A simulation program examining the use of ratios as raw variables in analyses of variance

An interactive, BASIC-PLUS, simulation program is described for performing a large number of multivariate analyses in accord with, or in violation of, known underlying models. Using a PDP 11/40 computer, random numbers are generated and converted into bivariate normal observations X and Y. These data are then analyzed according to three models. The three analyses are: (1) a standard analysis of variance ignoring the concomitant variable; (2) an analysis of covariance; (3) an analysis of variance on the ratio Y/X. The program can be used to examine the effect of performing multivariate analyses on data transformed into ratios. The utility of the program is the simplicity with which one can alter the underlying models and/or the mathematical relationships between X and Y. Output provides comparisons between models by accumulating rejections and other statistics on critical F-values for each model.     

Analysing Proportions that Arise from Factorial Experiments when the Underlying Proportions are Heterogeneous Within Groups

The analysis of proportions that arise from experiments that involve several factors is considered when there is heterogeneity of the underlying proportions within each combination of the levels of the factors. An analysis is described which can be implemented using a standard statistical program. This also provides an approximate analysis when the data are assumed to be Beta-binomially distributed.     

THE TECHNIQUE OF LABELLED MITOSES: ANALYSIS BY AUTOMATIC CURVE-FITTING

An improved method is described for the analysis of data obtained by the technique of labelled mitoses. It is a development of the method described by Barrett (1966) in which theoretical curves are computed on the basis of a model which assumes that the phases G¹, S and G² are described by independent log-normal distributions; the analysis consists in finding a form of this model which gives a labelled mitoses curve which is the best fit to the available data. This fitting procedure has now been made automatic. No comprehensive indication of the goodness of fit can be given, although in the analysis of over fifty sets of data the method appears to have worked well.
A supplementary computer program is described which, on the basis of three separate assumed modes of cell loss, calculates the form of the age distributions and theoretical continuous labelling curves. This allows growth fraction to be calculated in a way which takes account of the distribution of phase durations and the non-rectangular age distributions of expanding cell populations. It also gives an opportunity to study the implications of continuous labelling data as regards the mode of cell loss.
A comparison is made between the present method of labelled mitoses curve analysis and the empirical rules which have often been used.     

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.     

Programs for evaluating and characterising bacterial taxonomic data

Three programs are described for evaluating and characterisingdata collected during numerical taxonomic studies of bacteria.The program VARIANCE compares replicate cultures and evaluatesthe reproducibility of each character. Also it identifies thosecharacters that should be excluded from subsequent taxonomicanalysis because of their poor reproducibility. GPROPS summarisesthe properties of clusters of strains that have been definedfrom a cluster analysis, it can produce a probabilistic identificationmatrix and compares each strain within a cluster with the HypotheticalMean Organism (HMO) of that cluster. OVCLUST is an implementationof the program described by Sneath (1979) which calculates overlapstatistics between major clusters. These programs are designedto complement the CLUSTAN package (Wishart, 1982) which is oftenused for cluster analysis of bacterial taxonomic data. The programswere written in FORTRAN 77 and implemented on an IBM PC usingMS–DOS. Received on November 13, 1986; accepted on January 8, 1987     

Plant Growth Analysis: a Program for the Fitting of Lengthy Series of Data by the Method of B-splines*

A method is presented for fitting curves to lengthy and/or complicatedseries of data on plant growth. A computer program which derivesthe usual plant growth analytical quantities, and their errors,from these fitted curves is also described and offered for circulation.The fitted curves are splined cubic polynomial exponentials.Examples of their application are given, employing both realand artificial data. In any set of data the number of splines,and the position of the knots joining them, may be determinedeither by objective statistical tests or by the experimenterhimself, who thus retains a considerable degree of control overthe process but can call on the assistance of the program ifrequired. The value of this method is considered in relationto other curve-fitting approaches to plant growth analysis andit is concluded that, provided sufficient primary data are available,the method is free from many of the problems which beset earlierwork in this field, and also provides new possibilities of itsown. growth curves, approximating functions, empirical models, regression analysis, growth analysis     

A minicomputer program for automatic saccade detection and linear analysis of eye movement systems using sine wave stimulus

A FORTRAN IV program is described, which may be run interactively or in batch and which allows a user to obtain the frequency response amplitude ratio and phase resulting from the linear analysis of an eye movement system using sine wave stimuli. The response (eye position) signal may contain components contributed by the saccadic eye movements. The program can digitize analog signals and store data on a magnetic tape. With the aid of digital filters, the program can detect saccades without requiring any input parameters from the user. The program interpolates the saccade interval using a method of least square curve fitting with a sine wave. The interpolation is relatively noise immune and works well regardless of the stimulus frequencies and the width of a saccade interval. Moreover, the program can handle long duration of signals such as 90 min of data which covers about 5 cycles of a 0.001 Hz sine wave signal. Sample runs for the cases of 0.001 and 0.1 Hz are given. The resident driver and the overlayable segments of the program have been implemented on a DEC (Digital Equipment Corp.) LAB-11 minicomputer (PDP 11/20).     

A simple computer program for calculating, modifying and drawing circular restriction maps.

An HPL program is described which constructs and draws circular restriction maps given a set of cleavage sites, together with deletion of insertion data if required. This program is of great use in the routine interpretation of restriction patterns for the analysis of recombinant DNA molecules.     

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.     

Interactive map projection algorithm for illustrating protein surfaces

An interactive map projection algorithm and cluster analysis program are described which can be used in the display and analysis of protein surfaces. The application of the techniques to the analysis of protein charge distributions is described, and a brief discussion presented on various other applications.     

