Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Computer Programs And Programming”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 181 records · Page 10Linked to original sources
PubMed1979

Computer programs for the assembly of DNA sequences.

A collection of user-interactive computer programs is described which aid in the assembly of DNA sequences. This is achieved by searching for the positions of overlapping common nucleotide sequences within the blocks of sequence obtained as primary data. Such overlapping segments are then melded into one continuous string of nucleotides. Strategies for determining the accuracy of the sequence being analyzed and reducing the error rate resulting from the manual manipulation of sequence data are discussed. Sequences mapping from 97.3 to 100% of the Ad2 virus genome were used to demonstrate the performance of these programs.

Adenoviridae↗
PubMed1976

A computer program for an open two compartment system distinguishing three models.

A digital computer program is described for the estimation of parameters in an open two compartment system distinguishing 3 models. The mathematical function to be fitted to a given set of experimental data is given initial estimates for the parameters of the function. The program uses an iterative procedure to adjust the parameters until the sum of squares of residuals has converged to a minimum. Assuming that a given substance is introduced into compartment 1, the function can be fitted to the set of experiment data of that compartment. A set of experimental data from compartment 2 can also be included in the minimizing function. Two optional weighting functions are presented. From the constants of the two-exponential functions the physiological parameters of the three models are determined. Experimental observations of compartment 1 only allow for calculation of physiological parameters of two of the models.

Computers↗
PubMed1991

The use of a personal computer program for monitoring wound infections and other complications in orthopedics.

A personal computer program to monitor wound infections and other complications after orthopedic operations was developed, adopting international criteria and definitions. The program offers fixed data entry screens, and a free text editor, and produces user-specified variations of seven screen pages comprising most of the epidemiological data needed for surveillance and complication control. Furthermore a number of special lists can be generated for use in the daily work. For all reports and lists it is possible to generate subpopulations with up to twelve criteria. The program was tested in four danish orthopedic departments and serves well as a simple local tool for the operating staff, offering fast information on complication rates. Results consisting 2,583 operations are presented. The overall rates of complications were 1.8% superficial wound infections, 0.6% deep wound infections, 2.6% other infections and 3.8 other complications. The system is lowcost and an effective method of providing a widespread uniform surveillance of surgical wound infections and other complications in the orthopedic wards.

Adolescent↗
PubMed1992

A personal computer program for large-scale comparisons of related nucleotide sequences.

A personal computer program (COMPSEQ) has been developed which can present an informative listing of pre-aligned exonic nucleotide sequences and of their translations to amino acid sequences as well run triplet-oriented analyses on these sequences in a given reading frame. The sequence listing focuses on the differences between related sequences by suppressing the concordances between them.

Algorithms↗
PubMed1984

A computer program package for storing and retrieving DNA/RNA and protein sequence data.

A computer program package has been made available which contains five compound programs written in FORTRAN 10 (for DECsystem-10). Program DATBAS is for storing and improving DNA sequence data, especially those obtained by the sequencing method using M13 phages. Programs NUCDAT and PROTEN are for analyzing DNA/RNA and protein sequence data, respectively. They contain various options to help users in analyzing DNA/RNA and protein sequence data. With program NUCDAT, it is also possible to get access to the EMBO Nucleotide Data Library. This can be achieved by running program COPY to create two data files from the library. Program LITRAT enables users to prepare a scientific literature file convenient for writing scientific articles, and program STRAIN for storing information concerning bacterial and/or plasmid strains.

Amino Acid Sequence↗
PubMed1988

[Determination of antibiotype by a computer program. Epidemiological significance and antibiogram-identification correlates].

By means of a computer program disk diffusion diameter were analysed and an antibiotic susceptibility code (antibiotype) was determined for enterobacteriaceae. This code was a 6 figure-number. Each figure summarised susceptibility (susceptible or resistant) to 3 antibiotics. Thus a 18 serial antibiotics was necessary to calculate the 6 figure-code. At least following antibiotics were chosen for their characteristic behavior: amoxycillin, ticarcillin, amoxycillin + clavulanic acid, cephalothin, ticarcillin + clavulanic acid, cefotaxime, gentamycin, tobramycin, amikacin, nalidixic acid, pefloxacin, ciprofloxacin, fosfomycin and colistin. This code allowed three kind of utilisation: epidemiology by comparing biochemical and susceptibility patterns of same isolated species; laboratory control: a data base with main antibiotic susceptibility patterns for each species allowed a rapid compatibility control of biochemical identification with antibiogram. An inconsistent result lead to a checking of biochemical and susceptibility tests or to record a new code in a file to a further enrichment of the data base. Impression of a message depending of the code for a therapeutic purpose.

