Linkage Infrastructure, Equipment And Facilities - Grant ID: LE160100002
Funder
Australian Research Council
Funding Amount
$1,040,000.00
Summary
Distributed Memory Cluster for the Intersect consortium of universities. Distributed memory cluster:
This project aims to establish a new supercomputing facility. The NSW research community has used high performance computing (HPC) to achieve major breakthroughs across a diverse range of disciplines including astrophysics, bioinformatics, environmental science, information technology and engineering. As the use of HPC increases, the application-specific needs of the research community become mo ....Distributed Memory Cluster for the Intersect consortium of universities. Distributed memory cluster:
This project aims to establish a new supercomputing facility. The NSW research community has used high performance computing (HPC) to achieve major breakthroughs across a diverse range of disciplines including astrophysics, bioinformatics, environmental science, information technology and engineering. As the use of HPC increases, the application-specific needs of the research community become more diverse, requiring greater flexibility as well as higher performance. The present facility is no longer internationally competitive, and is hampering progress in cutting edge research. The new cluster is designed to provide a greater than 10-fold increase in computing capability.Read moreRead less
The genomic programming of complex organisms. The project will have far-reaching consequences in medicine, agriculture, biotechnology, engineering, information science and associated industries. It will provide a platform for the rationalization of genetic epidemiology and genetic improvement programs, the development of a wide range of new diagnostics and therapies, the development of new core technologies and practical approaches in genetics and genetic diversity, a framework for advanced gen ....The genomic programming of complex organisms. The project will have far-reaching consequences in medicine, agriculture, biotechnology, engineering, information science and associated industries. It will provide a platform for the rationalization of genetic epidemiology and genetic improvement programs, the development of a wide range of new diagnostics and therapies, the development of new core technologies and practical approaches in genetics and genetic diversity, a framework for advanced genetic engineering, the development of new principles and systems for information storage and transmission, and the design of artificial systems capable of self-referential assembly in other environments.Read moreRead less
Imaging mammalian organogenesis with adaptive optics. Optical and computational barriers to analysing cell movement have limited our understanding of mammalian organogenesis. We have built a super-resolution spinning disk confocal microscope with adaptive optics and developed machine learning-based image processing and cell segmentation workflows to overcome these long-standing barriers. We propose to combine these cutting-edge live imaging and analysis approaches to characterise the role of cel ....Imaging mammalian organogenesis with adaptive optics. Optical and computational barriers to analysing cell movement have limited our understanding of mammalian organogenesis. We have built a super-resolution spinning disk confocal microscope with adaptive optics and developed machine learning-based image processing and cell segmentation workflows to overcome these long-standing barriers. We propose to combine these cutting-edge live imaging and analysis approaches to characterise the role of cell movement in mammalian organ formation and develop advanced cell segmentation and tracking methods for use in the scientific community. We anticipate this project will generate fundamental insights into how cells interact to build complex organs.Read moreRead less
A paradigm of genomic discovery - an investigation of the allelic architecture of height. Understanding the complexities of the human body from its DNA sequence has proven difficult. Genomic discovery is best developed using stable, easily measurable and highly heritable characteristics such as height. By taking advantage of 2 large population surveys of adult and adolescent stature we shall apply modern molecular techniques and statistical strategies to identify and characterise the exact chang ....A paradigm of genomic discovery - an investigation of the allelic architecture of height. Understanding the complexities of the human body from its DNA sequence has proven difficult. Genomic discovery is best developed using stable, easily measurable and highly heritable characteristics such as height. By taking advantage of 2 large population surveys of adult and adolescent stature we shall apply modern molecular techniques and statistical strategies to identify and characterise the exact changes in DNA that determine height. This work builds on substantial preliminary leads from unique resources and complementary expertise in the scientific specialties. The results from this work will inform other genomic research and provide information about growth and bone biology.Read moreRead less
Linkage Infrastructure, Equipment And Facilities - Grant ID: LE0667981
Funder
Australian Research Council
Funding Amount
$200,000.00
Summary
Kangaroo Genome Resource Management Facility. Increasingly, large Australian multicentre research programs in biological and medical sciences have a genomics component that involves integration of biological information with sequencing data. The success of these research programs depends on rapid internet access to the research information by all participating scientists. The universal design of the proposed information management system means that it can be easily adapted to support a broad ran ....Kangaroo Genome Resource Management Facility. Increasingly, large Australian multicentre research programs in biological and medical sciences have a genomics component that involves integration of biological information with sequencing data. The success of these research programs depends on rapid internet access to the research information by all participating scientists. The universal design of the proposed information management system means that it can be easily adapted to support a broad range of research programs. The development of this software program therefore has the potential to benefit research scientists, academics and students in many related fields, as well as the broader community, through enhancing research outcomes.Read moreRead less
