnology, and agriculture.Read moreRead less
Processing large data sets on commodity data-parallel hardware. The project aims to reduce the costs of software development by improving the accessibility of massively data-parallel processors, termed graphics processing units (GPUs). The project seeks to develop a high-level programming system with data streaming support targeting GPUs and multi-GPU architectures. This would facilitate the difficult task of developing parallel applications for high-performance computing architectures. The comb ....Processing large data sets on commodity data-parallel hardware. The project aims to reduce the costs of software development by improving the accessibility of massively data-parallel processors, termed graphics processing units (GPUs). The project seeks to develop a high-level programming system with data streaming support targeting GPUs and multi-GPU architectures. This would facilitate the difficult task of developing parallel applications for high-performance computing architectures. The combination of parallelism and data streaming is designed to enable efficient processing of data too big to be held in device memory, which is a common problem in scientific computing, data analysis and machine learning. The project plans to integrate data streaming into an existing system, currently targeting single GPU architectures and which is successfully used in both industry and research.Read moreRead less
Grid Computing for Phylogenetic Analysis. This interdisciplinary project relates to information technology and bioinformatics, which both can be classified as Frontier Technology in the priority areas outlined by the ARC. Grid computing and using the state-of-art IT technologies to solve grand challenging problems in phylogenetic analysis are forefront research topics in information technology and bioinformatics. The analytical results and new technologies obtained in this project will certainly ....Grid Computing for Phylogenetic Analysis. This interdisciplinary project relates to information technology and bioinformatics, which both can be classified as Frontier Technology in the priority areas outlined by the ARC. Grid computing and using the state-of-art IT technologies to solve grand challenging problems in phylogenetic analysis are forefront research topics in information technology and bioinformatics. The analytical results and new technologies obtained in this project will certainly have significant implications in the relevant areas. New platforms and software developed could have commercial value. It is of great significance that Australia maintains its pioneering position and international reputation in research in Grid computing and its applications.Read moreRead less
Provably Correct on-chip Communication-based Design. This project falls in the priority area of Frontier Technologies for Building and Transforming Australian Industries. Embedded systems have complex communication architectures and functionalities due to their mission- and time-critical applications. This project will develop verifiable algorithms and techniques for design reuse to address them, help solve outstanding problems in the VLSI/SoC community and to lift the country's visibility and ....Provably Correct on-chip Communication-based Design. This project falls in the priority area of Frontier Technologies for Building and Transforming Australian Industries. Embedded systems have complex communication architectures and functionalities due to their mission- and time-critical applications. This project will develop verifiable algorithms and techniques for design reuse to address them, help solve outstanding problems in the VLSI/SoC community and to lift the country's visibility and credibility in the area. The economic benefits are better techniques for design reuse for embedded systems that may be integrated into existing Computer Aided Design environments, with potential to commercialise the algorithms to Electronic Design Automation and vendors.Read moreRead less
Sequencing and assembling microbial community metagenomes in real-time. This project aims to assemble metagenomes directly from environmental samples using nanopore sequencing. Short-read approaches to metagenomics cannot assemble mixed genomes from an environmental sample, so focus on describing which species and genes are present. Long-read nanopore sequencing enables the assembly of full genomes of multiple species in a sample. Assembling complete genomes in important resources such as water ....Sequencing and assembling microbial community metagenomes in real-time. This project aims to assemble metagenomes directly from environmental samples using nanopore sequencing. Short-read approaches to metagenomics cannot assemble mixed genomes from an environmental sample, so focus on describing which species and genes are present. Long-read nanopore sequencing enables the assembly of full genomes of multiple species in a sample. Assembling complete genomes in important resources such as water and soil should lead to deeper understanding of the dynamics, variation and transfer of genetic material within these resources’ microbial communities, strategies to manage microbial diversity, and improved productivity and long-term sustainability for these resources.Read moreRead less