Computer-assisted analysis of adenosine triphosphate data.

A computer program has been written to assist in the analysis of adenosine 5'-triphosphate data. The program is designed to calculate a dilution curve and to correct sample and adenosine 5'-triphosphate standard data for background and dilution effects. In addition, basic statistical parameters and estimates of biomass carbon are also calculated for each group of samples and printed in a convenient format. The versatility of the program to analyze data from both qauatic and terrestrial samples is noted as well as its potential use with various types of instrumentation and extraction techniques.     

An improved algorithm for finding diagnostic taxonomic descriptions

A computer program is described which finds sets of diagnostic characters for the recognition of species. Unlike previous algorithms, it finds all the possible sets requested and will also run with reasonable demands on computer time and storage. The program will search for sets with a specified size range and with a given minimum number of diagnostic characters to distinguish a taxon from all the others.     

A fortran IV computer program for automatic calculation of amino acid composition

A computer program is described which enables amino acid compositions to be calculated automatically and expressed in a variety of units. Calculations have been performed on protein hydrolyzates and cell extracts. The system is relatively simple and economical and could be applied to other column chromatographic analyses.     

A computer program for determining the size of DNA restriction fragments

A computer program has been developed for determining the sizes of DNA restriction fragments from their electrophoretic mobilities. A parabola is fitted to the mobilities of a set of standard fragments of known sizes and the sizes of the unknown fragments are then calculated from the fitted curve. This procedure is shown to yield estimated sizes which are accurate to within a few percentage, as judged by experiments with fragments obtained by digestion of pBR322 with the restriction endonuclease HaeIII. The program, which is written in BASIC, is simple to use and is very much faster than the graphical method that it replaces.     

A flexible new computer program for handling DNA sequence data.

A compact new computer program for handling nucleic acid sequence data is presented. It consists of a number of different subsets, which may be used according to a given code system. The program is designed for the determination of restriction enzyme and other recognition sites in correlation with translation patterns, and allows tabulation of codon frequencies and protein molecular weights within specified gene boundaries. The program is especially designed for detection of overlapping genes. The language, is FORTRAN and thus the program may be used on small computers; it may also be used without any prior computer experience. Copies are available on request.     

Application of microcomputers to the interpretation of high-resolution nuclear magnetic resonance spectra of asparagine-linked oligosaccharides: evaluation of high-mannose structures

A microcomputer program for determining primary oligosaccharide structures by high-resolution nuclear magnetic resonance is reported. The program uses the data base obtained from spectra of model compounds reported in the literature. A number of high-mannose-type asparagine-linked glycopeptide spectra containing tabulated chemical shifts measured at room temperature were tested to determine the ability of the computer to correctly assign carbohydrate units into a complete structure. High-mannose structures ranging from five to nine oligomannosyl units were completely and unambiguously analyzed to give complete structural assignments. The computer program will also resolve glycopeptide mixtures. The method provides investigators with a useful tool for accurately evaluating nuclear magnetic resonance spectra and should greatly facilitate the complicated and time-consuming evaluation of microheterogeneity in samples commonly isolated from biological systems.     

Image processing software for enhanced visualization of faint or noisy autoradiographic images

A computer program for digital image processing is described which can be implemented using scanning densitometer hardware pre-existing in most biology departments plus computer video hardware which may either pre-exist in the biology department or would represent a moderate upgrade over an already planned computer purchase. The primary purpose of this computer program is to provide contrast enhancement of faint or low contrast autoradiograph images and to implement background subtraction and digital smoothing methods which permit visualization of blurry electrophoresis bands against noisy backgrounds. However, the program also has modest editing capabilities that allow its use in the routine preparation of images for publication. Finally, the program has facilities for deblurring, edge enhancement and multiple image averaging, which give it usefulness in other forms of photographic analysis.     

Quantitative binding studies of a monoclonal antibody to immobilized protein-A.

Binding constants and column capacities are important factors for evaluating an affinity chromatography system. Scatchard plots based on classical equilibrium binding have been used to demonstrate how association constants and column capacities can be computed from simple binding experiments and a commercial computer program. The analysis has been demonstrated on a monoclonal antibody type IgG-1 Kappa against Serratia marcescens nuclease and a commercial protein-A column, Prosep-A. Additional analyses were performed with the same antibody and other protein-A affinity systems and the different binding constants and column capacities obtained confirmed the value of the analysis for evaluating an affinity system.     

Validation of a computer software program for statistical analysis of accelerated stability studies on biological standards.

Long-term stability is an essential requirement for biological measurement standards and it has been evaluated by applying the Arrhenius model to the data obtained from accelerated thermostability studies. A computer program DEGTEST suited to a mainframe computer has been used for evaluating the stability of biological standards for more than a decade. This paper describes the validation of a computer program executable in a personal computer Microsoft Windows XP environment for the analysis of accelerated thermostability study data.     

