A computational cloud framework for the study of gene families

用于研究基因家族的计算云框架

基本信息

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

项目摘要

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.

生命科学研究越来越多地变成数据密集的纪律。新的高通量测序技术生产大量的数字数据，需要有效地分析这些数据，以发现有趣的模式以进行新的生物学发现。大量数据会产生一个问题，因为它需要使用大量计算资源和复杂的计算技能来存储和分析。许多生物学实验室都难以为其计算需求拥有和维护大型计算集群。云计算框架已成为可行的替代方案，用于在付费模型上利用大型计算机功率，并且越来越多地进入主流生物学数据分析。 IPLANT-UK是由BBSRC资助的云计划，旨在为英国研究人员免费提供大型计算资源。 Iplant-UK Cloud专门针对满足生命科学社区的计算要求，并通过Web浏览器的舒适度提供了对大型计算基础架构的访问。通过此建议，我们希望开发一个计算工具包，以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，也称为抗抗性基因，这些基因负责病原体识别和植物中的抗病性反应。要了解一个物种中的基因家族，必须首先对该家族的所有成员进行分类，然后了解它们相对于对方以及相关物种的功能。这些数据集是通过下一代测序技术生成的，通常的音量很大。我们旨在开发专业软件，以分析Iplant-UK Compute云上的基因家族数据集。这样，我们可以为研究人员提供在大型且免费的计算资源上的专业工具。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，以使湿的生物学家专注于其核心研究，而不是担心云平台上的复杂计算。该项目中开发的代码将在开源许可下免费提供在公共领域中。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该提议。