Enhancing data sharing in collaborative research projects with DASH.

We describe a software framework, called DASH, that enables the facile access, maintenance, curation and sharing of computational biology data among collaborating research scientists. The DASH event-based framework enables members of team-based research projects to describe the multistep computational processing pipelines frequently required to generate data for sharing, monitors multiple distributed data stores for changes, and will then automatically invoke the appropriate processing pipeline(s). These pipelines can be used to communicate the results of data analyses to collaborators using mechanisms such as Web Services. We describe the overall design of the DASH system and the application of a simple DASH prototype to a collaborative pharmacogenomics research project involving several dozen researchers located at several different sites--the UCSF Pharmacogenetics of Membrane Transporters project.

UCSF Chimera--a visualization system for exploratory research and analysis.

The design, implementation, and capabilities of an extensible visualization system, UCSF Chimera, are discussed. Chimera is segmented into a core that provides basic services and visualization, and extensions that provide most higher level functionality. This architecture ensures that the extension mechanism satisfies the demands of outside developers who wish to incorporate new features. Two unusual extensions are presented: Multiscale, which adds the ability to visualize large-scale molecular assemblies such as viral coats, and Collaboratory, which allows researchers to share a Chimera session interactively despite being at separate locales. Other extensions include Multalign Viewer, for showing multiple sequence alignments and associated structures; ViewDock, for screening docked ligand orientations; Movie, for replaying molecular dynamics trajectories; and Volume Viewer, for display and analysis of volumetric data. A discussion of the usage of Chimera in real-world situations is given, along with anticipated future directions. Chimera includes full user documentation, is free to academic and nonprofit users, and is available for Microsoft Windows, Linux, Apple Mac OS X, SGI IRIX, and HP Tru64 Unix from http://www.cgl.ucsf.edu/chimera/.