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.

项目摘要标题：Cazyme研究云计算的探索我们的R01父项目（R01GM140370）打算开发四种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）特征新多糖的基本生物医学科学（或 Glycan）代谢酶和多糖利用率定位（脉冲，具有已知碳氢化物的基因簇底物）在人类肠道微生物组中，以及（ii）新兴的个性化营养实践（例如，使用肠微生物组测序是否是对某些饮食类似物或益生元的响应者的响应者。在过去的两年中，我们开发了DBCAN3（R01的AIM 1）和DBCAN-SEQ（R01的AIM 3），一个网络服务器和一个在线数据库，以允许用户提交自动化的任何微生物组的基因组数据 Cazyme，CGC和Glycan底物注释。现在两个网站都托管在我们实验室的独立桌面服务器（一台具有16核/32个线程CPU的六年级计算机），这不是安全且持续的解决方案，无法满足经常向服务器提交工作的用户的需求。为了例如，我们流行的DBCAN2 Web服务器（2012年启动的第二版DBCAN）处理了 35,000个用户在2022年通过这台台式计算机提交了作业。因此，存在挑战/风险，可能会破坏我们提供给数万美元的流行服务全世界的微生物组用户中，请求额外的支持以探索移动DBCAN3 到云计算平台，例如Amazon Web Services（AWS）。这些挑战包括：（i）我们的当地桌面服务器不再能够满足不断增长的工作提交，（ii）2017年构建的服务器（iii）已经由大学IT服务部经常报告服务器已不在保修中由于其旧操作系统和软件系统，具有许多安全漏洞。因此，该补充赠款提案的主要目标是探索和测试应用 Amazon Web服务（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，我们旨在测试我们在AWS上的DBCAN3网站的部署利用AWS Web托管服务和AWS批次进行自动工作负载分配，以及就其计算效率而言，与两个本地解决方案进行比较。为了实现这些目标，我们组建了一个多学科研究团队，包括三个教师，一个计算机专家和一名研究生。我们拥有生物信息学，云的所有必要专业知识计算和高性能计算。这个云探索项目的成功完成将使用AWS为我们的R01 Cazyme生物信息学工具开发大大提高了我们的知识。

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.