Digital Equipment Corporation VAX Research Articles

PAP: a protein analysis package

A program package has been assembled for the analysis of protein coordinates which are in the Brookhaven Protein Data Bank (PDB) format. These programs can be used to make two types of φ–ψ plots: a Ramachandran-style scatter plot, and a plot of φ and ψ values as a function of the linear sequence. Programs are also available for the display of distance diagonal plots for proteins. Two protein structures can be compared and the resulting r.m.s. differences in the structures plotted as a function of sequence. Temperature factors can be analyzed and plotted as a function of the linear sequence. In addition, various utilities are supplied for splitting PDB files which contain multiple subunits into individual files and also for renumbering PDB files. A utility is also provided for converting Amber-style PDB files into standard PDB files. Priestle's program RIBBON [J. Appl. Cryst. (1988), 21, 572–576] has been converted to run in a stand-alone mode with interactive rotation of the three-dimensional ribbon picture. Programs are Silicon Graphics four-dimensional level and have been tested on 4D70/GT and personal Iris workstations, although programs which give Postscript output have been converted to run on Digital Equipment Corporation VAX computers and Sun workstations.

A Real-Time, Mesoscale Numerical Weather-Prediction System Used for Research, Teaching, and Public Service at The Pennsylvania State University

A mesoscale modeling system is being applied on an experimental basis at The Pennsylvania State University (Penn State) for production of real-time, high resolution, numerical weather forecasts for the northeastern United States. The initial model experimentation is being supported by Penn State. It is believed to be the first time that a real-time, three-dimensional mesoscale model has been run routinely at an American university, although mesoscale models have been run in real time in government laboratories. A version of the Penn State/NCAR mesoscale model is employed, using a two-way interacting nested grid with a fine-grid increment of 30 km, a coarse-grid increment of 90 km, and 15 computational levels. The forecast cycle is initiated automatically by the Department of Meteorology's Digital Equipment Corporation VAX 8350 system when all the required 0000 UTC surface and upper-air National Weather Service (NWS) data have been received, quality checked, and archived. Lateral boundary conditions are ex...

Macromodel—an integrated software system for modeling organic and bioorganic molecules using molecular mechanics

AbstractAn integrated molecular modeling system for designing and studying organic and bioorganic molecules and their molecular complexes using molecular mechanics is described. The graphically controlled, atom‐based system allows the construction, display and manipulation of molecules and complexes having as many as 10,000 atoms and provides interactive, state‐of‐the‐art molecular mechanics on any subset of up to 1,000 atoms. The system semiautomates the graphical construction and analysis of complex structures ranging from polycyclic organic molecules to biopolymers to mixed molecular complexes. We have placed emphasis on providing effective searches of conformational space by a number of different methods and on highly optimized molecular mechanics energy calculations using widely used force fields which are supplied as external files. Little experience is required to operate the system effectively and even novices can use it to carry out sophisticated modeling operations. The software has been designed to run on Digital Equipment Corporation VAX computers interfaced to a variety of graphics devices ranging from inexpensive monochrome terminals to the sophisticated graphics displays of the Evans & Sutherland PS300 series.

Macintosh Workstations

OOP, GUI, AND LIBRARY WORKSTATION SOFTWARE. Digital Equipment Corporation (DEC) recently awarded large grants to the University of California and Pennsylvania State University jointly to link the massive bibliographic databases of both institutions together, in spite of varying hardware platforms and geography. At the workstation level, the University of California will create interfaces based on DECwindows, a form of the X Windows interface. The online bibliographic systems of Berkeley and Perm State handle 200,000 to 300,000 requests per week, and currently run on an IBM 3090 in California and a DEC VAX 9000 system in Pennsylvania. This interest in bibliographic interfaces has grown rapidly in the last few years thanks to hardware developments putting more computing muscle on the desktop for librarians, their programmers, and ultimately their patrons. Recent manifestations of graphic interfaces have appeared in many libraries as HyperCard shells built as intermediaries to mainframe bibliographic software. This grant by DEC indicates that this sort of work on graphic interfaces in libraries and the system offices on campuses has not gone without notice by major vendors. With the recent explosion in the number of graphic interfaces, it is important to review these tools and their basis in object oriented programming (OOP).

