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.     

NMR View: A computer program for the visualization and analysis of NMR data

Summary NMR View is a computer program designed for the visualization and analysis of NMR data. It allows the user to interact with a practically unlimited number of 2D, 3D and 4D NMR data files. Any number of spectral windows can be displayed on the screen in any size and location. Automatic peak picking and facilitated peak analysis features are included to aid in the assignment of complex NMR spectra. NMR View provides structure analysis features and data transfer to and from structure generation programs, allowing for a tight coupling between spectral analysis and structure generation. Visual correlation between structures and spectra can be done with the Molecular Data Viewer, a molecular graphics program with bidirectional communication to NMR View. The user interface can be customized and a command language is provided to allow for the automation of various tasks.Inquiries concerning the availability of NMR View and the Molecular Data Viewer should be sent via email to johnsonb@merck.com or to Bruce A. Johnson, Merck Research Laboratories, RY80Y-103, P.O. Box 2000, Rahway, NJ 07065, U.S.A.     

CyDAS: a cytogenetic data analysis system

For statistical analyses in cancer cytogenetics, the genomic changes encoded by the karyotype must be translated into numerical codes. We developed a program, which extracts chromosomal gains and losses as well as breakpoints from the karyotype. The changes are compiled in tables according to the chromosome bands involved and/or depicted in projection to the respective chromosome ideogram. The data are ready to be integrated into further statistical analyses. The program may be run as desktop or Internet application.     

EXCAVATOR: a computer program for efficiently mining gene expression data

Massive amounts of gene expression data are generated using microarrays for functional studies of genes and gene expression data clustering is a useful tool for studying the functional relationship among genes in a biological process. We have developed a computer package EXCAVATOR for clustering gene expression profiles based on our new framework for representing gene expression data as a minimum spanning tree. EXCAVATOR uses a number of rigorous and efficient clustering algorithms. This program has a number of unique features, including capabilities for: (i) data- constrained clustering; (ii) identification of genes with similar expression profiles to pre-specified seed genes; (iii) cluster identification from a noisy background; (iv) computational comparison between different clustering results of the same data set. EXCAVATOR can be run from a Unix/Linux/DOS shell, from a Java interface or from a Web server. The clustering results can be visualized as colored figures and 2-dimensional plots. Moreover, EXCAVATOR provides a wide range of options for data formats, distance measures, objective functions, clustering algorithms, methods to choose number of clusters, etc. The effectiveness of EXCAVATOR has been demonstrated on several experimental data sets. Its performance compares favorably against the popular K-means clustering method in terms of clustering quality and computing time.     

gimlet: a computer program for analysing genetic individual identification data

Growing interest in microsatellite genotyping, combined with noninvasive genetic sampling has led to the increased production of data. New tools to analyse these data are required. gimlet is a user‐friendly software package designed to perform several simple tasks: (i) construction of consensus genotypes from repeated genotyping; (ii) estimation of genotyping error rates; (iii) identification of identical genotypes; (iv) comparison of new genotypes to a set of reference genotypes; (v) determination of the kinship; and (vi) estimation of several population parameters such as allele frequencies, heterozygosity, probability of identity, and population size.     

A computer program for processing data from amino acid analysis and for the calculation of molecular weights from those data.

A computer program is described for the calculation of the complete amino acid composition of a protein from the analytical data. The program also derives a molecular weight on the basis of the amino acid composition. The use of the program for the determination of the molecular weights of the liver carboxylesterases of chicken, horse, ox, and sheep is described.     

Radioimmunoassay data handling and calculations with a graphics-statistics computer program.

This paper discusses the application of the data handling-graphics-statistics program Stata (Computing Resources Center, Santa Monica, CA) to radioimmunoassay. We have found that this program is more powerful and easier to use than a spreadsheet for analyzing various kinds of laboratory data generated from chromatography, radiolabeling experiments, enzyme-linked immunosorbent assays, and radioimmunoassays, to name several examples. Data from a radioimmunoassay procedure, originally analyzed using a spreadsheet, Lotus 1-2-3, have been processed with Stata. Simple programs (batch files) have been devised for computations and graphics. The original data and a comparison of results are presented.     

