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PubMed2003

A generic computer program for checking photon beam dose calculations.

A computer program for checking photon external beam dose calculations is described. It provides a check of the treatment planning calculation by the use of machine data that are independent of that used in the initial calculation. Data required to specify any radiation beam are easily and rapidly set up and the program works for all the major manufacturers' machines. The user interface uses an interactive screen for machine data input and also for dose checking, where dose calculation is performed in real time as data are entered. The dose resulting from the planned field parameters is calculated and compared with the prescribed dose with a warning provided if the agreement is outside a set range (+/-5%). Its purpose is to act as a final quality assurance check to ensure that no significant errors occur in the monitor unit calculation.

Algorithms↗
PubMed1984

Computer programs as theories in biology.

Complex theories in biology may be developed, refined, and tested by the use of computer programmed simulations. The computer is recognized as a powerful tool for theory development; it is, in fact, the only means of thoroughly testing and examining a large and intricate theory. A program as a text is a statement of a theory and when run on the computer it is model of that theory. As the program's behavior is then the major argument for the credibility of a large and complex theory, the program itself is the only irrefutable statement of the theory. Bur programs written in the currently available programming languages tend to be incomprehensible. We argue that the program should be the definitive statement of the theory. In addition, the program plus a series of abstractions is a vehicle for effective communication of complex theories in biology. Several techniques of computer science are borrowed, for the purpose of developing a methodology for abstraction and a language for representing abstractions. The arguments are fully illustrated with a recently published biological theory.

Communication↗
PubMed1990

A computer program to aid in the preparation of reagent solutions.

A computer program for calculating required amounts of reagents for making up chemical solutions is presented. The program also maintains a custom list of available reagents. Use of the interactive mode guides the novice in entering the required information. The program is written in the BASIC programming language for IBM compatible microcomputers. It is available without cost from the author.

Indicators and Reagents↗
PubMed1991

CASPER: a computer program used for structural analysis of carbohydrates.

The computer program CASPER and its algorithms are described. The program is aimed at facilitating the determination of structures of oligosaccharides and regular polysaccharides, requiring as input either the one-dimensional 1H or 13C NMR spectrum or the 2D C,H-correlation NMR spectrum together with information on components and linkages. The databases, the method of simulating spectra, options of the program, and techniques for faster calculations are described as well as an example of a structural determination.

Algorithms↗
PubMed1996

NCOMP--a windows-based computer program for noncompartmental analysis of pharmacokinetic data.

The computer program NCOMP performs noncompartmental analysis of pharmacokinetic data obtained from iv bolus, continuous infusion, and oral modes of administration. Integration of area-under-the-curve and area-under-the-first-moment-curve is done by either Lagrange polynomials or the hybrid method of Purves, which uses parabola-through-the-origin and log trapezoidal algorithms. Written for Microsoft Windows, NCOMP is designed to be used in conjunction with a spreadsheet program for graphical display and handling of data. NCOMP interactively aids the user in determining how best to extrapolate the areas to time infinity and in estimating the time zero concentration for iv bolus data.

Pharmacokinetics↗
PubMed1994

A computer program for construction of circular restriction maps.

The computer program COSMAP for construction of circular restriction maps has been developed. The generator is based on a permutational algorithm that puts forward all the possible maps that can be made with two enzymes, and the consistency checker compares the calculated and experimental double-digest fragment sizes within a predefined error bound. The output consists of the complete set of solutions ordered by a score number that is based on the matching degree between experimental and calculated double restriction fragment sizes. The program allows the application of heuristic rules which reduces the number of permutations to be checked and the number of sound solutions.

DNA, Circular↗
PubMed1987

Repetitive palindromic sequences in Escherichia coli. Detection and characterization with a new computer program.

We have made use of a new computer program which rapidly searches for DNA patterns irrespective of the exact sequence, in order to search systematically for repetitive palindromic structures on the Escherichia coli chromosome. By using a relatively restrictive criterion, we detected three families of palindromic structures. One is present in ribosomal RNA operons. Since seven identical ribosomal RNA operons are found on the E. coli genome, this constitutes a validation of the method. Another family is constituted by the extragenic palindromic units (PUs or REP) already described (Gilson et al., 1984). We propose a slightly different consensus for this highly repetitive and dispersed family. The last is a subclass of symmetrical transcription termination sites which we have identified. They are present in four attenuator sites and at least one terminator for convergent operons. We suggest that these symmetrical terminator sites may play a general role in the termination of transcription for convergent operons. We discuss briefly how this type of approach could be used to analyse the structure of genomes.

