We describe a network sharable, interactive computational tool for rapid and sensitive search and analysis of biomolecular sequence databases such as GenBank, GenPept, Protein Identification Resource, and SWISS-PROT. The resource is accessible via the World Wide Web using popular client software such as Mosaic and Netscape. The client software is freely available on a number of computing platforms including Macintosh, IBM-PC, and Unix workstations.

Rapid growth of protein structures database in recent years requires an effective approach for objective comparison and classification of deposited protein structures. We describe a novel method for structure comparison and classification based on the alignment of one-dimensional structure profiles. These profiles are obtained by calculating the OCCO pseudodihedral angles (formed by O-C-C-O atoms of carbonyl groups of consecutive amino acid residues) from protein three-dimensional coordinates. These angle measurements are then converted into a 24 letter alphabet, and the protein structures are represented by sequences of letter from this alphabet. The BioSCAN parallel computer, designed for primary sequence alignment, is used to rapidly align and classify these one-dimensional structure profiles. We have developed and implemented weighted scoring matrix to identify structural classes based on commonly found structural motifs. The results of our experiments are in good agreement with the traditional protein structure classification schemes. One-dimensional structure profiles significantly improve efficiency of structure comparison and classification.

VISTAnet is a three-year research effort that involves the deployment of prototype broadband switching systems interconnecting specialized supercomputers. The project partners include BellSouth, GTE, MCNC, North Carolina State University (NCSU), and the University of North Carolina at Chapel Hill (UNC-CH). In addition to the deployment and evaluation of experimental network facilities, the project supports research activities in several areas: gigabit communications, metacomputing, advanced visualization techniques, and medical treatment planning techniques, specifically dynamic radiation therapy planning. VISTAnet is organized as a testbed. It is an environment that has been established to experiment with and evaluate techniques associated with gigabit networking. These experiments include methods for moving data into and out of host computers from the application to the network at gigabit rates, demonstrations and evaluations of an application that requires gigabit networking, and interactive three-dimensional graphics techniques. The overall goal of the testbed is to advance the state-of-the-art in gigabit networking and its application. VISTAnet is one of five gigabit test beds coordinated by the Corporation for National Research Initiatives in cooperation with DARPA and NSF.>

As networks approach gigabit performance, supercomputer host interfaces are becoming the communication bottleneck.The Network Interface Unit (NIU) is a highperformance host interface for Pixel Planes 5, a custom graphics supercomputer.The design offers both performance and programmability through a balance of ahtamarshaling hardware and an embedded processor.In this paper, we describe the NW hardware and jirmware architecture.We present some prelitw"nary peq$ormance measurements and assess the applicability of this design for the targeted environment.We also comment on its suitability for other environments and outline plans for the future work.PemnissiOn to copy witkut fee df or pan of Ibis mat.xial is gmntaf, pmvikd that tbe copie6 are not made or diswilmted for direct commercial adva"lage, the ACM copyright nctice and ibe tide of the publication and 124 its date appear, and notice is given that copying is by permission of tbe Assxiation for Commting Machinery.To copy otbenvise, or to repubkb, requires a fee andkr specific permission.

A special-purpose computer system has been designed to accelerate scanning large databases of DNA and protein sequences (biosequences) for patterns of interest. The system consists of a custom-designed circuit board installed in a host workstation and associated software. The board features a variable number of identical full-custom ASICs. Each biological sequence comparative analysis node. (BioSCAN) ASIC, in turn, features a large one-dimensional systolic array of identical processing elements (PEs). The BioSCAN system scans approximately two million database elements per second. For typical problems this results in a 1000-fold speedup over current workstations.>