A COMPUTER MODEL FOR DAMA GE TOLERANCE ANALYSIS

ABSTRACTA computer model is being developed by the David Taylor Research Center (DTRC) to analyze the tolerance of surface ship combat systems to combat‐induced and self‐inflicted damage. The work is being done in support of the Navy's hull, mechanical and electrical design effort to improve the survivability of surface ship combat systems.The DDG‐51 Detailed Design Specifications (Section 072f) and the General Specifications for Ships of the U.S. Navy (1986 Section 072e) both require that damage tolerance analyses be performed.A damage tolerance analysis shows the effect of damage on vital auxiliary and electrical systems and relates these damage effects to the capability of the ship to continue performing its combat mission at a prescribed level. Designated the Computer Aided Design of Survivable Distributed Systems (CADSDiS) model, DTRC's deterministic analytical tool consists of portable software to be used by personnel at the activity responsible for the ship design. The model's graphics electrical module is now operating on Digital Equipment Corporation VAX computers at several Navy and commercial activities.Because CADSDiS is highly interactive, it becomes an integral part of the design cycle; this is its major benefit. Thus, damage tolerance analysis information is available to personnel designing the ship within hours or days rather than weeks or months. This computer model will help ensure that the survivability principles of separation and redundancy are incorporated into ship design and are realized in the ship as built.

Integrated, multivendor distributed data-acquisition system

A distributed data-acquisition system that used various computer hardware and software is being developed to support magnetic fusion experiments at Lawrence Livermore National Laboratory (LLNL). The experimental sequence of operations is controlled by a supervisory program, which coordinates software running on Digital Equipment Corporation (DEC) VAX computers, Hewlett–Packard (HP) UNIX-based workstations, and HP basic desktop computers. An interprocess communication system (IPCS) allows programs to communicate with one another in a standard manner regardless of program location in the network or of operating system and hardware differences. We discuss the design and implementation of this data-acquisition system with particular emphasis on the coordination model and the IPCS.

Information system for labor and delivery surveillance.

An on-line information system has been developed and implemented at St. Mary Medical Center in Long Beach, California, to support a ten-bed labor and delivery suite. A Digital Equipment Corporation VAX 750 was programmed to provide on-line multi-terminal clinical surveillance. The reports implemented include an obstetrical summary report, labor record, obstetrical clinical record, and the birth certificate. Computer terminals and monitors are placed at the nursing station and other work areas, such as the anesthesia on-call room, obstetrical supervisor's office, on-call room, neonatal ICU, O.R., admission room, and M.D. conference room. The system includes computer databases used to store information for medical quality assurance, management reports, obligatory statutory reports, and research, and to provide comparison of patient data with data from other hospitals.

The CERN Host Interface

The authors discuss the CERN Host Interface Project, which aims to provide modular interfaces between Digital Equipment Corporation's VAX series computers and two popular high-energy physics buses, the VMEbus and FASTBUS. These user-programmable interfaces contain a powerful central processing unit, large data memories, and ports that allow the user to configure the interface for the required host computer and target bus. The software support and the optical data connection are described.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>

Applications of the Connection Machine

The Connection Machine development effort was initiated in the belief that parallel processing and artificial intelligence could together accelerate the rate of progress toward truly intelligent machines. This progress is the result of the ease with which the machine can be programmed and the dramatic increase in compute power that the machine can bring to bear. The authors have been able to run many trials of experiments in instances where previously, running just one would have been considered an achievement and no further experimentation would have been done. This has enabled exploring a great many more hypotheses and to work on much larger problems that had been possible on previous-generation artificial intelligence workstations. The ease of programming is in part the result of a decision to use existing serial machines (the Symbolics 3600 or Digital Equipment Corporation VAX), thus leaving unchanged the operating systems, editors, file systems, debuggers, network communications systems, and so on, so as to provide familiar programming environments. The Connection Machine is programmed in conservative extensions of Common Lisp and C. Users familiar with these languages and with front-end computer systems have been able to produce results on the Connection Machine on the first day that theymore » use it.« less

