Standard Data File Research Articles

The CCP4 suite: programs for protein crystallography.

The CCP4 (Collaborative Computational Project, number 4) program suite is a collection of programs and associated data and subroutine libraries which can be used for macromolecular structure determination by X-ray crystallography. The suite is designed to be flexible, allowing users a number of methods of achieving their aims and so there may be more than one program to cover each function. The programs are written mainly in standard Fortran77. They are from a wide variety of sources but are connected by standard data file formats. The package has been ported to all the major platforms under both Unix and VMS. The suite is distributed by anonymous ftp from Daresbury Laboratory and is widely used throughout the world.

Note: Fire test data available for your purpose

AbstractThe EUREFIC (European Reaction to Fire Classification) has produced many fire test data made available through a Data Converting System (DCS). DCS is a simple PC‐based program which transfers data logger files into a standard fire test data format, given by FDMS (Fire Data Management System). DCS is also capable of transferring standard data files into data formats of common spreadsheets. The EUREFIC programme has made two models for assessing large‐scale performance of test materials. These models are integrated into a PC program called CT (Cone Tools).

A proposed standard data file format for hyperthermia treatments

One of the most critical areas of research essential to improve the clinical use of hyperthermia in cancer therapy is the determination and evaluation of temperature during therapy. In order to improve the dissemination of newly developed thermometry measurement and analysis programs and facilitate the transport of hyperthermia data files between computers for both intra- and inter- institutional use, we propose a standard file format, the Hyperthermia Data Standard (HDS), which can be used for all hyperthermia data. This data file consists of segments of which nine have been defined. The first is an initial /VERSION segment which identifies the file standard. This is followed by eight major segments: 2) a /IDENT segment which contains file and patient identification information; 3) a /TEXT segment containing additional miscellaneous documentation; 4) a /TUMOR segment which provides tumor and treatment site information; 5) a /HSETUP segment which contains treatment setup information; 6) a /FORMAT segment which defines the data segment structure; 7) a /DATA segment containing the actual thermometry data; 8) a /FOLLOWUP segment for documenting patient response; and 9) an /ANALYSIS segment containing summary information. All segments begin and end with a specified delimiter and, except for the first two (/VERSION and /IDENT), may be repeated more than once. For ease in debugging and verifying adherence to the standard, all information in the file is encoded in printable ASCII characters. All segments consist solely of records containing KEYWORDS and KEYWORD VALUES which identify specified information. Certain KEYWORDS are standard, i.e., having specified names and information formats as defined in this document. The /DATA segment consists of ASCII encoded chronological treatment thermometry and other data whose format and structure is identified in the /FORMAT segment. The /ANALYSIS segment provides the flexibility to store the results of any analysis program along with the actual data file for ease of data management. This thermometry data file standard is designed to provide both flexibility and extendability for all possible forms of hyperthermia treatment data. Furthermore, it is designed to provide a simple format which may be easily read by higher level languages. This document is intended for commercial manufacturers and others who are writing programs to document clinical hyperthermia treatments with the intention that they either use this format for their data storage or provide a means to convert their data into this format. Only by wide acceptance of this standard will it be of benefit to the scientific and clinical communities. Data analysis programs capable of reading this standard format are under development for the MS-DOS (Microsoft Corp.) and VAX/VMS (Digital Equipment (Corp.) operating systems.

Productivity analysis of a large multiproduct batch processing facility

Effective and efficient operation of multiproduct batch processing plants is often difficult. Such facilities are subject to uncertainties, delays, interferences and bottlenecks that shift with the product mix. Predicting the performance of such facilities is increasingly important as competitive forces both increase the number of products and shorten the lead times. This paper deals with the analysis, modeling and productivity investigation of a five-stage batch processing facility making over 100 different product types on more than 80 pieces of equipment. The dynamic simulation model explicitly deals with batch time variations, equipment cleanouts, delays due to operators, interferences due to batches competing for equipment, and periodic planned maintenance shutdowns. The model has been successfully used to help evaluate a number of changes, and it has now been turned over to plant personnel to help in facility planning, production planning and production scheduling. I do not intend to get into further details; this is not required to tell our story of how the model was developed or what it accomplished. I will note that the model was done in SIMSCRIPT II.5 ( Russell, 1983) and is now quite large. The effort to get a reasonable first stage prototype model developed and ready for review was roughly 2 man-months spread over a 4-month period. Roughly half was for data collection and operations description development and half was for model development (designing—writing—debugging the model). The final model with all its refinements and modifications has taken almost 1 man-yr of effort and the model is over 9000 lines of SIMSCRIPT code; almost half of this is for reading standard data files and for developing customized reports. It has been used to evaluate many cases. Documentation both on the modeling assumptions and logic and on how to use the model has been prepared. The model was developed on VAX computers, and the executable has been moved to the plant VAX 8300; this transfer was relatively easy. Plant engineers have indicated a keen interest in using the model. Since they were part of the development team, they feel it is valid, useful, and not someone's else's invention. As noted earlier, we were asked to develop a model that could help answer a number of detailed questions about the capacity and scheduling of a highly dynamic, large-scale batch production system. Since we needed to be able to determine the impact of rather small-scale changes in this system we developed a highly-detailed discrete simulation model of the total plant. We found out that if it had just focused on scheduling the filling operations (which some people advocated early on) we would have not captured the full magnitude of the shifting bottleneck characteristic nor would we have really addressed the full problem. This model is viewed as a good representation of the plant and is capable of addressing the questions originally asked. Results are having an impact on plant operations. Recently we have been working with the plant scheduler to: (1) have the model read several data files generated from off-plant sources; and (2) make it easier to routinely run the model to investigate a variety of questions which deal with the capability of the plant to meet specific tasks and how to schedule around difficulties. We feel this model clearly shows that simulation models can realistically represent large complex multiproduct batch plants and further shows that simulation based scheduling tools can provide a productivity gain and a resulting competitive edge.

