Thesis: Bioinformatics and Biomes: Developing Efficient Frameworks for Analysing Large Scale Microbial Surveys of Western Australian Soils
Ecological studies on microbial communities provide valuable insight on the relationship between the environmental factors present in ecosystems and the characteristics of the microorganisms present within. With the high throughput capabilities provided by the advent of next generation sequencing, large scale microbial surveys of environmental samples are now possible. The molecular data provided by these large scale surveys are paramount in the characterization of both diversity and functions present in microbial communities. Along with the quickly advancing technology associated with next generation sequencing is the need for a software framework with the ability to process the ever increasing data produced by the various sequencing platforms.
The PhD project I am undertaking looks at the state of current and upcoming next generation sequencing platforms and what bioinformatics techniques are required to handle the data produced. Foremost is the investigation of bioinformatics software currently in use and how they process data produced by the next generation sequencing. From these studies the project will seek to develop its own software framework which will be used to analyze environmental data collected from soils from various location around Western Australia. The project will work closely with the Microblitz Project (http://www.microblitz.com.au/) to create a biogeographical map of microbial communities present in Western Australian soils.
Why my research is important
With the ever increasing data produced by the rapid progress in next generation sequencing, there is a risk that a bottleneck may occur in the ability to process said data. There is a need develop new software frameworks that is able to cope with this increasing load. By investigating current software, the study will allow the development of a new framework by selecting computing elements that are desired and find out which ones need improvement. The proposed framework will include the ability to handle the increasing loads of data, make data available in a readily accessible and referable format and allow the visualization of results within a site specific context.
In conjunction with the Microblitz Project, the biogeographical map of Western Australia created with the assistance of the proposed framework will be used as a valuable reference tool for both ecological comparison and for bioremediation. Western Australia is prime candidate as a biogeographical reference due to the state containing multiple climatic regions as well as its varied soil types. The biogeographical map can also be a valuable tool in assisting environmental restoration by comparing the microbial communities in land use sites to pristine sites by tracking the progress of restoration efforts.