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 Chimera: A program for the interactive visualization and analysis of molecular structures and related data, including density maps, sequence alignments, docking results, and trajectories. Chimera is an extremely feature-rich program that continues to be highly used and cited.
- UCSF ChimeraX: The RBVI's next-generation program for the interactive visualization and analysis of molecular structures and related data, under active development to provide advanced rendering options, to facilitate working with large structures, integrative models, and microscopy datasets, and to support the development of plugins by the community.
- Virtual Reality: The RBVI develops virtual-reality capabilities for research within UCSF ChimeraX as well as the separate Molecular Zoo software for a more lighthearted introduction to molecules.
- 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 plugins.
- 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 Cytoscape analysis tools and protocols for single-cell RNA sequence data.
- Wynton: A large computing cluster available to all UCSF faculty.
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