Drug Resistance, Microbial↗
PubMed1984

Interactive computer programs for the graphic analysis of nucleotide sequence data.

A group of interactive computer programs have been developed which aid in the collection and graphical analysis of nucleotide and protein sequence data. The programs perform the following basic functions: a) enter, edit, list, and rearrange sequence data; b) permit automatic entry of nucleotide sequence data directly from an autoradiograph into the computer; c) search for restriction sites or other specified patterns and plot a linear or circular restriction map, or print their locations; d) plot base composition; e) analyze homology between sequences by plotting a two-dimensional graphic matrix; and f) aid in plotting predicted secondary structures of RNA molecules.

Amino Acid Sequence↗
PubMed1992

OLIGSCAN: a computer program to assist in the design of PCR primers homologous to multiple DNA sequences.

OLIGSCAN (oligonucleotide scanner) is a computer program for IBM-PC-compatible computers that allows the user to scan up to 200 DNA sequences for homology to oligonucleotide sequences of interest. Once a core sequence of longer than the user-defined minimum length is found, the remainder of the oligonucleotide is compared to the corresponding positions of the larger sequence to identify matches or mismatches flanking the core region. This algorithm results in identification of the longest possible homologous regions first. The program was originally designed to assist in the identification of potential annealing sites for polymerase chain reaction (PCR) primers in the genomic DNA of related strains of viruses. However, it may also be used for more general pattern-identification purposes, including scanning for various sequence motifs of functional importance. We present the analysis of homology to an oligonucleotide primer in 16 complete genomic sequences of the human and simian immunodeficiency viruses.

Algorithms↗
PubMed1991

A compiled computer program for assisting the diagnosis of gastrointestinal helminths of humans and animals.

A compiled computer program for assisting the diagnosis of gastrointestinal helminths in fecal examinations of humans and animals is described. The characteristics of this program which distinguish it from previous similar programs are that it does not require specific software, it does not need a lot of computer memory, and it covers both humans and animals, making it easier to use.

Animals↗
PubMed1979

A computer program for analysis of clotting factor assays and other parallel-line bioassays.

A computer program for the analysis of coagulation factor assays is presented. It can be run on small computers utilizing FORTRAN. It allows considerable flexibility in assay design, accommodates any sample dilution scheme, different numbers of standard and test doses, and missing data points. The report lists the input data for each assay, the analysis of variance for the regression lines, and the potency ratio, as well as statistics that allow estimates of the precision of the potency ratio. It is suggested that interpretation of clotting factor assay results would be facilitated if reports regularly included such information about the reliability of the potency ratio measurements.

Analysis of Variance↗
PubMed1977

A computer program for the analysis of controllability, observability and structural identifiability of biological compartmental systems.

A computer program to check structural identifiability of biological compartmental systems, that is the priori possibility of estamating all unknown system parameters through a multi input-multi output tracer experiment is presented. The procedure, as based only on the adopted compartmental structure and the chosen input-output experiment, is independent of the numerical values of the parameters: therefore the program can be usefully employed before parameter estimation algorithms, to assure that all the unknown parameters evidenced in the model can be estimated from the experimental data. After a short review on compartmental models, controllability observability and structural identifiability are defined and techniques to check them are provided. The digital computer implementation of the whole procedure is discussed in detail. Some typical program runs regarding the application to biological systems are given.

Computers↗
PubMed1991

A computer program for many-beam image simulation of amplitude-contrast images.

A computer program for the simulation of amplitude-contrast electron micrographs is described. The program is based on the n-beam dynamical theory of diffraction contrast as described by Howie and Whelan (see Howie, A., and Whelan, M.J. (1961) Proc. R. Soc. Lond. [Biol]). The displacement fields associated with crystal lattice defects are calculated using linear anisotropic elasticity. The program can be used to simulate images of crystals containing line or planar defects or combinations of these defects. The line defects can be oriented freely within the foil, and are not restricted to being mutually parallel, but must be straight. Different techniques available for solving the diffraction problem, with or without the column approximation, are discussed.

Crystallization↗
PubMed1983

Computer program for evaluating the thermal environment.

