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PubMed1989

GENPRO: automatic generation of Prolog clause files for knowledge-based systems in the biomedical sciences.

With the increasing interest in using knowledge-based approaches for protein structure prediction and modelling, there is a requirement for general techniques to convert molecular biological data into structures that can be interpreted by artificial intelligence programming languages (e.g. Prolog). We describe here an interactive program that generates files in Prolog clausal form from the most commonly distributed protein structural data collections. The program is flexible and enables a variety of clause structures to be defined by the user through a general schema definition system. Our method can be extended to include other types of molecular biological database or those containing non-structural information, thus providing a uniform framework for handling the increasing volume of data available to knowledge-based systems in biomedicine.

Database Management Systems↗
PubMedDate not supplied

Community-based computerized donor record systems.

Computer programs for management of donor information have been developed for the Champaign County Blood Bank, a division of the Regional Health Resource Center, Urbana, Illinois. The system provides the blood bank with reports from the donor files, incorporating the donor's last donation dates, ABO groups and Rh factors, memberships in assurance programs, and rare donor information to generate lists to meet either daily or emergency inventory needs. The system was designed to decrease time requirements for donor recruitment, improve donor base sampling, aid in support of special recruitment programs, and provide statistical profiles of the community donor base. Experiences in the development and use of the system indicate requirements for effective development of such systems include careful design, strict monitoring of performance, use of a versatile programming language, and incorporation of program modifications via staff-programmer interaction throughout implementation.

Blood Donors↗
PubMedDate not supplied

A Pascal program for the semi-automation of laboratory cell counting procedures.

A program that allows a microcomputer to function as a semi-automatic multi-keyed laboratory cell counter is presented. Using a microcomputer as a cell counter allows laboratory personnel to work faster, more efficiently and more accurately than the traditional multi-keyed laboratory counter. Automatic data storage, automatic calculation of results and error trapping are also available. The program is presented in the Pascal programming language.

Cell Count↗
PubMedDate not supplied

How to draw irregular radiation beams in 3-D treatment plans.

We describe a general method for computing the outline which an irregular field originating from some arbitrary angle makes on a plane which may be oriented obliquely within the patient. We describe the mathematical theory of the method, which is based on coordinate transformations expressed as matrix multiplications. Then we describe the implementation of the method in the Pascal programming language, emphasizing language-independent optimizations which ensure fast interactive response. Finally, we describe a systematic program testing procedure that is derived from the mathematical theory, which improves our confidence that the method is coded correctly.

Computer Graphics↗
PubMed1992

Object Command Language: a formalism to build molecular models and to analyze structural parameters in macromolecules, with applications to nucleic acids.

We have written a programming language OCL (Object Command Language) to solve, in a general way, two recurring problems that arise during the construction of molecular models and during the geometrical characterization of macromolecules: how to move precisely and reproducibly any part of a molecular model in any user-defined local reference axes; and how to calculate standard or user-defined structural parameters that characterize the complex geometries of any macromolecule. OCL endows the user with three main capabilities: the definition of subsets of the macromolecule, called objects in OCL, with a formalism from elementary set theory or lexical analysis; the definition of sequences of elementary geometrical operations, called procedures in OCL, enabling one to build arbitrary three-dimensional (3D) orthonormal reference frames, to be associated with previously defined objects; and the transmission of these definitions to programs that allow one to display, to modify and to analyze interactively the molecular structure, or to programs that perform energy minimizations or molecular dynamics. Several applications to nucleic acids are presented.

Computer Graphics↗
PubMed1975

Provision of a language index for severely and profoundly retarded individuals.

The development of habilitative language programming for severely and profoundly retarded individuals requires detailed knowledge of their current levels of competence. Specific information is needed regarding the particular language skills characteristically displayed, the frequency with which such skills are used, and the proportion of severely retarded individuals who evidence linguistic abilities at the various levels. An index of language proficiency has been developed utilizing a standardized system of direct observation of subjects in their usual, familiar environment. Data on a group of ambulant, institutionalized, severely and profoundly retarded individuals were described. Some type of vocal or gestural communication was observed for about 75 percent of the subjects; almost 60 percent evidenced some vocal or verbal expression. One in four subjects demonstrated meaningful, articulate speech. Associations between language and factors such as sex, chronological and mental age, diagnosis, and biosocial history were investigated. Implications of these findings were discussed in relation to programs for language development.

Adaptation, Psychological↗
PubMed1991

A fast 80X86 assembly language module to low-pass filter digital data.

This short assembly language procedure, which can be called from a high level language program, will low-pass filter an array of digital data. This is a well known algorithm coded in assembly language for speed: it filters 512 data points in 5 ms in a 16 MHz 386 microcomputer. The procedure can handle up to 32 kb of binary data, 12-16 bits wide, from an on-line experiment or from an already stored file. The user chooses the cutoff frequency selecting a factor and how many times the data are passed through the filter. The filter has an excellent time-domain response which makes it ideal for physiological pulse recording. The listings of the source assembly routine and of a sample Pascal program that calls it are provided in the text.

