Understanding somatic mutation in plants: new methods, new software, new data. Somatic mutations accumulate as plants grow, affecting everything from short-term ecological interactions to long-term evolutionary dynamics. These mutations have important consequences for plant industry and conservation, but because they are so hard to measure almost nothing is known about them. This project aims to develop new methods and software to detect, analyse, and compare the genome-wide history of somatic m ....Understanding somatic mutation in plants: new methods, new software, new data. Somatic mutations accumulate as plants grow, affecting everything from short-term ecological interactions to long-term evolutionary dynamics. These mutations have important consequences for plant industry and conservation, but because they are so hard to measure almost nothing is known about them. This project aims to develop new methods and software to detect, analyse, and compare the genome-wide history of somatic mutation in individual plants, providing an unprecedented level of detail into an important but understudied source of biological variation. By applying these methods to an iconic experimental population, This project aims to provide the first insights into the genome-wide causes and consequences of somatic mutation in plants.Read moreRead less
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
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
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
Achieving Tailored Industrial Software Process Improvement with Experience Repositories and Electronic Process Guides. There is a well-recognised need for organisations to improve their software development processes in order to achieve higher software quality and greater efficiencies in development. The use of electronic process guides and experience repositories have been two technologies independently proposed to achieve these aims. This research will develop a framework, methods and tools ....Achieving Tailored Industrial Software Process Improvement with Experience Repositories and Electronic Process Guides. There is a well-recognised need for organisations to improve their software development processes in order to achieve higher software quality and greater efficiencies in development. The use of electronic process guides and experience repositories have been two technologies independently proposed to achieve these aims. This research will develop a framework, methods and tools to allow integration of experience repositories and electronic process guides to facilitate process tailoring, process improvement, and project management. The result will be significant improvements in software development productivity and quality.Read moreRead less
Exploring novel coding genomic features through integrative proteogenomics. Knowledge of the full extent to which the human genome is made into proteins is of fundamental importance in the study of health and disease. New technological advances are now enabling functional studies of genomes with increasing detail. This project aims to develop and apply cutting edge bioinformatics methods to perform an integrative and comprehensive exploration of the extent to which the genes of a human cell line ....Exploring novel coding genomic features through integrative proteogenomics. Knowledge of the full extent to which the human genome is made into proteins is of fundamental importance in the study of health and disease. New technological advances are now enabling functional studies of genomes with increasing detail. This project aims to develop and apply cutting edge bioinformatics methods to perform an integrative and comprehensive exploration of the extent to which the genes of a human cell line are made into proteins. The project will improve our understanding of the human genome and deliver cutting edge methodology applicable for genome annotation in all living organisms.Read moreRead less
Eat and Dream: effective automatic testing and debugging for real-life embedded wireless communications software. Embedded software is a key enabling technology for the majority of Australian manufacturing industries, including strategically important sectors such as the automotive industry. Embedded wireless communication technologies are playing an increasingly significant role in Australia with a wide range of critical applications ranging from natural disaster early warning to personal healt ....Eat and Dream: effective automatic testing and debugging for real-life embedded wireless communications software. Embedded software is a key enabling technology for the majority of Australian manufacturing industries, including strategically important sectors such as the automotive industry. Embedded wireless communication technologies are playing an increasingly significant role in Australia with a wide range of critical applications ranging from natural disaster early warning to personal health monitoring. Embedded wireless communications software, however, is difficult to test and debug owing to the complexity of the operational environment and complications arising from the interplay between software and hardware. This project will develop an effective and automatic technology to alleviate these difficulties and achieve higher quality software.Read moreRead less
A Generic Software Architecture for Web-Based Applications on Micro-Mobile Systems. The next generation of computers that will capture the imagination of the society are likely to be micro-mobile devices such as personal digital assistants, mobile phones, smartcards and chips embedded in home and office items. Developing applications for information processing using a wireless network of such devices is an emerging challenge. This project will develop and evaluate a generic architecture for web- ....A Generic Software Architecture for Web-Based Applications on Micro-Mobile Systems. The next generation of computers that will capture the imagination of the society are likely to be micro-mobile devices such as personal digital assistants, mobile phones, smartcards and chips embedded in home and office items. Developing applications for information processing using a wireless network of such devices is an emerging challenge. This project will develop and evaluate a generic architecture for web-based applications on micro-mobile devices. This will make it easy to design applications that can seamlessly interact with different kinds of devices. The project will be carried out in partnership with Total Internet Centre, a Newcastle based regional enterprise.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
Preparing Australia For Genomic Medicine: A Proposal By The Australian Genomics Health Alliance
Funder
National Health and Medical Research Council
Funding Amount
$25,000,000.00
Summary
The sequencing of the human genome brings the possibility of more accurate identification of the underlying basis of many diseases. This technology has moved so rapidly, however, that clinical access has been limited. In this application, a national alliance of clinicians, researchers, health economists and policymakers will evaluate the case for clinical genomics across inherited disease and cancer, determine how best to deliver this to the patient and train a capable workforce.