Colour molecular graphics on a microcomputer

Software has been developed on a microcomputer to provide a low-level but useful graphics system. The programs have been written to aid in the fitting of electron density maps, provide various representations of protein models and allow the comparison of protein structures. The work demonstrates that an 8-bit microcomputer has sufficient power to perform quite complex calculations and provide an interactive tool for probing protein structure; and even very low resolution graphics (300 × 150 pixels) is sufficient, with colour, to give a good representation of a model containing as many as 830 atoms.     

Plotting genetic maps on a microcomputer

Maps of genetic linkage and restriction enzyme cleavage sites can be quickly prepared on an IBM PC microcomputer with the commercially available program Lotus 1-2-3. Data can be entered on the keyboard or imported from other programs. The maps can be displayed on the screen or with a printer or plotter. These procedures should be useful in the research laboratory, in preparing figures for publication and in teaching.     

Linear algebraic transformations of the bidomain equations: Implications for numerical methods

A mathematical framework is presented for the treatment of the bidomain equations used to model propagation in cardiac tissue. This framework is independent of the model used to represent membrane ionic currents and incorporates boundary conditions and other constraints. By representing the bidomain equations in the operator notation , various algebraic transformations can be expressed as , where P and Q are linear operators. The authors show how previous work fits into this framework and discuss the implications of various transformation for numerical methods of solution. Although such transformations allow many choices of independent variable, these results emphasize the fundamental importance of the transmembrane potential.     

Optimal alignments of biological sequences on a microcomputer

An algorithm and a program have been developed which enableoptimal alignments of biological sequences on an 8–bitmicrocomputer. The compiled program can process sequences upto 1000 residues on a Commodore 64. Since this program was writtenoriginally in the BASIC language, it may readily be adaptedto other microcomputers with small changes. Received on March 11, 1985; accepted on March 14, 1985     

Nonlinear regression on a microcomputer: which program?

Eleven published programs for performing nonlinear regressionusing a microcomputer have been reviewed. They have been assessedaccording to many criteria, especially: application, programlanguage, algorithm used, method for calculating partial differentials,facility for weighting, desirable input and output features,robustness during execution, memory requirements, accessability,ease of implementation and evaluation and testing. No one programcontains all the desirable characteristics discussed, but guidanceis given as to which might be the most suitable for a particularpurpose or for a given microcomputer system.     

Fast and sensitive multiple sequence alignments on a microcomputer

A strategy is described for the rapid alignment of many longnucleic acid or protein sequences on a microcomputer. The programdescribed can handle up to 100 sequences of 1200 residues each.The approach is based on progressively aligning sequences accordingto the branching order in an initial phylogenetic tree. Theresults obtained using the package appear to be as sensitiveas those from any other available method. Received on October 7, 1988; accepted on December 6, 1988     

Allergy screening using a microcomputer.

Data are presented to show that a microcomputer can be programmed to: (1) analyse a standard allergy questionnaire, (2) reliably predict the ranked order probabilities with which IgE antibody tests will produce positive results, (3) store the IgE test results, and (4) print a comprehensive report that summarises and integrates the clinical and laboratory data. Consequently, the practitioner who refers a blood sample and a questionnaire completed by the patient to a centre where both can be analysed will obtain enough practical information to decide whether to treat or refer that patient to a specialist. The microcomputer is therefore potentially of great value in any preliminary allergy investigation.     

Timing pulse and sampling programs implemented on a laboratory microcomputer

This paper presents two programs implemented on a microcomputer for analog-to-digital (A-to-D) conversion of neurophysiological signals. The first program, TIMET, sets flexible pulse trains for the timing of the A-to-D conversions, executed by the second program, ADC8. TIMET contains options for a continuous or a triggered pulse train with variable onset delay. ADC8 allows sampling up to 30 kHz for one channel and 9 kHz for the maximum of 7 channels, with about 8 microseconds lag between channels. The digitized data are displayed with interactive gain control from keyboard input, and selected sweeps can be stored on disk files.     

CLUSTAL: a package for performing multiple sequence alignment on a microcomputer

An approach for performing multiple alignments of large numbers of amino acid or nucleotide sequences is described. The method is based on first deriving a phylogenetic tree from a matrix of all pairwise sequence similarity scores, obtained using a fast pairwise alignment algorithm. Then the multiple alignment is achieved from a series of pairwise alignments of clusters of sequences, following the order of branching in the tree. The method is sufficiently fast and economical with memory to be easily implemented on a microcomputer, and yet the results obtained are comparable to those from packages requiring mainframe computer facilities.     

Solving the heart mechanics equations with Newton and quasi Newton methods--a comparison

The non-linear elasticity equations of heart mechanics are solved while emulating the effects of a propagating activation wave. The dynamics of a 1 cm(3) slab of active cardiac tissue was simulated as the electrical wave traversed the muscular heart wall transmurally. The regular Newton (Newton-Raphson) method was compared to two modified Newton approaches, and also to a third approach that delayed update only of some selected Jacobian elements. In addition, the impact of changing the time step (0.01, 0.1 and 1 ms) and the relative non-linear convergence tolerance (10(-4), 10(-3) and 10(-2)) was investigated. Updating the Jacobian only when slow convergence occurred was by far the most efficient approach, giving time savings of 83-96%. For each of the four methods, CPU times were reduced by 48-90% when the time step was increased by a factor 10. Increasing the convergence tolerance by the same factor gave time savings of 3-71%. Different combinations of activation wave speed, stress rate and bulk modulus revealed that the fastest method became relatively even faster as stress rate and bulk modulus was decreased, while the activation speed had negligible influence in this respect.     

A Pascal program for weighted least squares regression on a microcomputer

Weighted least-squares regression has been programmed in Pascal for a microcomputer. A double precision Pascal compiler and the Motorola 6809 assembler produce a fast machine-code program occupying 22,000 bytes of memory when appended to the Pascal run-time module. Large data sets fit in the remaining memory. A regression with 72 observations and 24 parameters runs in 7 min, excluding optional print out of large matrices. The maximum dimensions of the design matrix, X, can be altered by modifying two Pascal constants. Minor changes to the Pascal source program will make it compatible with other Pascal compilers. The program optionally orthogonalises the X matrix to detect linearly-dependent columns in X, and/or generate orthogonal parameter estimates. After orthogonalizing X and fitting the model, the parameter estimates for the original X can be retrieved by the program. Regressions on a repeatedly reduced model are performed through elimination of columns in X until the minimum adequate model is obtained.     

Solving inverse problems for biological models using the collage method for differential equations

In the first part of this paper we show how inverse problems for differential equations can be solved using the so-called collage method. Inverse problems can be solved by minimizing the collage distance in an appropriate metric space. We then provide several numerical examples in mathematical biology. We consider applications of this approach to the following areas: population dynamics, mRNA and protein concentration, bacteria and amoeba cells interaction, tumor growth.     

Description of electrophysiological data using a microcomputer*

ABSTRACT. Customization of an inexpensive microcomputer and peripherals to produce hard copy outputs of electrophysiological data is described. The system uses any of the Apple II series computers and a common A/D+D/A card together with a digital plotter. For the 1–2 s recordings normally used in studies of insect chemoreception, this computer configuration can replace more laborious permanent hard copy production techniques. Additional analytical programs can easily use the three data files produced by the current sytem.