Along with the develoipment of high-throughput sequencing technologies,both sample size and SNP number are increasing rapidly in genome-wide association studies(GWAS),and the associated computation is more challenging...Along with the develoipment of high-throughput sequencing technologies,both sample size and SNP number are increasing rapidly in genome-wide association studies(GWAS),and the associated computation is more challenging than ever.Here,we present a memory-efficient,visualization-enhanced,and parallel-accelerated R package called“r MVP”to address the need for improved GWAS computation.r MVP can 1)effectively process large GWAS data,2)rapidly evaluate population structure,3)efficiently estimate variance components by Efficient Mixed-Model Association e Xpedited(EMMAX),Factored Spectrally Transformed Linear Mixed Models(Fa ST-LMM),and Haseman-Elston(HE)regression algorithms,4)implement parallel-accelerated association tests of markers using general linear model(GLM),mixed linear model(MLM),and fixed and random model circulating probability unification(Farm CPU)methods,5)compute fast with a globally efficient design in the GWAS processes,and 6)generate various visualizations of GWASrelated information.Accelerated by block matrix multiplication strategy and multiple threads,the association test methods embedded in r MVP are significantly faster than PLINK,GEMMA,and Farm CPU_pkg.r MVP is freely available at https://github.com/xiaolei-lab/r MVP.展开更多
实验室管理系统旨在提供全面的解决方案,以管理实验室的设备、仪表、材料、实验项目、研究人员和学生等重要信息。实验室管理系统不仅简化了实验室资源的跟踪和管理,而且增强了实验项目的组织和监控,从而确保研究过程的透明度和数据的...实验室管理系统旨在提供全面的解决方案,以管理实验室的设备、仪表、材料、实验项目、研究人员和学生等重要信息。实验室管理系统不仅简化了实验室资源的跟踪和管理,而且增强了实验项目的组织和监控,从而确保研究过程的透明度和数据的完整性。该系统采用Java技术栈,包括SpringBoot、Spring Security和Spring Data JPA,作为后端开发框架,结合HTML、CSS、JavaScript以及React作为前端技术,构建了一个用户友好且功能强大的实验室管理平台。通过数据库设计和优化,系统实现了实验室资源的高效管理、实验项目的追踪和评估、用户权限的灵活控制以及数据的可视化分析。展开更多
The three-dimensional discontinuous deformation analysis(3D-DDA) is a promising numerical method for both static and dynamic analyses of rock systems. Lacking mature software, its popularity is far behind its ability....The three-dimensional discontinuous deformation analysis(3D-DDA) is a promising numerical method for both static and dynamic analyses of rock systems. Lacking mature software, its popularity is far behind its ability. To address this problem, this paper presents a new software architecture from a software engineering viewpoint. Based on 3D-DDA characteristics, the implementation of the proposed architecture has the following merits. Firstly, the software architecture separates data, computing, visualization, and signal control into individual modules. Secondly, data storage and parallel access are fully considered for different conditions. Thirdly, an open computing framework is provided which supports most numerical computing methods; common tools for equation solving and parallel computing are provided for further development. Fourthly, efficient visualization functions are provided by integrating a variety of visualization algorithms. A user-friendly graphical user interface is designed to improve the user experience. Finally, through a set of examples, the software is verified against both analytical solutions and the original code by Dr. Shi Gen Hua.展开更多
基金supported by the National Natural Science Foundation of China(Grant Nos.31730089,31672391,31702087,and 31701144)the National Key R&D Program of China(Grant No.2016YFD0101900)+2 种基金the Fundamental Research Funds for the Central Universities,China(Grant Nos.2662020DKPY007 and 2662019PY011)the National Science Foundation,USA(Grant No.DBI 1661348)the National Swine System Industry Technology System,China(Grant No.CARS-35)。
文摘Along with the develoipment of high-throughput sequencing technologies,both sample size and SNP number are increasing rapidly in genome-wide association studies(GWAS),and the associated computation is more challenging than ever.Here,we present a memory-efficient,visualization-enhanced,and parallel-accelerated R package called“r MVP”to address the need for improved GWAS computation.r MVP can 1)effectively process large GWAS data,2)rapidly evaluate population structure,3)efficiently estimate variance components by Efficient Mixed-Model Association e Xpedited(EMMAX),Factored Spectrally Transformed Linear Mixed Models(Fa ST-LMM),and Haseman-Elston(HE)regression algorithms,4)implement parallel-accelerated association tests of markers using general linear model(GLM),mixed linear model(MLM),and fixed and random model circulating probability unification(Farm CPU)methods,5)compute fast with a globally efficient design in the GWAS processes,and 6)generate various visualizations of GWASrelated information.Accelerated by block matrix multiplication strategy and multiple threads,the association test methods embedded in r MVP are significantly faster than PLINK,GEMMA,and Farm CPU_pkg.r MVP is freely available at https://github.com/xiaolei-lab/r MVP.
文摘实验室管理系统旨在提供全面的解决方案,以管理实验室的设备、仪表、材料、实验项目、研究人员和学生等重要信息。实验室管理系统不仅简化了实验室资源的跟踪和管理,而且增强了实验项目的组织和监控,从而确保研究过程的透明度和数据的完整性。该系统采用Java技术栈,包括SpringBoot、Spring Security和Spring Data JPA,作为后端开发框架,结合HTML、CSS、JavaScript以及React作为前端技术,构建了一个用户友好且功能强大的实验室管理平台。通过数据库设计和优化,系统实现了实验室资源的高效管理、实验项目的追踪和评估、用户权限的灵活控制以及数据的可视化分析。
基金supported by the National Natural Science Foundation of China(Grant No.61471338)the Knowledge Innovation Program of the Chinese Academy of Sciences,Youth Innovation Promotion Association CAS,President Fund of UCASCRSRI Open Research Program(Grant No.CKWV2015217/KY)
文摘The three-dimensional discontinuous deformation analysis(3D-DDA) is a promising numerical method for both static and dynamic analyses of rock systems. Lacking mature software, its popularity is far behind its ability. To address this problem, this paper presents a new software architecture from a software engineering viewpoint. Based on 3D-DDA characteristics, the implementation of the proposed architecture has the following merits. Firstly, the software architecture separates data, computing, visualization, and signal control into individual modules. Secondly, data storage and parallel access are fully considered for different conditions. Thirdly, an open computing framework is provided which supports most numerical computing methods; common tools for equation solving and parallel computing are provided for further development. Fourthly, efficient visualization functions are provided by integrating a variety of visualization algorithms. A user-friendly graphical user interface is designed to improve the user experience. Finally, through a set of examples, the software is verified against both analytical solutions and the original code by Dr. Shi Gen Hua.
