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Visualisation and interaction tool for bioinformatics laboratories

PROJECT CONTEXT

Next generation sequencing has become a necessity for the biological sciences to investigate how genes are expressed and regulated in health and diseases as well as under different physiological conditions such as growth, development, proliferation and death. Deep sequencing produces high volume data and requires biologists with skills in informatics or computer science to analyse these data and express them in a manner that is easily interpreted by biologists. Although there are many available tools, algorithms and pipelines to investigate high throughput data from next generation sequencing currently, these are not standardised but most importantly they are not user friendly for biologists with little computational skills.

The goal within the scope of this project is the exploration of methods and techniques in the field of visualisation and human-computer interaction and adapt these to the needs in computational biology. Biologists shall be provided with a software platform that allows them to gain deeper understanding of high volume data, and decrease cognitive load of processing the sheer large amount of data. After a first exploration of potential visualisation and interaction models, a platform that copes with the daily biologist laboratory tasks shall be developed as a user friendly application.

RESEARCH DIRECTIONS

Rather than investigating methods utilised in bioinformatics to process biological data, the project is centred on user centred and visualisation aspects. The project shall address the bottleneck of bioinformaticians to deal with large amounts of data, and how this data can be interactively visualised. The project outcome shall benefit skilled bioinformaticians to overcome the high load of information that they are confronted with. Consequently, the project requires an interface in the form of a simplified user friendly software platform for biologists. The platform shall come with the capabilities to upload common data formats of sequencing data and simplify the following analysis process. The actual bioinformatics pipelines are not part of this process, but the development of a tool that supports the bioinformatician in the analysis process with advanced visualisation and interaction features. The vision of the project is to create a tool that is adapted to the needs of biological laboratory analysis, and created in tight cooperation with bioinformaticians and laboratory workers.

ADDITIONAL INFORMATION

The project will be conducted in cooperation with the University of Western Australia (UWA). Students will be provided with the latest technologies,  e.g. the Curtin’s Hub for Immersive Visualisation and eResearch (HIVE), 3D virtual and augmented glasses, brain-interfaces, eye trackers, or biofeedback sensors to conduct their research.

The HIVE