Mutagenesis and combinatorial algorithms for sequencing problematic genomic regions. This project will develop a remarkable and original approach to DNA sequencing with potential to radically improve the speed, accuracy and effectiveness of existing sequencing technologies. It is especially useful for dealing with difficult-to-sequence genomic regions and has implications for all sequencing projects, including completion of the Human Genome Project. The approach involves generating, and wholly o ....Mutagenesis and combinatorial algorithms for sequencing problematic genomic regions. This project will develop a remarkable and original approach to DNA sequencing with potential to radically improve the speed, accuracy and effectiveness of existing sequencing technologies. It is especially useful for dealing with difficult-to-sequence genomic regions and has implications for all sequencing projects, including completion of the Human Genome Project. The approach involves generating, and wholly or partially sequencing, mutated copies of problematic regions of the target genome. Advanced combinatorial algorithms are then used to form highly probable alignments between strings and determine the unknown sequence. The approach has additional benefits in detecting single-nucleotide polymorphisms and sequencing errors.Read moreRead less
A genomic approach to the mechanism of meiotic recombination in Neurospora. Recombination shuffles DNA sequences between homologous chromosomes during the reduction division in the life cycle of higher organisms. Along with mutation, it is a key process in evolution. Understanding of the molecular processes involved in recombination is largely based on yeast, which is intolerant of significant levels of sequence mismatch, limiting the resolution of analyses of normal recombination events. We hav ....A genomic approach to the mechanism of meiotic recombination in Neurospora. Recombination shuffles DNA sequences between homologous chromosomes during the reduction division in the life cycle of higher organisms. Along with mutation, it is a key process in evolution. Understanding of the molecular processes involved in recombination is largely based on yeast, which is intolerant of significant levels of sequence mismatch, limiting the resolution of analyses of normal recombination events. We have shown that Neurospora, like other less tractable multicellular eukaryotes, is tolerant of sequence mismatch, allowing high resolution analysis of individual recombination events. This project will build on fundamental advances we have already made in understanding how recombination occurs.Read moreRead less
Genetic variation in narrow leafed lupin (NLL) accessions and breeding programs. The centre of origin of a crop plant is expected to have the greatest extant genetic variation of wild relatives. Development of modern cultivars may be accompanied by a severe genetic bottleneck, whereby subsequent breeding efforts are hampered by lack of significant genetic variation within domesticated breeding material. This proposal will research the extent to which the available genetic variation in wild acces ....Genetic variation in narrow leafed lupin (NLL) accessions and breeding programs. The centre of origin of a crop plant is expected to have the greatest extant genetic variation of wild relatives. Development of modern cultivars may be accompanied by a severe genetic bottleneck, whereby subsequent breeding efforts are hampered by lack of significant genetic variation within domesticated breeding material. This proposal will research the extent to which the available genetic variation in wild accessions of the recently developed crop Lupinus angustifolius has been utilised in breeding programs around the world. Results will be applied to broaden the gene pool and improve adaptation of new cultivars in the National Lupin Improvement Program.Read moreRead less
Linkage Infrastructure, Equipment And Facilities - Grant ID: LE0775726
Funder
Australian Research Council
Funding Amount
$306,270.00
Summary
Australian Mirror of the UCSC Genome Database and Browser. Modern medical, biological, agricultural, and environmental research and industries are being transformed by access to genomic information that details the DNA sequence of various species, as well as of different strains and individuals within populations. This information is being generated at an exponentially increasing speed, and requires large computational resources. This facility will provide Australian researchers, R&D organizati ....Australian Mirror of the UCSC Genome Database and Browser. Modern medical, biological, agricultural, and environmental research and industries are being transformed by access to genomic information that details the DNA sequence of various species, as well as of different strains and individuals within populations. This information is being generated at an exponentially increasing speed, and requires large computational resources. This facility will provide Australian researchers, R&D organizations and industry with state-of-the-art genomic data storage and analysis capability, which will permit both public and proprietary access, and accelerate Australian research and development in genetic medicine, pharmaceuticals, animal breeding and biodiversity.Read moreRead less
Intron encoded RNA regulatory networks in yeast. This project has the capacity to transform our understanding of the evolution, development and genetic variation of complex organisms, as well as the self-organization of complex systems in general. The national and community benefits of the project will be to maintain Australian leadership in advanced genetics and genome-phenome informatics. It will provide a platform for many applications in biology and biotechnology, including new genetic diagn ....Intron encoded RNA regulatory networks in yeast. This project has the capacity to transform our understanding of the evolution, development and genetic variation of complex organisms, as well as the self-organization of complex systems in general. The national and community benefits of the project will be to maintain Australian leadership in advanced genetics and genome-phenome informatics. It will provide a platform for many applications in biology and biotechnology, including new genetic diagnostics and an informed basis for the engineering of complex traits in agriculture. The project will also provide insights into the structure of biological communication and control systems with applications in information science and the programming of integrated complex systems in other domains.Read moreRead less