A quantitative approach to cytoarchitectonics: software and hardware aspects of a system for the evaluation and analysis of structural inhomogeneities in nervous tissue

Cytoarchitectonic studies are based on the analysis of structural inhomogeneities in nervous tissue. Boundaries of brain regions are established where local structural properties such as numerical cell density, size, shape or orientation change. The measurement of these properties from histological sections with automatic devices is biased due to the thickness of the sections. In this study, the grey level index (GLI) is measured with a TV-based image analyzer from routine histological sections. This parameter is a biased estimate of the volume density of Nissl-positive structures. The histological section is digitized into GLI values by a computer-controlled scanning procedure. The result is stored in an image matrix which is processed by digital filtering in order to visualize the laminar pattern. GLI statistics of brain regions are evaluated from the pictorial data by delineating these regions with a cursor on a hard copy fixed to digitizer. Information from a series of sections is stored in a standardized data file and combined by specific application programs.

Software Reviews : Ci2 SYSTEM 100, Version 1.1 Reviewed by Frank M. Howell, Mississippi State University Publisher: Sawtooth Software, Inc., P.O. Box 3429, 208 Spruce North, Ketchum, ID 83340 (telephone: 208-726-7772) Year of Publication: 1985 Materials: Three diskettes (system disk, installation disk, sample questionnaire; demo disk available at no charge); 148-page manual; summary card for color-codes used in Logic program

Summary: A major-league software package implementing computer-directed and computer-assisted interviewing using the microcomputer. The Ci2 SYSTEM comes in several versions, both for research and teaching purposes, and is the most complete and lowest-priced software of its type on the market. It maintains a compatibility with other packages through the capacity to export standard ASCII data files and implements some of the most current techniques of survey research-such as randomization of item-sets, use of color visuals, and branching. The capacity for programming the logic underlying questionnaire branching is powerful, yet easy to use. Telephone user- support is very good. C~2 will be of serious interest to all those involved in (non-mail) survey research.

WOCE/TOGA Historical Oceanographic Data Subgroup

The Oceanographic Historical Data Subgroup of the World Ocean Circulation Experiment (WOCE)/Tropical Ocean and Global Atmosphere program (TOGA) Data Management Working Group was organized to assess both the quantity and quality of historical standard oceanographic data files (e.g., temperature and salinity profiles and current meter, drifter, and ship drift data) for WOCE/TOGA studies and to estimate the amount of existing data that is not to be found in National Oceanogrphic Data Center (NODC) files and formulate a strategy for adding these data to the historical files.

Score system for behaviour of radiologically diagnosed approximal carious lesions.

The evolution of systems which monitor changes in the severity of approximal carious lesions diagnosed from serial bitewing radiographs is reviewed. These systems derive a 'score' for each individual lesion based upon the extent of its progression. A new lesion behaviour score system is described which, unlike its predecessors, allows both lesion regression and data from partially overlapped but readable surfaces to contribute to scores. It employs scoring codes from a previously proposed standardized grading system which is compatible with WHO recommendations for grading clinical caries. The score system is designed to be used as a computer program capable of running on a variety of readily available microcomputers; this allows the incorporation of a flexible range of additional options which use the standard data files to calculate scores according to differing conventions. These accommodate variations in: the threshold at which restorative intervention is practiced, the treatment of reversals of caries diagnosis, the threshold of caries diagnosis and the way in which partially overlapped surfaces are scored. These options allow the system to be configured to suit the local needs of different investigations and workers, and also permit the study of the effects of these various methodologies.

PHASE: An interactive appraisal package for whole hospital design

PHASE (Package for Hospital Architecture Simulation and Evaluation) aims to provide a more informed basis for design decision-making during the early stages of hospital design. This is done by tracing the consequences of design decision through a range of design criteria. The completed package will consist of three programs. The building program is at present operational: the network and structures programs are under development. Input to the building program is structured into four data files — a standard data file, a solution file, a project file and a scheme file. Output is presented at two levels — synoptic and detailed. The full output consists of measures of department location, boilerhouse location, capital and energy costs. Applications for the package include the evaluation of alternative design strategies, upgrading of existing buildings, selection of hospital sites and investigation of phasing strategies.

Magnetic Tape Data Interface for Multiple Ge(Li) Spectrometers

A buffered electronic Data Transfer Interface has been developed for acquiring data from 1-14 Ge(Li) and/or NaI(Tl) gamma spectrometers and processing this data in an IBM 1130 Minicomputer System. Sample instrument and spectrum data are transferred between remote spectrometers and mass storage buffer and between buffer and processor as standard formatted data files. Spectrometers and the processor are serviced on a time-sharing basis in accordance with a multiple service demand queue. The first record of each magnetic tape data file consists of a serial file number and all samples and instrument data. Sample and instrument data, including sample number, sample group code, accummulate time, configuration code, energy range code, energy calibration code, instrument number and analysis code, are entered from punched sample cards, thumbwheel switches and a time of year clock. All subsequent data file records consist of spectra data. Operation of the data interface is initiated from individual spectrometers, the data interface Control and Data Unit or from the processor. Part of the data interface was installed and placed in continuous operation with one Ge(Li) spectrometer in 1970. Additional spectrometers and interface equipment are currently being added to complete the system.