Ansig for Windows: An interactive computer program for semiautomatic assignment of protein NMR spectra

Assignment of NMR spectra is a prerequisite for structure determination of proteins using NMR. The time spent on the assignment is comparatively long compared to that spent on other parts in the protein structure determination process, but it can be shortened by using either interactive or fully automated computer programs. To benefit from the advantages of both types of program we have developed a version of the interactive assignment program ANSIG to include automatized, yet user-supervised, routines. The new program includes tools for (i) semiautomatic sequential assignment, (ii) plotting of distances from PDB structure files directly in NMR spectra and (iii) statistical analysis of distance restraint violations with the possibility to directly zoom to violated NOEs in NOESY spectra.     

Index selection for genetic improvement of quantitative characters

Summary This paper reviews the basic theory and summarizes various modifications of the selection index. The limitations of selection index are discussed in four parts: (1) changes of parameters due to selection. (2) sampling errors of parameter estimation. (3) evaluation of relative economic weights and (4) internal deterrents to index selection.     

Computer system for simulating population dynamic patterns of polygenes and mobile genetic elements upon truncation selection for a quantitative trait

A computer system was developed for simulation of population dynamics of interacting polygene patterns and mobile genetic elements (MGEs) under selection for a quantitative trait. The system is stochastic (Monte Carlo) and takes into account the main sources of random change in the patterns (recombinations, transpositions, excisions), genetic drift, and determined trends of selection and other genetic processes in a finite population. Using this model, it is possible to analyze the dynamics of many population parameters that cannot be experimentally estimated: frequencies of polygenic alleles, proportions of adaptive and random fixations, average heterozygosities of polygenes and MGEs, coefficient of inbreeding, heritability, etc. In addition, the model can be used to test various hypotheses on polygene-MGE interaction.     

A teaching exercise for the identification of bacteria using an interactive computer program

An interactive computer program written in Fortran is described which provides an exercise in the identification of bacteria. The program, IDEN, provides a novel way of enhancing a student's approach to systematic bacteriology and numerical identification procedures. An unknown bacterium is assigned to a student who is provided with a list of possible species and a list of tests which may be carried out. The student's objective is the correct identification of the unknown in the most economical manner. An indication is given concerning the way in which this program can be used to enhance theoretical instruction and practical investigation.     

An computer information system for genetic engineering

The article describes the vectors data base and the software for its use (the VECTOR-PC system). At present the prototype versions of data base and VECTOR-PC exist and are in test exploitation. The original data base entry format contains 17 main fields for specific genetic engineering information. The VECTOR-PC system includes programs for data base search and support, and also the "genetic engineering designer", which allows the user to design his own hypothetic structures from the objects of data base and to receive detailed information about them. The system is destined for IBM PC or compatible computers.     

An interactive computer system for the analysis of cell lineages.

We have developed an interactive computer system for analysing cell lineage data. It can be utilized in studies of cell motility, cell division, cell differentiation, and cell aging. It has enabled us to document the heterogeneity of human foreskin fibroblasts in culture and to propose that loss of proliferative potential may mean that cells enter a state of differentiation which makes them unable to respond to mitotic stimulation. Our method, which enables us to apply immunological and cytochemical probes after recording the history of a cell lineage, should allow us to define precisely features which uniquely distinguish cycling from noncycling cells on an individual cell basis.     

A computer program for selection of oligonucleotide primers for polymerase chain reactions.

We have designed a computer program which rapidly scans nucleic acid sequences to select all possible pairs of oligonucleotides suitable for use as primers to direct efficient DNA amplification by the polymerase chain reaction. This program is based on a set of rules which define in generic terms both the sequence composition of the primers and the amplified region of DNA. These rules (1) enhance primer-to-target sequence hybridization avidity at critical 3'-end extension initiation sites, (2) facilitate attainment of full length extension during the 72 degrees C phase, by minimizing generation of incomplete or nonspecific product and (3) limit primer losses occurring from primer-self or primer-primer homologies. Three examples of primer sets chosen by the program that correctly amplified the target regions starting from RNA are shown. This program should facilitate the rapid selection of effective and specific primers from long gene sequences while providing a flexible choice of various primers to focus study on particular regions of interest.     

An interactive microcomputer program for the computation of most probable number

An interactive computer program for the rapid computation of Most Probable Numbers (MPN) with 95% confidence intervals and goodness-of-fit, is presented. The program, written in ‘MICROSOFT BASIC’ employs an iterative algorithm based on a modification of the Newton-Raphson method and accomodates any number of replicates up to ten dilutions. It is applicable to most microcomputers with little or no modification. Since the computed MPN, confidence interval,a nd goodness-of-fit tests are displayed simultaneously, MPN tables are no longer required.     