The calculations required to evaluate the thermal environment can be tedious and time consuming. To reduce this effort to a minimum, a computer program is presented that requires only five basic measurements to calculate and print out a complete evaluation of the thermal environment at a specific location. These are the dry bulb, natural wet bulb, psychrometric wet bulb and black globe temperatures, and the air velocity. Any reference to charts, tables and nomographs is unnecessary, since all other quantities are contained within, or computed by, the program.

Computers↗
PubMed1989

[A computer program that draws pedigree charts for inbred strains of animals].

We produced a computer program that draws pedigree charts for inbred strains of animals such as mice or rats. This program is composed of four subprograms, which are (1) inputting the data, (2) drawing pedigree charts, (3) listing the data which have been input, and (4) backup of the system and the data. Pedigree charts and lists of data can be displayed on a TV screen and printed out on the papers. Using this program, we drew the pedigree charts of the inbred strains of rats which we are maintaining by brother-sister inbreeding in our institute and found that there were three sublines in one of the strains, WKAH/Hkm, because of unsuitable maintenance. This program is very convenient to draw the pedigree charts and useful for checking the maintenance of inbred strains or the strains of animal models of human diseases.

Animals↗
PubMed1991

A Macintosh computer program for designing DNA sequences that code for specific peptides and proteins.

A computer program (PINCERS) is described for use in the design of synthetic genes and mixed-probe DNA sequences. A protein sequence is reverse translated with generation of synonymous codons at each position producing a degenerate sequence. In order to locate potential restriction enzyme sites, the degenerate sequence is searched with a library of restriction enzymes for sites that utilize any combination of synonymous codons. These sites are indicated in a map so that they may be incorporated into the synthetic gene sequence. The program allows the user to select the appropriate codon usage table for the organism of interest and then to set a threshold usage frequency below which codons are not generated. PINCERS may also be used to assist in planning the synthesis of mixed-probe DNA sequences for cross-hybridization experiments. It can identify regions of specified length with the protein sequence that have the least overall degeneracy, thereby minimizing the number of probes to be synthesized and, therefore, maximizing the concentration of a given probe sequence.

DNA↗
PubMed1986

Accuracy of computerized electrocardiographic identification of left ventricular hypertrophy as determined by echocardiographic measurements of left ventricular mass: evaluation of a widely used computer program.

The Hewlett-Packard 1000 electrocardiographic management system employs a user-interactive computer with revisable software. The diagnostic accuracy of this system in predicting left ventricular hypertrophy has been evaluated by comparing computer-predicted with anatomic left ventricular hypertrophy. The latter was defined as a left ventricular mass greater than 247 g as determined by M-mode echocardiography within 1 week of the computerized electrocardiogram. In this study, the Hewlett-Packard system was evaluated in 134 consecutive patients having anatomic left ventricular hypertrophy and 157 similarly studied patients with a normal left ventricular mass. By means of various combinations of voltage criteria, ST-T wave changes, abnormal QRS duration or ventricular activation time, left atrial enlargement and left axis deviation, the computer correctly identified 43 of 134 patients with left ventricular hypertrophy (sensitivity 32%); left ventricular hypertrophy was suggested or identified in an additional 18 patients with a normal left ventricular mass (specificity 89%). Graded probability statements (that is, the "strength" of the left ventricular hypertrophy diagnosis) increased with ventricular mass not only in patients with anatomic left ventricular hypertrophy but also in the patients with a "false positive" computerized electrocardiogram. Overall diagnostic accuracy was improved only in men by adjusting the definition of left ventricular hypertrophy for sex (at least 300 g for men and 220 g for women). Diagnostic accuracy was significantly better in patients 65 years of age and younger than in older patients (p = 0.007). It is concluded that the overall performance of this computer program (version ECLSB6) requires modification to improve its accuracy in identifying left ventricular hypertrophy.

Age Factors↗
PubMedDate not supplied

A computer program for on-line measurement, storage, analysis and retrieval of urodynamic data.

A computer program is presented which allows for direct connection of a minicomputer to a urodynamic set-up. The program stores measured pressure and flow data in a random access disc file with minimal intervention of the urodynamicist, and enables the direct application of a number of methods of analysis to the data. The program is modular, and other analysis methods are easily added. Results of analyses are stored in the same disc file, and both results and measured data can be quickly and easily retrieved. The program is written in FORTRAN; hardware-dependent functions (analog input, graphics display, and random access disc storage) are implemented in subroutines (partly assembler) which can easily be replaced.

Computers↗