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ViCE Helps Smooth Scientific Workflows

January 1, 2006


A typical ViCE workflow that shows a scientist using the BLAST search technology to search three protein sequence databases (nr, the main protein sequence database; topsecret, an example of proprietary data; and pdb, the Protein Structure Databank), then extracting the resulting sequences and aliging them

DSD’s work in higher-level interfaces to the Grid has led to the development of a visual programming tool, ViCE, that is used to collaboratively develop and execute complex scientific workflows.

Scientific projects today are frequently large collaborations among geographically and organizationally distributed teams. ViCE is designed to support scientists collaborating over a visual description of their workflow. A workflow is represented as a set of nodes and links. The nodes represent actions, such as querying a protein sequence database, and links represent the data transfer between nodes. By dragging and dropping a series of domain- specific nodes onto a palette, a scientist can construct a complete workflow.

The accompanying figure shows a typical visual workflow description from biology. The biologists are searching several protein sequence databases, looking for a likely match to a newly sequenced protein.

ViCE supports collaboration by allowing multiple groups to have the same view of the changing workflow description. They can use integrated chat tools to discuss the workflow. Future versions will support the collaborative editing of the visual workflow description.


About Computing Sciences at Berkeley Lab

The Lawrence Berkeley National Laboratory (Berkeley Lab) Computing Sciences organization provides the computing and networking resources and expertise critical to advancing the Department of Energy's research missions: developing new energy sources, improving energy efficiency, developing new materials and increasing our understanding of ourselves, our world and our universe.

ESnet, the Energy Sciences Network, provides the high-bandwidth, reliable connections that link scientists at 40 DOE research sites to each other and to experimental facilities and supercomputing centers around the country. The National Energy Research Scientific Computing Center (NERSC) powers the discoveries of 7,000-plus scientists at national laboratories and universities, including those at Berkeley Lab's Computational Research Division (CRD). CRD conducts research and development in mathematical modeling and simulation, algorithm design, data storage, management and analysis, computer system architecture and high-performance software implementation. NERSC and ESnet are Department of Energy Office of Science User Facilities.

Lawrence Berkeley National Laboratory addresses the world's most urgent scientific challenges by advancing sustainable energy, protecting human health, creating new materials, and revealing the origin and fate of the universe. Founded in 1931, Berkeley Lab's scientific expertise has been recognized with 13 Nobel prizes. The University of California manages Berkeley Lab for the DOE’s Office of Science.

DOE’s Office of Science is the single largest supporter of basic research in the physical sciences in the United States, and is working to address some of the most pressing challenges of our time. For more information, please visit science.energy.gov.