Scientific Data and Software



PDBtool and CIFters



The Protein Data Bank collects macro-molecular structure data for biochemists and crystallographers. It currently contains 900 molecules and is expected to grow to 6000 by the end of the decade. Dr. Pu is leading the design and implementation of an interoperable database backend of an object-oriented toolbox for the Protein Data Bank. The goal is to provide biologists with a state-of-the-art tookit that handles data management for data with complex structures in an efficient way. The beta release of the PDBtool, an object-oriented toolbox for macromolecular structure verification, is described in PDBtool Home Page.

This work is in collaboration with Dr. Phil Bourne, who is the principal investigator of the project.



Weather Data Management



This work on computational biology has been developed into an architecture for scientific data management, to be applied in a joint project with George Taylor of Oregon Climate Service and Prof. Gad Levy of College of Atmospheric and Oceanographic Sciences at the Oregon State University, and the Department of Atmospheric Sciences at the University of Washington. The collaboration has two thrusts: (1) development of Internet software to make climate data accessible to the public, particularly Oregon people, and (2) data assimilation in large weather data sets of the future.


Environmental Data Management



A third collaboration with scientists is the joint project with Prof. Antonio Baptista of Center for Coastal and Land Margin Research and Department of Environmental Sciences and Engineering of OGI. This project is developing software for the collection, integration, and processing of environmental data in a regional scale.

This work is in collaboration with Prof. Darrell Long of University of California, Santa Cruz, who is working in the REINAS project. Two papers describe REINAS: "REINAS: the Real-Time Environmental Information Network and Analysis System" and "The REINAS System Design" .

REINAS System Map



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