Sonification of biological sequences

Supervisors: Dr Daniel Barker, Professor Thomas Meagher

Project Description:

Visualisation of DNA, protein and genome sequences has been central to our understanding of biological complexity. Visualisation is how we comprehend the sequence of covalently bonded residues along a strand of DNA, RNA or protein. However, in the era of bioinformatics, with a step change in volume and scope of information, visualisation becomes increasingly challenging as we become overwhelmed with detail. This exciting PhD project directly addresses this challenge through development of an alternative means of human interface with biological information. Instead of converting data – in our case, base-pairs, amino acids and chromosomes – to visual information, sonification converts data to sound. There have been promising results with sonification in bioinformatics (e.g. Temple 2017, BMC Bioinformatics 18:221), but the field is under-developed. Consequently, the potential for sonification of biological sequences, to represent and understand sequences, variation, function and evolution, remains largely untapped. The proposed project will develop and apply sonification techniques to represent biological sequences. The goal is to develop algorithms and software with broad applicability to research and education in life sciences and to public engagement with science. An ideal candidate is likely to have previous experience of bioinformatics and an interest in music. The project will involve scripting (e.g. in Python or Perl), use of the Linux command-line and processing of biological sequence data, from single genes or proteins to sets of thousands of eukaryotic genomes. The supervisors together have experience in bioinformatics, music performance, genetics, statistics, software engineering, research, education and public engagement and will provide guidance in these areas. The student will be left with a range of skills broadly applicable within bioinformatics, computational science and algorithmic music composition.

If you wish to apply for this project, please go to this link.