Psyxpert: An expert system prototype for aiding psychiatrists in the diagnosis of psychotic disorders

Psyxpert is an expert computer system prototype disigned to aid psychiatrists in the diagnosis of mental disorders, in cases where psychotic features are the prominent part of the presenting clinical picture. The knowledge base contains psychiatric knowledge in the form of production rules. The system uses a backward-chaining control strategy to guide the consultation. Psyxpert provides a menu-driven user interface and an explanation subsystem. The system uses certainty and importance measures to produce a diagnosis with an attached certainty factor and recommendations for further evaluation or therapy. Psyxpert is written in Virginia Tech HC Prolog and runs on Digital Equipment Corporation's VAX 11 780 under the VMS operating system.

Use of a new array processor in the restrained least-squares procedure of Hendrickson and Konnert

The restrained least-squares refinement procedure of Hendrickson & Konnert [Hendrickson (1985). Methods in Enzymology, Vol. 115, edited by H. W. Wyckoff, C. H. W. Hirs & S. N. Timasheff, pp. 252–270. Orlando: Academic Press] has been implemented on a Digital Equipment Corporation VAX 11/780 equipped with a 30 MFLOP (million floating point operations per second) Numerix MARS-432 array processor. The modified program executes in only one twentieth of the time required for the unmodified version on the same VAX and an estimated half of the time required for execution on an IBM 3081.

Physics analysis database for the DIII-D tokamak

Centralized databases for handling reduced data for physics analysis have been implemented for the DIII-D tokamak. Each database record corresponds to a specific snapshot in time for a selected discharge. Features of the database environment include automatic updating, data integrity checks, and data traceability. Reduced data from each diagnostic comprises a dedicated dataset (a subset of the database) with quality assurance provided by a physicist. For the confinement database, these datasets will be used to create profile datasets which will be input to a transport code to create a transport dataset. The databases are implemented on a Digital Equipment Corporation VAX 8600 running VMS. The database management system is S1032 from Software House, Inc.

MBIS--an integrated system for the retrieval and analyses of sequence data from nucleic acids and proteins.

A computer-based system termed MBIS (the Molecular Biological Information Service), written in FORTRAN77 and Digital Command Language (DCL) and running on a Digital Equipment Corporation VAX computer under the VMS operating system (V4.1) is in use at the Division of Molecular Biology. MBIS consists of three main sections: 1) The utility section, used by the system's manager to tailor the five commonly available databases so that they are useable by the applications programmes running on the system; 2) The retrieval section, used to find and extract specific sequences or bibliographic information, and 3) The analytical section, used to analyse and compare sequences either extracted from the databases or input by the user. The nucleotide databases maintained are GenBank, EMBL and PIR (Protein Identification Resource, National Biomedical Research Foundation) and the peptide databases are PIR and NEWAT. In addition, users can originate and maintain their own databases. Those programmes which feature graphics output are compatible with most emulators of the Tektronix 4010 terminal.

A Three-Dimensional Vision by Off-Shelf System with Multi-Cameras

A three-dimnensional vision system for on-line operation that aids a collision avoidance system for an industrial robot is developed. Because of the real-time requirement, the process that locates and describes the obstacles must be fast. To satisfy the safety requirement, the obstacle model should always contain the physical obstacle entirely. This condition leads to the bounding box description of the obstacle, which is simple for the computer to process. The image processing is performed by a Machine Intelligence Corporation VS-100 machine vision system. The control and object perception is performed by the developed software on a host Digital Equipment Corporation VAX 11/780 Computer. The resultant system outputs a file of the locations and bounding descriptions for each object found. When the system is properly calibrated, the bounding descriptions always completely envelop the obstacle. The response time is data-dependent. When using two cameras and processed on UNIX time sharing mode, the average response time will be less than 2 s if eight or fewer objects are present. When using all three cameras, the average response time will be less than 4 s if eight or fewer objects are present.

