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Identifying residue coupling relationships within a protein family can provide important insights into the family's evolutionary record, and has significant applications in analyzing and optimizing sequence-structure-function relationships. We present the first algorithm to infer an undirected graphical model representing residue coupling in protein(More)
Pattern languages are representations that have been used in architecture and urban designer about twenty years. They J~cus on the interaction between physical j@m and social behavior, and express design solutions in an understandable and generalizable j@m. But pattern languages are not simptv set of patterns intended to be universally applied; instead,(More)
The methods currently used to assure the safety of planned changes to our air transportation systems were developed 50 years ago for systems composed primarily of hardware components and of much less complexity than the systems we are building today. These methods are not powerful enough to handle the complex, human and software intensive systems being(More)
ed underlying grid infrastructure to an application) allowed us to reuse an existing game engine without the need to make any significant changes to it. In this paper we examine the design elements needed by an MMOG and provide a practical implementation example—the extension of the id Software Quake IIt game engine using OptimalGrid middleware. A key(More)
A new hazard analysis technique, called System-Theoretic Process Analysis, is capable of identifying potential hazardous design flaws, including software and system design errors and unsafe interactions among multiple system components. Detailed procedures for performing the hazard analysis were developed and the feasibility and utility of using it on(More)
Most of the basic design decisions affecting safety are made in the concept development stage of system development. Once these decisions are made, the cost of changing them later in development is often enormous and perhaps even infeasible. At the same time, most hazard analysis methods require a fairly complete design to be most useful. By the time enough(More)
This paper develops an approach for designing protein variants by sampling sequences that satisfy residue constraints encoded in an undirected probabilistic graphical model. Due to evolutionary pressures on proteins to maintain structure and function, the sequence record of a protein family contains valuable information regarding position-specific residue(More)
Protein-protein interactions are mediated by complementary amino acids defining complementary surfaces. Typically not all members of a family of related proteins interact equally well with all members of a partner family; thus analysis of the sequence record can reveal the complementary amino acid partners that confer interaction specificity. This article(More)
We present a case study in the use of virtual environment technology for cultural heritage applications, describing a collaborative effort to construct two cultural heritage exhibits for a five month exhibition at the New Orleans Museum of Art. To illustrate the factors that shape museum exhibit design, we explore the initial conceptual phase and discuss(More)
Computer system users today are inundated with a flood of semi-structured information, such as documents, electronic mail, programs, and images. Today, this information is typically stored in filesystems that provide limited support for organizing, searching, and operating upon this data, all operations that are vital to the ability of users to effectively(More)