The Internet technology has already changed the Information Society in profound ways, and will continue to do so. Nowadays many people foresee that there is a similar trajectory for the next generation of Internet - G...The Internet technology has already changed the Information Society in profound ways, and will continue to do so. Nowadays many people foresee that there is a similar trajectory for the next generation of Internet - Grid Technology. As an emerging computational and networking infrastructure, Grid Computing is designed to provide pervasive, uniform and reliable access to data, computational and human resources distributed in a dynamic, heterogeneous environment. On the other hand, the development of Geographic Information System （GIS） has been highly influenced by the evolution of information technology such as the Internet, telecommunications, software and various types of computing technology. In particular, in the distributed GIS domain, the development However, due to the closed and centralized has made significant impact in the past decade. legacy of the architecture and the lack of interoperability, modularity, and flexibility, current distributed GIS still cannot fully accommodate the distributed, dynamic, heterogeneous and speedy development in network and computing environments. Hence, the development of a high performance distributed GIS system is still a challenging task. So, the development of Grid computing technology undoubtedly provides a unique opportunity for distributed GIS, and a Grid Computing based GIS paradigm becomes inevitable. This paper proposes a new computing platform based distributed GIS framework - the Grid Geographic Information System （G^2IS）.展开更多
Data visualization empowers researchers to communicate their results that support scientific reasoning in an intuitive way.Three-dimension(3D)spatially resolved transcriptomic atlases constructed from multi-view and h...Data visualization empowers researchers to communicate their results that support scientific reasoning in an intuitive way.Three-dimension(3D)spatially resolved transcriptomic atlases constructed from multi-view and high-dimensional data have rapidly emerged as a powerful tool to unravel spatial gene expression patterns and cell type distribution in biological samples,revolutionizing the understanding of gene regulatory interactions and cell niches.However,limited accessible tools for data visualization impede the potential impact and application of this technology.Here we introduce VT3D,a visualization toolbox that allows users to explore 3D transcriptomic data,enabling gene expression projection to any 2D plane of interest,2D virtual slice creation and visualization,and interactive 3D data browsing with surface model plots.In addition,it can either work on personal devices in standalone mode or be hosted as a web-based server.We apply VT3D to multiple datasets produced by the most popular techniques,including both sequencing-based approaches(Stereo-seq,spatial transcriptomics,and Slide-seq)and imaging-based approaches(MERFISH and STARMap),and successfully build a 3D atlas database that allows interactive data browsing.We demonstrate that VT3D bridges the gap between researchers and spatially resolved transcriptomics,thus accelerating related studies such as embryogenesis and organogenesis processes.The source code of VT3D is available at https://github.com/BGI-Qingdao/VT3D,and the modeled atlas database is available at http://www.bgiocean.com/vt3d_example.展开更多
In large spatial,temporal,and spatio-temporal databases,the concept of dimensions–time and space–is central and their efficient processing has always been a great concern.A Geographic Information System(GIS)is widel...In large spatial,temporal,and spatio-temporal databases,the concept of dimensions–time and space–is central and their efficient processing has always been a great concern.A Geographic Information System(GIS)is widely known for its efficient and sophisticated handling of the spatial databases;however,integration of the time domain introduces additional complexities.Considerable research is ongoing in this area.Though numerous approaches have already been proposed in the literature to address the time-related challenges in GIS community,such as the development of temporal GIS data models,this study contributes to these ongoing efforts through extensions to the Parametric Data Model.Parametric database approaches(Parametric Data Model)have been developed to handle dimensional data such as space,time,belief,etc.In this study,the time dimension is of specific interest and we propose the integration of parametric approaches to GIS to absorb the temporal burden.The temporal processing of the data is done using parametric approaches that address the limitation of GIS to support temporal queries and temporal analysis of phenomena.Using the AutoConViz tool,developed for spatio-temporal data modeling and visualization,results can be directly integrated into standard GIS software programs such as ArcGIS and further processed seamlessly along with and in a similar manner to other attributes.展开更多
文摘The Internet technology has already changed the Information Society in profound ways, and will continue to do so. Nowadays many people foresee that there is a similar trajectory for the next generation of Internet - Grid Technology. As an emerging computational and networking infrastructure, Grid Computing is designed to provide pervasive, uniform and reliable access to data, computational and human resources distributed in a dynamic, heterogeneous environment. On the other hand, the development of Geographic Information System （GIS） has been highly influenced by the evolution of information technology such as the Internet, telecommunications, software and various types of computing technology. In particular, in the distributed GIS domain, the development However, due to the closed and centralized has made significant impact in the past decade. legacy of the architecture and the lack of interoperability, modularity, and flexibility, current distributed GIS still cannot fully accommodate the distributed, dynamic, heterogeneous and speedy development in network and computing environments. Hence, the development of a high performance distributed GIS system is still a challenging task. So, the development of Grid computing technology undoubtedly provides a unique opportunity for distributed GIS, and a Grid Computing based GIS paradigm becomes inevitable. This paper proposes a new computing platform based distributed GIS framework - the Grid Geographic Information System （G^2IS）.
基金supported by the General Program(Key Program,Major Research Plan)of National Natural Science Foundation of China(No.32170439).
文摘Data visualization empowers researchers to communicate their results that support scientific reasoning in an intuitive way.Three-dimension(3D)spatially resolved transcriptomic atlases constructed from multi-view and high-dimensional data have rapidly emerged as a powerful tool to unravel spatial gene expression patterns and cell type distribution in biological samples,revolutionizing the understanding of gene regulatory interactions and cell niches.However,limited accessible tools for data visualization impede the potential impact and application of this technology.Here we introduce VT3D,a visualization toolbox that allows users to explore 3D transcriptomic data,enabling gene expression projection to any 2D plane of interest,2D virtual slice creation and visualization,and interactive 3D data browsing with surface model plots.In addition,it can either work on personal devices in standalone mode or be hosted as a web-based server.We apply VT3D to multiple datasets produced by the most popular techniques,including both sequencing-based approaches(Stereo-seq,spatial transcriptomics,and Slide-seq)and imaging-based approaches(MERFISH and STARMap),and successfully build a 3D atlas database that allows interactive data browsing.We demonstrate that VT3D bridges the gap between researchers and spatially resolved transcriptomics,thus accelerating related studies such as embryogenesis and organogenesis processes.The source code of VT3D is available at https://github.com/BGI-Qingdao/VT3D,and the modeled atlas database is available at http://www.bgiocean.com/vt3d_example.
文摘In large spatial,temporal,and spatio-temporal databases,the concept of dimensions–time and space–is central and their efficient processing has always been a great concern.A Geographic Information System(GIS)is widely known for its efficient and sophisticated handling of the spatial databases;however,integration of the time domain introduces additional complexities.Considerable research is ongoing in this area.Though numerous approaches have already been proposed in the literature to address the time-related challenges in GIS community,such as the development of temporal GIS data models,this study contributes to these ongoing efforts through extensions to the Parametric Data Model.Parametric database approaches(Parametric Data Model)have been developed to handle dimensional data such as space,time,belief,etc.In this study,the time dimension is of specific interest and we propose the integration of parametric approaches to GIS to absorb the temporal burden.The temporal processing of the data is done using parametric approaches that address the limitation of GIS to support temporal queries and temporal analysis of phenomena.Using the AutoConViz tool,developed for spatio-temporal data modeling and visualization,results can be directly integrated into standard GIS software programs such as ArcGIS and further processed seamlessly along with and in a similar manner to other attributes.