Performance monitoring on a multiaccess system

This paper describes the need for performance monitoring of a multiaccess operating system and outlines the methods that can be used to perform monitoring. The study describes the monitoring that has been carried out on a Digital Equipment Corporation.† VAX is a trademark of Digital Equipment Corporation VAX 11/750 (running ‡ 4.1 Berkeley Source Distribution 4.1BSD) which has been running under varying workload conditions for approximately eight months. The results that were collected are presented and some conclusions drawn. Areas of further studies are indicated.

Selection of a standard programming language for an oil service consultancy

Abstract Criteria for selection of a standard programming language for an oil service company involved in creating and applying data bases for the petroleum industry are discussed. Computer languages for a popular minimainframe computer, the Digital Equipment Corporation VAX, are considered in the light of these criteria. The authors selected the language PL/1 as best fulfilling the requirements of the company. It is suggested that the selection criteria might be pertinent to computer geology, in general, and that the computer languages considered may be representative of those known and normally available to this community of users.

A comprehensive set of sequence analysis programs for the VAX.

The University of Wisconsin Genetics Computer Group (UWGCG) has been organized to develop computational tools for the analysis and publication of biological sequence data. A group of programs that will interact with each other has been developed for the Digital Equipment Corporation VAX computer using the VMS operating system. The programs available and the conditions for transfer are described.

CSNET protocol software

CSNET is built on the Department of Defense network (ARPANET), public packet-switched physical networks (Telenet), and a telephone-based relay network (Phonenet). Some CSNET sites have direct connections to ARPANET, some have direct connections to Telenet, and some have connections only to telephone-based relay machines. The chief objective of CSNET is to provide a network interconnection for all groups engaged in Computer Science Research. CSNET has adopted TCP/IP as its standard transport level protocols. The Transmission Control Protocol (TCP) [POST81] is an end-to-end protocol. It establishes communications between two processes that are running on different machines, detects and corrects errors, controls data flow, and provides reliable communications. Application programs call TCP to transfer data across the network. TCP, in turn, uses the Internet Protocol (IP) [POST81] to send data to the appropriate network. CSNET communications such as file transfer, remote login, and process-to-process communication over the network assume that a TCP interface is available at CSNET sites. Since ARPANET sites are required to support the TCP/IP protocols, CSNET sites connected directly to the ARPANET automatically have access to TCP/IP. Phonenet relays connect directly to the ARPANET; they too have access to TCP to relay mail onto the ARPANET. Telenet does not use the TCP/IP protocols. Consequently, CSNET sites that are connected only to Telenet need additional software before they can communicate on CSNET. That software is described in this paper -- it provides an interface between the public packet - switched protocol X.25 [CCITT78] and TCP/IP. Although the design outlined here is applicable to any vendor's system, our implemention is for a Digital Equipment Corporation VAX running the Western Electric UNIX [UNIX78] operating system as modified by the University of California at Berkeley. This report focuses on the technical issues involved in building software to interface TCP/IP and X.25. The tariff structure for public networks is discussed only to the extent that it influences our design. Other issues such as access control, and protocol selection are beyond the scope of this report.

Towards an efficient, machine-independent language for microprogramming

A machine independent low level language YALLL is presented. This language produces microcode for two very different machines: Hewlett Packard HP 300 and Digital Equipment Corporation VAX 11/780. The efficiency of this language is tested by comparing two examples on both machines to microassembly coded versions. To our best knowledge, this is the first time programs have been compiled and executed on two different microarchitectures. These examples also let us compare the efficiency of the microarchitectures and macroarchitectures of these machines and re-examine the benefits of microprogramming versus macroprogramming. We conclude this paper with comments upon transportability of high level microprogramming languages.