Algorithms↗
PubMedDate not supplied

Authoring options for computer assisted nursing instruction.

Nurse educators who want to control the content of computer assisted instructional courseware may want to write their own programs. Traditional programming languages, authoring systems, and authoring languages are the three principal approaches to coding courseware, and each approach has advantages and disadvantages. The use of an authoring language or an authoring system may be the easiest courseware development method for the nurse educator who is unfamiliar with programming techniques. Whatever approach is chosen, it is important that the approach support the instructional strategy of the lesson.

Computer-Assisted Instruction↗
PubMed1986

Programming for the DNA analysis of FCM data on an IBM microcomputer.

The analysis of data generated on a flow cytometer (FCM) is often performed on a computer obtained especially for dedicated use with the flow cytometer. This computer component can be expensive and also presents the FCM user with the added burden of mastering specialized programming language or of accepting the secret analytical processes of protected proprietary program routines. We believe that the evolution of more accurate and efficient FCM analyses that have the power to consider complex signal distributions can be assisted by the availability of analysis programs written in languages common to many users. DNA analysis routines written for a relatively inexpensive microcomputer (IBM PC/XT) in Basic and Pascal are described here. The routines can automatically process multiple FCM data files and can provide high-resolution graphic hardcopy. A foreground/background utilization is also described that allows the computer to be available for other uses in the laboratory.

Animals↗
PubMed1991

Parallelizing genetic linkage analysis: a case study for applying parallel computation in molecular biology.

Parallel computers offer a solution to improve the lengthy computation time of many conventional, sequential programs used in molecular biology. On a parallel computer, different pieces of the computation are performed simultaneously on different processors. LINKMAP is a sequential program widely used by scientists to perform genetic linkage analysis. We have converted LINKMAP to run on a parallel computer, using the machine-independent parallel programming language, Linda. Using the parallelization of LINKMAP as a case study, the paper outlines an approach to converting existing highly iterative programs to a parallel form. The paper describes the steps involved in converting the sequential program to a parallel program. It presents performance benchmarks comparing the sequential version of LINKMAP with the parallel version running on different parallel machines. The paper also discusses alternative approaches to the problem of "load balancing," making sure the computational load is shared as evenly as possible among the available processors.

Chromosome Mapping↗
PubMed1991

CANEST: a microcomputer program for estimating cancer in a cohort.

Certain diseases and symptoms carry an overrepresentation of cancer. To be able to measure the strength of such an association it is necessary to be able to predict cancer development in the group being observed. A computer program for computers running under the MS DOS operating system has been developed for this purpose. The program is written in the CLIPPER programming language. The estimates are based on incidence and prevalence data from the Swedish Cancer Registry for the years 1958 to 1986. The program also computes confidence intervals based on the Poisson distribution. The results can be printed out or exported to other programs for further analysis.

Cohort Studies↗
PubMed1989

A microcomputer data base system for maternal serum alpha fetoprotein screening programmed in BASIC.

A computer program was developed for the IBM PC computer to be used for maternal serum alpha fetoprotein screening (MSAFP). This program, written in BASIC, 1) maintains a data base for patients tested, 2) allows input and storage of MSAFP results, 3) calculates the gestational age dependent result in multiple of the median (MOM), 4) makes an individualized interpretation of the result based on maternal age, weight and diabetes, 5) makes an appropriate recommendation for subsequent action based on the result, and 6) prints a report containing the above information. In addition, the program will print a daily log of patients tested, provides a follow-up sheet to assist in tracking abnormal results to term, converts the data files into files which can be easily intergrated into more powerful data base programs, and generates a monthly statement for billing purposes. The program can be easily modified by someone with minimal training in the BASIC programming language.

Female↗
PubMed1992

On the assessment of bioequivalence in a two-period cross-over design.

The results obtained with Meineke and De Mey's algorithm for posterior probability distributions in the nonparametric evaluation of two-period cross-over bioequivalence studies are critically discussed. Suggestions for improvement of their program NEWPARM are given. It is shown that this program in its present form cannot handle the results from bioequivalence studies in which more than 15 subjects participated. For larger study sizes, conversion to a more powerful programming language capable of handling large three-dimensional arrays, is mandatory. An alternative algorithm, allowing large sample sizes to be analysed nonparametrically without program conversion, is offered. A general bioequivalence program written by the author, into which this alternative algorithm is implemented, has been in use by a number of pharmaceutical companies and drug regulatory agencies since February 1990; its most recent update is Version 3.7 (BIOEQV37.EXE) of October 1990.

Algorithms↗