RBVI Projects

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The RBVI seeks to advance the frontiers of biomedical research while developing new applications of immediate use to scientists. Our projects generate high-quality software and websites for the analysis of biomedical data ranging from molecular and cellular structures to sequences, networks, and multi-omics data.

UCSF ChimeraX: The RBVI's next-generation program for the interactive visualization and analysis of molecular structures and related data, including cryo-EM and X-ray density maps, sequence alignments, docking results, trajectories and much more. ChimeraX provides advanced rendering options, to facilitate working with large structures, integrative models, and microscopy datasets, and supports plugin development by the community.

Virtual Reality: The RBVI develops virtual-reality capabilities for research within ChimeraX as well as the separate Molecular Zoo software for pre-college students to learn about biomolecules.

Cytoscape: An open-source platform for the visualization and analysis of complex networks. The RBVI contributes to the Cytoscape core and has developed several highly used Cytoscape Apps.

Scalable Precision Medicine Oriented Knowledge Engine (SPOKE): A heterogeneous network incorporating diseases, compounds, genes, proteins, pathways, and other data from multiple sources. Pooling such diverse data allows identifying new connections, with implications for drug repurposing, personalized medicine, and other biomedical applications.

Human Cell Atlas: A global collaboration to map and characterize all of the cell types in a healthy human body. The RBVI is developing tools to analyze the associated data, such as the scNetViz Cytoscape app for showing networks of differentially expressed genes from single-cell RNA sequencing.

Wynton: A large computing cluster available to all UCSF faculty.