Algorithms↗
PubMed1992

A BASIC computer program for analyzing endpoint assays.

We present a computer program that is based on Karber's approximation of endpoint titers, written in GW-BASIC and provides an easy means for analyzing the results of dilution endpoint assays. The program provides estimates of standard error that are not possible from other statistical procedures for this type of data.

Indicator Dilution Techniques↗
PubMed1991

[PEDINFUS computer program for total parenteral nutrition of children].

The computer program PEDINFUS permits the fast and simple definition of the individual nutrient amounts and infusion volumes in accordance with age, weight and possible metabolic complications for children up to 18 years. All components needed for total parenteral nutrition are taken into account. The conditions necessary for the optimal satisfaction of the individual needs of each patient by means of combined solutions have thus been created.

Adolescent↗
PubMed1982

Interactive computer program for self-distributed medical questionnaire in a population health screening.

The questionnaire is an important element of a medical screening investigation, just as important as the biometrical screening tests. There are several difficulties in realizing interactive computer programs for such tasks. In the present report, we describe the design, operation and results of an interactive computer program for self-distributed medical questionnaire in which the screening subjects are informed and instructed on the terminal routines, and answer, check, confirm and record the questions direct in the computer terminals by means of simple keyboard functions. This program was possible to construct as an integrated component of the interactive computer system monitoring our multiphasic health screening in a standard minicomputer environment.

Computers↗
PubMed1997

Computer program for the equations describing the steady state of enzyme reactions.

MOTIVATION: The derivation of steady-state equations is frequently carried out in enzyme kinetic studies. Done manually, this becomes tedious and prone to human error. The computer programs now available which are able to accept reaction mechanisms of some complexity are focused only on the strict steady-state approach. RESULTS: Here we present a computer program called REFERASS, with a short computation time and a user-friendly format for the input and output files, able to derive the strict steady-state equations and/or those corresponding to the usual assumption that one ore more of the reversible steps are in rapid equilibrium. This program handles enzyme-catalysed reactions with mechanisms involving up to 255 enzyme species connected by up to 255 reaction steps, subject to limits imposed by the memory and disk space available.

Algorithms↗
PubMed1996

A networked computer program for managing a national external quality assurance scheme in cytopathology.

We described a computer program to manage a national external quality assurance (EQA) scheme in cytopathology which uses the international computer network, the Internet, to collect data directly from participants, thereby reducing errors of transcription and administrative costs. Feedback to screeners and pathologists is provided as high quality images of the diagnostic areas on the slide which are only available once all users at a centre have entered their answers. This allows comparison with the original material while it is still available at this site. Users are encouraged to register differences of opinion by labelling areas on images of the slides on the computer. The program performs the statistical analysis of the data for each centre and each slide.

Computer Communication Networks↗
PubMed1991

A computer program that simulates cloning of DNA.

Easy Cloner is a computer program that manipulates DNA sequences as in cloning experiments and produces maps of the resulting plasmids. The program runs in the graphics mode of an IBM PC or compatible computer and is operated by using a mouse to point to the required actions. The program is available in the public domain.

Cloning, Molecular↗
PubMedDate not supplied

Computer programs that teach the interpretation of image-based laboratory tests.

OBJECTIVE: To review the effort of the University of Washington (UW) Department of Laboratory Medicine to develop and use personal computer programs to teach the interpretation of image-based clinical laboratory tests to medical technologists and other health care workers. DATA SOURCES: Professional journals and books; Software owned by and licensed by the University of Washington. STUDY SELECTION: Not applicable. DATA EXTRACTION: Not applicable. DATA SYNTHESIS: We have been developing interactive personal computer (PC) programs for teaching image-based laboratory tests to medical technologists and other health care workers. The programs, called "Laboratory Tutors," are useful for teaching microscope-based tests and tests based on electrophoresis. Our programs include ANA-Tutor, which teaches the immunofluorescence assay for anti-nuclear antibodies; Gram Stain-Tutor, which teaches the direct Gram stain; Electrophoresis-Tutor, which teaches the interpretation of agarose gel protein electrophoretic patterns; Urinalysis-Tutor, which teaches the microscopic examination of urine sediment; in addition to other programs. The tutorials are all based on high-quality digital images that were acquired and processed using digital imaging systems. They require minimal computer literacy and have a number of advantages over standard approaches to teaching image-based laboratory tests. The computer tutorials are used in UW's medical technology and medical school curriculum, where they are used as supplements to traditional instruction. CONCLUSION: Laboratory tutors are computer programs that use high resolution digital images to teach the interpretation of image-based laboratory tests. We plan to continue to develop these programs, study their educational effectiveness, and update them periodically.

