Exact Calculation of Permutational Distributions for Two Dependent Samples I

A simple Fortran subroutine is given for the calculation of permutational distributions. Important special cases are Fisher's randomization test, the Wilcoxon signed ranks test and the sign test. The algorithm works in polynomial time. Thus it can be used even for micro-computers within justifiable time limits.     

Statistical comparison of power spectra: A computer program

A general computer program, of interest to neurobiologists, for comparison of uncorrelated power spectra is presented. The program, ALPHAF, is written in Fortran V language and is easily compiled and executed in any computer with a Fortran software package. The purpose of the program is to read power spectral density (PSD) values into a computer from digital tape and then perform the following functions: (1) compute and report power; (2) compute and report averages of the computed power values over selected frequency bands and (3) compute and report statistical standardised normal distributions for a frequency spectrum of interest. The standardised normal distribution statistic is derived by using equation 7.20, page 250 of Random data: Analysis and measurement procedures (Bendat and Piersol, 1971).     

Automatic Fortran to C++ conversion with FABLE

Background

In scientific computing, Fortran was the dominant implementation language throughout most of the second part of the 20th century. The many tools accumulated during this time have been difficult to integrate with modern software, which is now dominated by object-oriented languages.

Results

Driven by the requirements of a large-scale scientific software project, we have developed a Fortran to C++ source-to-source conversion tool named FABLE. This enables the continued development of new methods even while switching languages. We report the application of FABLE in three major projects and present detailed comparisons of Fortran and C++ runtime performances.

Conclusions

Our experience suggests that most Fortran 77 codes can be converted with an effort that is minor (measured in days) compared to the original development time (often measured in years). With FABLE it is possible to reuse and evolve legacy work in modern object-oriented environments, in a portable and maintainable way. FABLE is available under a nonrestrictive open source license. In FABLE the analysis of the Fortran sources is separated from the generation of the C++ sources. Therefore parts of FABLE could be reused for other target languages.     

How to perfect a chocolate soufflé and other important problems

When learning to achieve a goal through a complex series of actions, humans often group several actions into a subroutine and evaluate whether the subroutine achieved a specific subgoal. A new study reports brain responses consistent with such "hierarchical reinforcement learning."     

A FORTRAN subroutine to compute inbreeding and kinship coefficients according to the number of ancestral generations

This paper presents a FORTRAN IV subroutine to calculate inbreedingand kinship coefficients from pedigree information in a diploidpopulation without self-fertilization. The user can specifythe number of ancestral generations to be taken into account.It is thus possible to determine contributions of succeedingancestral generations to the inbreeding and kinship coefficientsunder consideration. The subroutine is based on a recursiveprocedure that generates systematically all paths connectingtwo individuals, NP and NM, whose kinship coefficient is tobe calculated (or between the father NP and the mother NM ofthe individual whose inbreeding coefficient is to be calculated).These paths obey the following conditions: (i) a given pathdoes not contain the same parent—offspring link more thanonce; (ii) the vertex of a path is an ancestor common to individualsNP and NM, with a rank lower or equal to the parameter specifiedin input. Constraints regarding the size of the corpus of genealogicaldata and the storage method are discussed, as well as the interestof this subroutine compared to the existing ones. An exampleof application is given. Received on October 20, 1988; accepted on March 21, 1989     

Computer analysis of rapid eye movements

Simulation of the saccadic eye movement mechanism and, more recently, diagnosis of neuromuscular disorders associated with saccades rely on accurate recording and analysis of saccade characteristics. Traditionally, eye movements are monitored objectively by registering a transduced voltage correlate of eye position on a pen or cathode ray oscillograph. Analysis of the record obtained is tedious and often inaccurate. The advent of small digital computers with analog-to-digital capability permits more efficient recording. However, computer programs reviewed are limited to the analysis of specific saccade parameters or partly depend on manual operations. The computer program described stores the entire saccadic event of each eye between pre-defined limits including the pre- and post-saccade intervals. Preliminary operations including artifact identification, location of onset, elimination of RC decay, DC offset and amplitude scaling prepare the data for display and subsequent analysis. The program also includes a subroutine to derive the mean and standard deviation of successive saccades.     

A CORBA-Based Distributed Component Environment for Wrapping and Coupling Legacy Scientific Codes

Within NASA's High Performance Computing and Communication (HPCC) program, the NASA Glenn Research Center (GRC) is developing a large scale, detailed simulation environment for the analysis and design of aircraft engines called the Numerical Propulsion System Simulation (NPSS). The three major aspects of modeling capabilities focused in NPSS, including integration of different engine components, coupling of multiple disciplines, and engine component zooming at appropriate level of fidelity, require relatively tight coupling of different analysis codes. Most of these codes in aerodynamics and solid mechanics are written in Fortran. Refitting these legacy Fortran codes with distributed objects can increase these codes reusability. In this paper, we describe our experiences in building a CORBA-based component development environment for programmers to easily wrap and couple legacy Fortran codes. This environment consists of a C++ wrapper library to hide the details of CORBA and an efficient remote variable scheme to facilitate data exchange between the client and the server. We also report empirical performance evaluation results and describe current applications.     

A concept of a general computer program for the iterative calculation of maximum likelihood estimators with application to qualitative dose response analyses

In this article we describe the construction of a general computer program for the iterative calculation of maximum likelihood estimators. The program is general in the sense that it allows the maximization of any given likelihood function. The user only has to write a subroutine LKLHD, in which the special likelihood function and their first and second derivatives will be calculated. This subroutine is an input parameter of the optimization program. This enables the user to employ one main program for the maximization of various likelihood functions. This advantage will be shown for the evaluation of qualitative dose response relationships (quantal assays: probit-, logit-analysis).     