An integrated model for simulating interactive thermal processes in human–clothing system

Stolwijk's multi-node model is modified by considering the sweat accumulation on the skin surface and is applied to simulate the human physiological regulatory response. This human model is interfaced with a coupled heat and moisture model of clothing materials that takes into consideration the adsorption of water vapor in the fibers. Furthermore, a multi-layer clothing system is developed and integrated with the human model. The result agrees well with the published experimental data.     

An interactive toxicological data handling system for a PDP-12 computer.

This paper describes a program developed for the cataloguing, storage and retrieval of toxicological data. The user can, through dialogue with the program, enter and update data, and request reports with statistical analyses. The system is written in the FOCAL-12 language for a PDP-12 laboratory computer, and is suitable for a larger number of moderately-sized experiments.     

An interactive microcomputer-based system for the quantitative analysis of stratified tissue sections

This paper describes a microcomputer-based system that allows diagnostically relevant properties of stratified tissue sections to be objectively measured. The results of detailed nuclear image analyses are examined in the broader context of the position of nuclei within the tissue section and relative to histologic structures and each other. Quantitative measures are obtained for important morphometric and densitometric properties of individual nuclei and mitotic figures and especially for their distribution and orientation within the tissue section relative to the stratum germinativum and each other. Recorded karyometric and histometric parameters include measures of nuclear DNA content (based on optical density measurements), size, roundness, texture, shape, distance to the basal layer, angle with the stratum germinativum, epithelial height and proximate nuclear distance. Statistics generated describe normalized mitotic density as a function of depth in the epithelium, and a composite mitotic index is produced based upon weighting of these densities relative to their distance from the stratum germinativum. These properties and derived statistics may be examined as a function of epithelial depth and nuclear type and may be plotted as a function of other diagnostic features in addition to the observed stratum. The system is one part of microTICAS-STRATEX, an expert diagnostic system for the clinical evaluation of stratified tissue sections, now under development as an outgrowth of the microTICAS system. Results of measurements made with this system will be compared with site-specific and diagnosis-specific reference profiles and used in conjunction with clinical data derived from a data base at the University of Chicago of over 1.5 million patients to generate diagnostic and prognostic evaluations.     

SEQ-ED: an interactive computer program for editing, analysis and storage of long DNA sequences

The rapidly growing body of sequenced DNA demands efficientcomputer programs for its analysis and storage. The programdescribed in this paper, SEQ-ED, has been designed to handlea large number of DNA sequences up to 200 kilobases [kb] longstored in a sequence library. In order to minimize the requiredstorage space, the sequences are stored in a compressed formatusing three binary digits per base. In the development of thisprogram, special care has been given to make it easy to usefor molecular biologists without any previous computer experience. Received on September 10, 1984; accepted on October 30, 1984     

Novel genetic selection system for quantitative trait loci of quality protein maize

Quality protein maize combines a high-lysine trait with kernel hardness, for which a new, simpler genetic selection was designed.     

POWSIM: a computer program for assessing statistical power when testing for genetic differentiation

Knowledge of statistical power is essential for sampling design and data evaluation when testing for genetic differentiation. Yet, such information is typically missing in studies of conservation and evolutionary genetics, most likely because of complex interactions between the many factors that affect power. powsim is a 32‐bit Windows/DOS simulation‐based computer program that estimates power (and α error) for chi‐square and Fisher's exact tests when evaluating the hypothesis of genetic homogeneity. Optional combinations include the number of samples, sample sizes, number of loci and alleles, allele frequencies, and degree of differentiation (quantified as F_ST). powsim is available at http://www.zoologi.su.se/~ryman .     

A stochastic computer model for simulating population growth

A model is described for investigating the interactions of age-specific birth and death rates, age distribution and density-governing factors determining the growth form of single-species populations. It employs Monte Carlo techniques to simulate the births and deaths of individuals while density-governing factors are represented by simple algebraic equations relating survival and fecundity to population density. In all respects the model's behavior agrees with the results of more conventional mathematical approaches, including the logistic model andLotka's Law, which predicts a relationship betwen age-specific rates, rate of increase and age distribution. Situations involving exponential growth, three different age-independent density functions affecting survival, three affecting fecundity and their nine combinations were tested. The one function meeting the assumptions of the logistic model produced a logistic growth curve embodying the correct values or r_m and K. The others generated sigmoid curves to which arbitrary logistic curves could be fitted with varying success. Because of populational time lags, two of the functions affecting fecundity produced overshoots and damped oscillations during the initial approach to the steady state. The general behavior of age-dependent density functions is briefly explored and a complex example is described that produces population fluctuations by an egg cannibalism mechanism similar to that found in the flour beetle Tribolium. The model is free of inherent time lags found in other discrete time models yet these may be easily introduced. Because it manipulates separate individuals, the model may be combined readily with the Monte Carlo simulation models of population genetics to study eco-genetic phenomena.     

An experimental test of quantitative genetic theory

Theoretical and Applied Genetics - An experiment was conducted withDrosophila melanogaster to test a theory of quantitative inheritance. The covariances among half and full sibs did not increase...