Generating samples under a Wright-Fisher neutral model of genetic variation

A Monte Carlo computer program is available to generate samples drawn from a population evolving according to a Wright-Fisher neutral model. The program assumes an infinite-sites model of mutation, and allows recombination, gene conversion, symmetric migration among subpopulations, and a variety of demographic histories. The samples produced can be used to investigate the sampling properties of any sample statistic under these neutral models.     

Computer aided stress analysis of long bones utilizing computed tomography

A computer aided analysis method has been developed which utilizes computed tomography (CT) and a finite element (FE) computer program to determine the stress-displacement pattern in a long bone section. The CT data file provides the geometry, the apparent density and the elastic properties for the three-dimensional FE model. A developed pre-processor generates the FE model of a human diaphyseal tibia section which is then analyzed by the SAP IV finite element program. The results obtained are sorted and displayed by a developed post-processor and compared with stresses and deformations from the literature. The model generation method was verified by applying it to a model of simple geometry and boundary conditions, then comparing the results with the analytical solution of the same problem. The convergence behavior of nodal displacements was tested as a function of mesh refinement. This method provides an automatic, versatile, non-invasive and accurate tool of long bone modeling for finite element stress analysis.     

Analysis of data from the analytical ultracentrifuge by nonlinear least-squares techniques.

Least-squares analysis of experimental data from the analytical ultracentrifuge is discussed in detail, with particular attention to the use of interference optics in studying nonideal self-associating macromolecular systems. Several samples are given that describe the application of the technique, the expected precision of the results, and some of its limitations. A FORTRAN IV computer program is available from the authors.     

DIODA: delineation and feature extraction of microscopical objects.

A computer program is described for delineation and measurement of microscopical objects, such as cells and chromosomes, which may have been scanned using absorbance, fluorescence or reflectance microscopy. The quality of the object delineation is optimized through the controur ratio, which is simply computed from the object contour. Geometrical features, like the perimeter and area are computed. A new definition is introduced for the background region, especially suited for the analysis of closely packed objects. This definition is based upon a comparison between total staining material content values resulting from a variety of methods and circumstances. The program is principally intended for use in the on-line real-time environment of a small laboratory computer, but may be used off-line as well. It has facilities for displaying the results and the process by which they are produced. A program module is described for displaying scan data on a bilevel display using an adaptation of the sigma-delta method.     

Plant Taxonomy Today

A computer program for genetic models which has some useful and labour saving features is described. The program allows students with only a rudimentary knowledge of programming to cope easily with complex genetic models. Some applications of the program are discussed.     

A nonlinear regression program for small computers

A BASIC computer program for performing weighted nonlinear regression is described and a listing of the program is given. The program, which is small and simple to use, has been designed to be run by users with little knowledge of mathematics or computers. Robust methods of analysis are described which may be applied to data in which experimental errors are not normally distributed, and the program incorporates one such method. It is shown that the program is useful for the analysis of data conforming to the Michaelis-Menten equation, a single exponential, and to binding equations, and other applications are discussed.     

The Education and Training of Biology Teachers

A technique for the numerical identification of bacteria using normalized likelihoods calculated from a probabilistic database is described, and the principles of the technique are explained. A simple computer program, which can be used to perform the calculations and identifications on a microcomputer in undergraduate classes, is presented. The program is annotated so that the steps in the calculation can be linked to the equivalent steps in the program to assist in teaching the principles of programming. Specimen results from the program, and examples of how they should be interpreted and explained, are given. It is expected that the program will be of use to teachers of undergraduates to teach the principles of numerical identification and an important use of computers in biology.     

A DNA sequence handling program

A computer program that aids in recording, editing, and analysis of the base sequences of DNA and RNA is presented. A tape containing copies of the program and the user manual for it are available at cost.     

Measurement of H2S in Crude Oil and Crude Oil Headspace Using Multidimensional Gas Chromatography,Deans Switching and Sulfur-selective Detection

A method for the analysis of dissolved hydrogen sulfide in crude oil samples is demonstrated using gas chromatography. In order to effectively eliminate interferences, a two dimensional column configuration is used, with a Deans switch employed to transfer hydrogen sulfide from the first to the second column (heart-cutting). Liquid crude samples are first separated on a dimethylpolysiloxane column, and light gases are heart-cut and further separated on a bonded porous layer open tubular (PLOT) column that is able to separate hydrogen sulfide from other light sulfur species. Hydrogen sulfide is then detected with a sulfur chemiluminescence detector, adding an additional layer of selectivity. Following separation and detection of hydrogen sulfide, the system is backflushed to remove the high-boiling hydrocarbons present in the crude samples and to preserve chromatographic integrity. Dissolved hydrogen sulfide has been quantified in liquid samples from 1.1 to 500 ppm, demonstrating wide applicability to a range of samples. The method has also been successfully applied for the analysis of gas samples from crude oil headspace and process gas bags, with measurement from 0.7 to 9,700 ppm hydrogen sulfide.