Global Kinetic Explorer: A new computer program for dynamic simulation and fitting of kinetic data

We describe a new dynamic kinetic simulation program that allows multiple data sets to be fit simultaneously to a single model based on numerical integration of the rate equations describing the reaction mechanism. Unlike other programs that allow fitting based on numerical integration of rate equations, in the dynamic simulation rate constants, output factors, and starting concentrations of reactants can be scrolled while observing the change in the shape of the simulated reaction curves. Fast dynamic simulation facilitates the exploration of initial parameters that serve as the starting point for nonlinear regression in fitting data and facilitates exploration of the relationships between individual constants and observable reactions. The exploration of parameter space by dynamic simulation provides a powerful tool for learning kinetics and for evaluating the extent to which parameters are constrained by the data. This feature is critical to avoid overly complex models that are not supported by the data.     

A computer program for the analysis of crossover designs.

We describe a program, CROSS, which we have written to obtain potency estimates and other parameters for bioassay data from assays of crossover design. The program permits testing of all assays for statistical validity and calculates the complete analysis of variance for assays of balanced design. The form of data input and the complete documentation of assay results make this program particularly useful for anyone carrying out crossover assays on a routine basis. The analysis of variance presented is also useful for more general biological or medical situations.     

A computer program for the analysis of dental models.

This paper presents the details and logic of a Fortran computer program which carries out routine clinical analysis of dental models resulting from impressions of the teeth and related structures, which are subsequently cast in plaster of Paris. The program is primarily intended for use by the orthodontist who is engaged in research or clinical practice, and is useful in studies related to changes in the dentition as a result of orthodontic treatment.     

CGH-Explorer: a program for analysis of array-CGH data

SUMMARY: CGH-Explorer is a program for visualization and statistical analysis of microarray-based comparative genomic hybridization (array-CGH) data. The program has preprocessing facilities, tools for graphical exploration of individual arrays or groups of arrays, and tools for statistical identification of regions of amplification and deletion.     

Design and analysis of accelerated degradation tests for the stability of biological standards II. A flexible computer program for data analysis

The accelerated degradation test is commonly used to predict the stability of a biological standard during long-term storage at low temperature. A flexible computer program is described which has been written to analyse degradation test results by the method of maximum likelihood. In addition to predicting the degradation rate at low temperature, the program furnishes estimates of statistical precision and it carried out a test of goodness of fit of the data to the assumed Arrhenius equation model.     

A computer program for Wiener filtering of evoked potential data.

We have developed a computer program for Wiener filtering of evoked potential data. The basic algorithm involves computation of the difference berween the power spectrum of the sweep sum and the sum of power spectra of individual sweeps. Power spectra are computed by means of the discrete Fourier transform. The program is now being run on a LSI-11 computer in a neurophysiology research laboratory to analyze somatic evoked potential data from monkeys.     

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.     

Quantitative infrared spectroscopy of lipids in solution: III. Automated data collection and computer aided calculations of lipid analysis.

In the third part of this series, a data acquisition system is described which digitizes the analog signal from a commercial infrared spectrometer and records the data on paper tape. The paper tape is then processed off-line with a microcomputer and an infrared spectrum is printed. The correction routine for absorbance due to the O-H stretching band is discussed as well as the integration limits for calculation of integrated intensities of the C-H stretching band. The computer program is briefly described and statistical data on correlation between integrated intensity and lipid concentration given.     

DSLINK: a computer program for gene-centromere linkage analysis in families with a trisomic offspring.

Trisomic individuals provide information for gene-centromere mapping, since two of the four chromatids in a meiotic tetrad can be recovered. When centromeric markers are available, linkage analysis between the centromere and any marker locus can be performed in nuclear families having one or more trisomic offspring. Since conventional linkage programs consider only disomic individuals, we have written a FORTRAN computer program, DSLINK, that performs gene-centromere linkage analysis on the basis of information on trisomic and disomic offspring. This program makes it possible to study the relationship between recombination and chromosome segregation.