(WCUB) Sonification of biological sequences

DNA、蛋白质和基因组序列的可视化一直是我们理解生物复杂性的核心。可视化是我们如何理解沿DNA、RNA或蛋白质链的共价结合残基的序列。然而，在生物信息学时代，随着信息量和信息范围的逐步变化，可视化变得越来越具有挑战性，因为我们被细节淹没了。这个令人兴奋的博士项目通过开发一种与生物信息交互的替代方法直接解决了这一挑战。而不是转换数据-在我们的情况下，碱基对，氨基酸和染色体-视觉信息，超声转换数据为声音。超声在生物信息学方面已经取得了可喜的成果（例如Temple 2017， BMC bioinformatics 18:21），但该领域尚不发达。因此，生物序列的超声化潜力，以表示和理解序列，变异，功能和进化，仍在很大程度上尚未开发。拟议的项目将开发和应用超声技术来表示生物序列。目标是开发广泛适用于生命科学研究和教育以及公众参与科学的算法和软件。理想的候选人可能有生物信息学方面的经验，并对音乐感兴趣。该项目将涉及脚本编写（例如Python或Perl），使用Linux命令行和处理生物序列数据，从单个基因或蛋白质到数千个真核生物基因组。这些导师在生物信息学、音乐表演、遗传学、统计学、软件工程、研究、教育和公众参与方面都有经验，并将在这些领域提供指导。学生将拥有广泛适用于生物信息学、计算科学和算法音乐创作的一系列技能。

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.