Clinical Laboratory Information Systems↗
PubMed1999

Using 'off the shelf', computer programs to mine additional insights from published data: diurnal variation in potency of ACTH stimulation of cortisol secretion revealed.

We describe the use of available computer programs to mine additional insights from published data. Graphs from four studies of ACTH and cortisol plasma levels collected throughout the 24 h day in humans were scanned into digital form and the data points extracted. To investigate the magnitude of ACTH stimulation of cortisol secretion across the 24 h, Monte Carlo methods were used to fit the parameters of a computer model of the ACTH-adrenal axis to the extracted data. ACTH was found to have a greater effect on cortisol secretion during the peaks of the cycle than at the nadir. This finding could not be explained by previously published dose response curves of ACTH effect. This implies that other modulators influence the effect of ACTH on the adrenal. This study also demonstrates how available computer programs can be used to examine models of physiologic regulation using data already available in the literature.

Adrenocorticotropic Hormone↗
PubMed1998

Developing a dose-volume histogram computation program for brachytherapy.

A dose-volume histogram (DVH) computation program was developed for brachytherapy treatment planning in an attempt to benefit from the DVH's ability to present graphically information on 3D dose distributions. The program is incorporated into a planning system that utilizes a pair of orthogonal radiographs to localize the radiation sources. DVHs are calculated for the volume of tissue enclosed by an isodose surface (e.g. half the value of the reference isodose). The calculation algorithm is based on a non-uniform random sampling that gives a denser point distribution at the centre of the implants. Our program was tested and proved to be fast enough for clinical use and sufficiently accurate (i.e. computation time of 20 s and less than 2% relative error for one point source, for 100,000 calculation points). The accuracy improves when a larger calculation point number is used, but the computation time also increases proportionally. The DVH is presented in the form of a simple graph or table, or as Anderson's 'natural' DVH graph. The cumulative DVH tables can be used to extract a series of indexes characterizing the homogeneity and the dose levels of the distribution in the treatment volume and the surrounding tissues. If a reference plan is available, the DVH results can be assessed relative to the reference plan's DVH.

Brachytherapy↗
PubMed2000

The reliability and internal consistency of an Internet-capable computer program for measuring utilities.

OBJECTIVE: The purpose of this study was to assess the reliability and internal consistency of measurements of utilities performed with a computer program (iMPACT2) designed for Internet surveys and Internet patient decision-support systems. METHODS: We implemented the Internet Multimedia Preference Assessor Construction Tool, version 2 (iMPACT2) program using the combination of a web server, HTML files, and a web-accessible database. The program randomized subjects, screened their responses for missing data and failures of internal consistency, assisted patients with resolving certain inconsistencies, and, upon a subject's completion of the protocol, provided a report of results to the research assistant administering the program. To validate the iMPACT2 program, we recruited 60 healthy community volunteers and elicited preferences in a research-lab setting using a visual analog scale (VAS) and the standard gamble (SG) for subject's current health and three hypothetical states. For purposes of comparison, we also administered a Short Form-12 (SF-12) health-assessment questionnaire. Subjects used the computer software on two occasions separated by 2-4 weeks of time. RESULTS: Visual analog scale and standard gamble ratings for subjects' current health were reliable (intraclass correlation coefficient (ICC) of 0.82 and 0.84 (two outliers excluded -0.60 without exclusions), respectively) were comparable with the reliability of the Physical and Mental Component scales of the SF-12 (ICCs of 0.84 and 0.75, respectively). Subjects could easily discriminate between hypothetical states (D scores 0.74 for SG and 0.90 for VAS), and 94% had a completely internally consistent ordering of preference ratings for states. CONCLUSIONS: iMPACT2 produces measurements of standard gamble utilities that are reliable and have a high degree of internal consistency. Procedures for assessment of utilities developed for desktop computer programs can be translated to software designed for the Internet, facilitating the use of utilities and endpoints in clinical trials and development of web-based decision-support applications for patients. However, further testing, including direct comparisons with traditional interviewer administered utility elicitation protocols, is needed.

Analysis of Variance↗