Combinatorial image analysis of DNA microarray features

MOTIVATION: DNA and protein microarrays have become an established leading-edge technology for large-scale analysis of gene and protein content and activity. Contact-printed microarrays has emerged as a relatively simple and cost effective method of choice but its reliability is especially susceptible to quality of pixel information obtained from digital scans of spotted features in the microarray image. RESULTS: We address the statistical computation requirements for optimizing data acquisition and processing of digital scans. We consider the use of median filters to reduce noise levels in images and top-hat filters to correct for trends in background values. We also consider, as alternative estimators of spot intensity, discs of fixed radius, proportions of histograms and k-means clustering, either with or without a square-root intensity transformation and background subtraction. We identify, using combinatoric procedures, optimal filter and estimator parameters, in achieving consistency among the replicates of a gene on each microarray. Our results, using test data from microarrays of HCMV, indicate that a highly effective approach for improving reliability and quality of microarray data is to apply a 21 by 21 top-hat filter, then estimate spot intensity as the mean of the largest 20% of pixel values in the target region, after a square-root transformation, and corrected for background, by subtracting the mean of the smallest 70% of pixel values. AVAILABILITY: Fortran90 subroutines implementing these methods are available from the authors, or at http://www.bioss.ac.uk/~chris.     

The Routine Fitting of Kinetic Data to Models: A Mathematical Formalism for Digital Computers

A mathematical formalism is presented for use with digital computers to permit the routine fitting of data to physical and mathematical models. Given a set of data, the mathematical equations describing a model, initial conditions for an experiment, and initial estimates for the values of model parameters, the computer program automatically proceeds to obtain a least squares fit of the data by an iterative adjustment of the values of the parameters. When the experimental measures are linear combinations of functions, the linear coefficients for a least squares fit may also be calculated. The values of both the parameters of the model and the coefficients for the sum of functions may be unknown independent variables, unknown dependent variables, or known constants. In the case of dependence, only linear dependencies are provided for in routine use. The computer program includes a number of subroutines, each one of which performs a special task. This permits flexibility in choosing various types of solutions and procedures. One subroutine, for example, handles linear differential equations, another, special non-linear functions, etc. The use of analytic or numerical solutions of equations is possible.     

Sixty million connections per second

The purpose of this note is to report processing in a feedforward neural network at a peak speed of 59.9 million connections per second. The network algorithm was coded in Fortran and executed on a CRAY XMP-1, a high speed general purpose vector machine.     

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.     

Computer programs for the analysis and the management of DNA sequences.

A program package is described for the management and the analysis of DNA sequence data. The programs - with the exception of a few Fortran routines - are written in the programming language APL. They are best used interactively although batch processing is possible. The package has been in constant use for about 3 years and contains programs for most of the routine problems presently found in a DNA sequencing laboratory.     

Exact Calculation of Permutational Distributions for Two Independent Samples

A simple Fortran Subroutine is given for the exact calculation of permutational distributions for two independent samples. Important special cases are the Fisher-Pitman randomization test, the Mann-Whitney U-test, the Mantel-Haenszel-test and the exact test for 2×k contingency tables. The algorithm needs polynomial time and is of use even for personal- or microcomputers.     

A new model describing the coordination pattern of the legs of a walking stick insect

A computer (Fortran) model is proposed that describes the temporal and spatial coordination pattern of straight walking stick insects (Carausius morosus) for a broad speed range. It provides a stable pattern independent of the different starting positions. The model is based on six relaxation oscillators. The leading oscillator corresponds to a frontleg. Therefore the information flow runs from front to rear in contrast to earlier models (Graham, 1972; Wendler, 1968).Supported by DFG     

TetraploidMap: construction of a linkage map in autotetraploid species

TetraploidMap is a suite of Fortran 90 routines run from Microsoft Windows with a text-based input and output. TetraploidMap enables the user to assemble a linkage map from dominant and codominant (multiallelic) marker loci scored for the parents and full-sib progeny of a cross in an autotetraploid species. It includes routines for the inference of the parental genotypes, identification of linkage groups, two-point analysis to estimate the recombination frequency and LOD score between all pairs of marker in a linkage group, and locus ordering by simulated annealing.     

A calculator program for least-squares parameter estimation according to the one-compartment kinetic model with zero-order input

A calculator program that performs a nonlinear least-squares fit to data conforming to the one-compartment model with zero-order input is described. The program, which is designed for the Hewlett-Packard HP-41 CV calculator, is based on the Gauss-Newton iterative algorithm as modified by Hartley. A subroutine for calculation of initial parameter estimates is incorporated into the program. Plasma concentration data relative to a single oral dose of a sustained-release theophylline formulation are used to demonstrate the practical application of the program.     

Sequential and parallel molecular mechanics calculations

This article describes a gradient algorithm for the computational optimization of model molecular structures, and discusses the various compromises inherent in the practical expression of the algorithm in a Fortran computer program (VULCAN) for both sequential and parallel computers. Details are given of some previously undiscussed properties of gradient algorithms; various acceleration techniques are compared: and some traps for the unwary are highlighted.     

Supercomputer analysis of purine and pyrimidine metabolism leading to DNA synthesis

A model-system is established to analyze purine and pyrimidine metabolism leading to DNA synthesis. The principal aim is to explore the flow and regulation of terminal deoxynucleoside triophosphates (dNTPs) in various input and parametric conditions. A series of flow equations are established, which are subsequently converted to differential equations. These are programmed (Fortran) and analyzed on a Cray X-MP/48 supercomputer. The pool concentrations are presented as a function of time in conditions in which various pertinent parameters of the system are modified. The system is formulated by 100 differential equations.