WormGUIDES: an interactive single cell developmental atlas and tool for collaborative multidimensional data exploration

• DOI: 10.1186/s12859-015-0627-8
• Publication Date: 2015-06-07T23:34:34Z
• Authors: Anthony Santella; Raúl Catena; Ismar Kovacevic; Pavak Shah; Zidong Yu; Javier Marquina-S...; Abhishek Kumar; Yicong Wu; James Schaff; Daniel Colón-Ramos; Hari Shroff; William A. Mohler; Zhirong Bao
• Keywords: 0301 basic medicine; User-Computer Interface; 03 medical and health sciences; Databases, Factual; Animals; Single-Cell Analysis; Caenorhabditis elegans; Biochemistry; Molecular Biology; Nervous System; Software; Computer Science Applications

Imaging and image analysis advances are yielding increasingly complete complicated records of cellular events in tissues whole embryos. The ability to follow hundreds thousands cells at the individual level demands a spatio-temporal data infrastructure: tools assemble collate knowledge about development spatially manner analogous geographic information systems (GIS). Just as GIS indexes items or based on their 4D location Earth these would organize within Developmental processes highly context-specific, but complexity environment which they unfold is barrier assembling an understanding any particular process from diverse sources information. In same way that aids use geo-located large sets, software can, with proper frame reference, allow biological sets be understood spatially. Intuitive needed navigate spatial structure complex tissue, existing this help users derive hypotheses developmental mechanisms.Toward goal we have developed WormGUIDES, mobile application presents atlas for Caenorhabditis elegans. WormGUIDES app enables 3D model depicting nuclear positions all developing embryo. identity each cell can queried tap, community databases searched available cell. Information ancestry, fate gene expression used label craft customized visualizations highlight potential players event interest. Scenes easily saved, shared published other users. Android iOS platforms.WormGUIDES provides important tool examining mechanistic control. Critically, it typical end user intuitive interface sharing custom processes. Equally important, because select position search them, also serves organized index into body C. elegans online. Moreover, create publish result exploration: interactive content brings researchers students directly point insight. Ultimately will incorporate detailed time lapse record shape, beginning neurons. This add key understand coordinated precise emergence anatomy, particularly wiring nervous system.