(WCUB) Sonification of biological sequences

(WCUB) 生物序列的可听化

• 批准号: 2672549
• 金额: --
• 依托单位: University of Edinburgh
• 依托单位国家: 英国
• 项目类别: Studentship
• 财政年份: 2019
• 资助国家: 英国
• 起止时间: 2019 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=studentship-2672549
• 关键词: WCUB; Sonification; biological; sequences

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.

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着DNA、RNA或蛋白质链沿着共价键合的残基的序列。然而，在生物信息学时代，随着信息量和范围的逐步变化，可视化变得越来越具有挑战性，因为我们变得对细节不知所措。这个令人兴奋的博士项目通过开发人类与生物信息交互的替代手段直接解决了这一挑战。在我们的例子中，不是将数据（碱基对、氨基酸和染色体）转换为视觉信息，而是将数据转换为声音。生物信息学中的声化已经有了有希望的结果（例如Temple 2017，BMC Bioinformatics 18：221），但该领域尚未开发。因此，生物序列的声化的潜力，以表示和理解序列，变异，功能和进化，仍然在很大程度上尚未开发。拟议的项目将开发和应用声化技术来表示生物序列。目标是开发算法和软件，广泛适用于生命科学的研究和教育以及公众参与科学。一个理想的候选人可能有生物信息学的经验和对音乐的兴趣。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基因组。导师们在生物信息学、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。学生将获得广泛适用于生物信息学，计算科学和算法音乐作曲的一系列技能。