A computer program using a nested analysis of variance in morphometric sampling

The quality of the sample set is absolutely essential in a morphometric analysis. In this paper a computer program is described which uses a nested analysis of variance in defining the sample. The program denotes those levels of the sampling protocol at which additional sampling should be performed to reduce the variance within the sample set. Furthermore, the program is written for use on a microcomputer which allows it to be used routinely in monitoring a sample set.     

Three-dimensional computer-assisted design of craniofacial surgical procedures: optimization and interaction with cephalometric and CT-based models

A computer program is described which aids the clinician in planning craniofacial surgical procedures. It operates on a three-dimensional landmark data base derived by combining posteroanterior and lateral cephalograms from the patient and from the Bolton normative standards. A three-dimensional surgical simulation program based on computerized tomographic (CT) data is also described which can be linked to the cephalometrically based program. After the clinician has selected the number and type of osteotomies to be performed on the patient, an automated optimization program computes the postoperative positions of these fragments which best fit the appropriate normal cephalometric form. The clinician then interactively modifies the design to account for such variables as bone-graft resorption, relapse tendency, occlusal disparities, and the condition of the overlying soft-tissue matrix. Osteotomy movement specifications are easily transferred between the CT-based and the cephalometrically based surgical simulation programs. This allows the automated positioning step to be performed on the cephalometrically based model while the interactive step is performed using the superior image provided by the CT-based model.     

Multi-user system for analysis of data from flow cytometry.

A new program is described for the analysis of DNA histograms from flow cytometry. The fundamental model representing the cell population is similar to one described previously. It assumes the population is grouped into compartments, each consisting of cells having approximately the same DNA content. After staining the cells with an appropriate fluorochrome, the fluorescence distribution of cells within each compartment is assumed to be Gaussian. In the present algorithm, the parameters of the model can either be computed directly by the program from the data, or can be specified as input by the user. When synchronous cell populations lacking distinct G1 and G2/M phases are analyzed, the parameter values must first be obtained using an appropriate control. Percentages of cells in the various compartments are computed using a gradient search method described by Bevington.     

Automatic determination of glucose, ethanol, amino nitrogen, and ammonia. Cell counting and data processing

Automated methods for analysis of growth kinetics and culture media of yeast populations are presented. Assays of sugar, alcohol, amino nitrogen, and ammonia are described. Microbial growth was automatically sized with a continuously working cell counter. The data thus obtained are processed by a computer program which evaluates metabolic parameters and carbon balances at any time of growth. The system can be applied to batch and continuous cultures and allows extension to microbial populations other than yeasts.     

Computer-aided construction of nucleic acid restriction maps using defined vectors

A new algorithm is described that will rapidly produce restrictionmaps of cloned DNA fragments. Information concerning the vectoris stored as a data file and used in constructing probable maps.As the program is based upon a permutation analysis it has twoprimary uses. First, preliminary restriction maps can be createdfrom fragment length data as a starting point for further analysis.Second, existing maps can be confirmed as being highly probable,and other probable maps examined to ensure certain combinationshave not been overlooked. Although primarily designed for linearvectors, the program can be used to calculate circular maps. Received on June 5, 1985; accepted on September 27, 1985     

A set of programs for analysis of kinetic and equilibrium data

A program package that can be used for analysis of a wide rangeof kinetic and equilibrium data is described. The four programswere written in Turbo Pascal and run on PC, XT, AT and compatibles.The first of the programs allows the user to fit data with 16predefined and one user-defined function, using two differentnon-linear least-squares procedures. Two additional programsare used to test both the evaluation of model functions andthe least-squares fits. One of these programs uses two simpleprocedures to generate a Gaussian-distributed random variablethat is used to simulate the experimental error of measurements.The last program simulates kinetics described by differentialequations that cannot be solved analytically, using numericalintegration. This program helps the user to judge the validityof steady-state assumptions or treatment of kinetic measurementsas relaxations. Received on September 19, 1989; accepted on March 16, 1990     

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.     

TNT version 1.5, including a full implementation of phylogenetic morphometrics

Version 1.5 of the computer program TNT completely integrates landmark data into phylogenetic analysis. Landmark data consist of coordinates (in two or three dimensions) for the terminal taxa; TNT reconstructs shapes for the internal nodes such that the difference between ancestor and descendant shapes for all tree branches sums up to a minimum; this sum is used as tree score. Landmark data can be analysed alone or in combination with standard characters; all the applicable commands and options in TNT can be used transparently after reading a landmark data set. The program continues implementing all the types of analyses in former versions, including discrete and continuous characters (which can now be read at any scale, and automatically rescaled by TNT). Using algorithms described in this paper, searches for landmark data can be made tens to hundreds of times faster than it was possible before (from T to 3T times faster, where T is the number of taxa), thus making phylogenetic analysis of landmarks feasible even on standard personal computers.     

A computer program for the morphometric analysis of cell profiles.

A computer program which yields values for the volumes, surface areas, and volume/surface area ratios of cell profiles is described for use on a desktop calculator (minicomputer). This program uses standard morphometric procedures, and incorporates data obtained from electron micrographs at two levels of sampling. The main program yields values for the 'average cell volume' at the tissue level of sampling. Two options at the cellular level of sampling are also included which yield values for the volumes, surface areas and volume/surface area ratios for the organelles. The first option allows an analysis of 'whole cells' containing equatorial profiles through the nucleus, while the second option permits a 'fractional' approach using segments of the cells. Finally, some of the advantages of the two options are discussed.