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Exploration of cloud computing for CAZyme research

CAZyme 研究的云计算探索

基本信息

批准号：
10827621
负责人：
Yanbin Yin
金额：
$ 21.93万
依托单位：
UNIVERSITY OF NEBRASKA LINCOLN
依托单位国家：
美国
项目类别：
财政年份：
2021
资助国家：
美国
起止时间：
2021-05-01 至 2025-02-28
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10827621
关键词：
6 year old Activities of Daily Living Applications Grants Automated Annotation Bioinformatics Carbohydrates Cloud Computing Communities Computer software Computers Country Data Databases Development Enzymes Evaluation Faculty Family Funding Gene Cluster Goals Growth Health High Performance Computing Human Human Microbiome Inherited Interdisciplinary Study Internet Knowledge Longevity Maintenance Memory Metabolic Methods Monitor Occupations Operating System Paper Parents Persons Polysaccharides Process Publications Publishing Reporting Research Risk Running Science Secure Security Services Shotguns Specialist Testing Time Universities Whole-Genome Shotgun Sequencing Workload acronyms base bioinformatics tool computational platform computing resources cost dietary genomic data graduate student gut microbes gut microbiome gut microbiota improved microbiome microbiome sequencing migration novel nutrition parent project prebiotics software systems success tool tool development web server web services web site whole genome

项目摘要

PROJECT SUMMARY Title: Exploration of cloud computing for CAZyme research Our R01 parent project (R01GM140370) intends to develop four bioinformatics tools for automated annotation of CAZymes (Carbohydrate Active Enzymes) and CAZyme Gene Clusters (CGCs) in human gut microbiome. These automated tools will enhance: (i) the basic biomedical science to characterize new polysaccharide (or glycan) metabolic enzymes and polysaccharide utilization loci (PULs, gene clusters with known carbohydrate substrates) in the human gut microbiome, and (ii) the emerging personalized nutrition practice (e.g., using gut microbiome sequencing to infer if a person is a responder to certain dietary glycans or prebiotics). In the past two years, we have developed dbCAN3 (Aim 1 of R01) and dbCAN-seq (Aim 3 of R01), one web server and one online database, to allow users submit their genomic data of any microbiomes for automated CAZyme, CGC, and glycan substrate annotation. Both websites are now hosted on our lab’s standalone desktop server (a six-year-old computer with 16-core/32-thread CPU), which is not a secure and sustained solution and cannot meet the increasing demand from users who routinely submit jobs to our servers. For example, our popular dbCAN2 web server (the second version of dbCAN that started in 2012) processed over 35,000 user submitted jobs in 2022 all by this desktop computer. Therefore, challenges/risks exist that may disrupt the popular service we provide to tens of thousands of microbiome users all over the world and additional support is requested to explore moving dbCAN3 to a cloud computing platform, e.g., Amazon Web Services (AWS). These challenges include: (i) our local desktop server is no longer able to meet the continuously growing job submissions, (ii) the server built in 2017 is already out of warranty, (iii) the server have been frequently reported by the University IT service department to have numerous security vulnerabilities due to its old operating system and software system. Therefore, the major goal of this supplement grant proposal is to explore and test the application of Amazon Web Services (AWS) to support the CAZyme bioinformatics tool development objective of our R01 parent project. In this one-year project, we aim to test the deployment of our dbCAN3 website on AWS by taking advantage of AWS web hosting service and AWS Batch for automatic workload distribution, and compare with two on-prem solutions in terms of their computational efficiency. To achieve these goals, we have assembled a multi-disciplinary research team including three faculty, one computer specialist, and one graduate students. We have all necessary expertise in bioinformatics, cloud computing, and high-performance computing. The successful completion of this cloud exploration project will significantly increase our knowledge using AWS for our R01 CAZyme bioinformatics tool development.

项目概要标题：CAZyme 研究的云计算探索我们的 R01 父项目 (R01GM140370) 打算开发四种用于自动注释的生物信息学工具人类肠道微生物组中的 CAZymes（碳水化合物活性酶）和 CAZyme 基因簇 (CGC)。这些自动化工具将增强：（i）表征新多糖（或聚糖）代谢酶和多糖利用位点（PUL，具有已知碳水化合物的基因簇）底物）在人类肠道微生物群中，以及（ii）新兴的个性化营养实践（例如，使用肠道微生物组测序来推断一个人是否对某些膳食聚糖或益生元有反应）。近两年我们开发了dbCAN3（R01的Aim 1）和dbCAN-seq（R01的Aim 3），一个web 服务器和一个在线数据库，允许用户提交任何微生物组的基因组数据以进行自动化 CAZyme、CGC 和聚糖底物注释。这两个网站现在都托管在我们实验室的独立服务器上桌面服务器（具有 6 年历史的计算机，具有 16 核/32 线程 CPU），这不是一个安全和可持续的解决方案，无法满足定期向我们的服务器提交作业的用户日益增长的需求。为了例如，我们流行的 dbCAN2 Web 服务器（2012 年启动的 dbCAN 的第二个版本）处理了 2022 年，35,000 个用户全部通过这台台式计算机提交了作业。因此，存在的挑战/风险可能会扰乱我们为数以万计的人提供的流行服务世界各地的微生物组用户，需要额外的支持来探索移动 dbCAN3 到云计算平台，例如亚马逊网络服务（AWS）。这些挑战包括：(i) 我们当地桌面服务器已无法满足不断增长的作业提交，（ii）2017年建成的服务器已过保修期，(iii) 服务器经常被大学 IT 服务部门报告由于其旧的操作系统和软件系统，存在许多安全漏洞。因此，本补充赠款提案的主要目标是探索和测试 Amazon Web Services (AWS) 支持我们 R01 的 CAZyme 生物信息学工具开发目标父项目。在这个为期一年的项目中，我们的目标是通过以下方式测试 dbCAN3 网站在 AWS 上的部署：利用 AWS Web 托管服务和 AWS Batch 进行自动工作负载分配，以及与两个本地解决方案的计算效率进行比较。为了实现这些目标，我们组建了一个多学科研究团队，包括三名教师、一名计算机专家，一名研究生。我们拥有生物信息学、云计算方面所有必要的专业知识计算、高性能计算。此次云探索项目的顺利完成，将使用 AWS 进行 R01 CAZyme 生物信息学工具开发，显着增加我们的知识。

项目成果

期刊论文数量（13）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

dbCAN-seq update: CAZyme gene clusters and substrates in microbiomes.

DOI：
10.1093/nar/gkac1068
发表时间：
2023-01-06
期刊：
NUCLEIC ACIDS RESEARCH
影响因子：
14.9
作者：
Zheng, Jinfang;Hu, Boyang;Zhang, Xinpeng;Ge, Qiwei;Yan, Yuchen;Akresi, Jerry;Piyush, Ved;Huang, Le;Yin, Yanbin
通讯作者：
Yin, Yanbin

Cadmium stress triggers significant metabolic reprogramming in Enterococcus faecium CX 2-6.