A computational cloud framework for the study of gene families

用于研究基因家族的计算云框架

• 批准号: BB/N023145/1
• 负责人: Anthony Hall
• 金额: $ 18.77万
• 依托单位: Earlham Institute
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2017
• 资助国家: 英国
• 起止时间: 2017 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FN023145%2F1
• 关键词: computational; cloud; framework; study; gene

Life science research is increasingly turning into data-intensive discipline. New high-throughput sequencing technologies produce vast amounts of digital data that needs to be efficiently analyzed in order to discover interesting patterns to make new biological discoveries. The large volume of data produces a problem of its own, as it needs to be stored and analyzed using large computing resources and sophisticated computing skills. Many biology labs struggle to own and maintain large computing clusters for their computing needs. Cloud computing frameworks have emerged as feasible alternative for availing large computer power on a pay-as-you-go model and are increasingly making inroads into mainstream biological data analysis. iPlant-UK is a cloud initiative funded by BBSRC to make large computing resources available for free of cost to UK researchers. iPlant-UK cloud is specifically tailored to meet the computing requirements of life sciences community and provides access to large computing infrastructures through the comforts of web-browser. Through this proposal, we want to develop a computational toolkit for analysis of gene family datasets. An example of a gene family in plants is R genes, also known as Resistance genes that are responsible for pathogen recognition and disease resistance responses in plants. To understand a gene family in a species, one must first catalogue all members of the family, and then understand their function with respect to other each other, as well as related species. These datasets are generated through next generation sequencing techniques and are usually large in volume. We aim to develop specialized software for analysis of gene family datasets on the iPlant-UK compute cloud. This way, we can provide researchers access a specialized tool on a large and free computing resource. Further, we want to simplify the use of the toolkit by providing graphical user interfaces that can be accessed through web-browsers to enable wet-lab biologists to focus on their core research rather than worry about the complex computation on a cloud platform. The code developed in this project will be available in public domain for free under open-source license. By building the workflow in iplant we will ensure its sustainability and visibality beyond this proposal.

生命科学研究正日益成为数据密集型学科。新的高通量测序技术产生了大量的数字数据，需要对这些数据进行有效分析，以发现有趣的模式，从而做出新的生物学发现。大量的数据产生了自己的问题，因为它需要使用大量的计算资源和复杂的计算技能来存储和分析。许多生物实验室都在努力拥有和维护大型计算集群以满足其计算需求。云计算框架已经成为在现收现付模式下利用大型计算机能力的可行替代方案，并且越来越多地进入主流生物数据分析。iPlant-UK是由BBSRC资助的一项云计划，旨在为英国研究人员提供免费的大型计算资源。iPlant-UK云是专门为满足生命科学社区的计算需求而量身定制的，并通过舒适的Web浏览器提供对大型计算基础设施的访问。通过这个建议，我们希望开发一个计算工具包，用于分析基因家族数据集。植物中基因家族的一个例子是R基因，也称为抗性基因，其负责植物中的病原体识别和抗病反应。要了解一个物种中的基因家族，首先必须对该家族的所有成员进行分类，然后了解它们彼此之间以及相关物种之间的功能。这些数据集是通过下一代测序技术生成的，通常体积很大。我们的目标是开发专门的软件，用于在iPlant-UK计算云上分析基因家族数据集。通过这种方式，我们可以为研究人员提供在大型免费计算资源上访问专用工具的机会。此外，我们希望通过提供可以通过Web浏览器访问的图形用户界面来简化工具包的使用，使湿实验室生物学家能够专注于他们的核心研究，而不是担心云平台上的复杂计算。在这个项目中开发的代码将在开源许可证下免费提供给公共领域。通过在iplant中构建工作流程，我们将确保其可持续性和可见性超出本提案。

项目成果

Circadian regulation of the transcriptome in a complex polyploid crop.

• DOI: 10.1371/journal.pbio.3001802
• 发表时间: 2022-10
• 期刊: PLoS biology
• 影响因子: 9.8