API-CALC 1.0: a computer program for calculating the average probability of identity allowing for substructure, inbreeding and the presence of close relatives

Individual identification via DNA profiling is important in molecular ecology, particularly in the case of noninvasive sampling. A key quantity in determining the number of loci required is the probability of identity (PIave), the probability of observing two copies of any profile in the population. Previously this has been calculated assuming no inbreeding or population structure. Here we introduce formulae that account for these factors, whilst also accounting for relatedness structure in the population. These formulae are implemented in API-CALC 1.0, which calculates PIave for either a specified value, or a range of values, for F-IS and F-ST.

ExtSym: a program to aid space-group determination from powder diffraction data

Once unit-cell dimensions have been determined from a powder diffraction data set and therefore the crystal system is known (e.g. orthorhombic), the method presented by Markvardsen, David, Johnson & Shankland [Acta Cryst. (2001), A57, 47-54] can be used to generate a table ranking the extinction symbols of the given crystal system according to probability. Markvardsen et al. tested a computer program (ExtSym) implementing the method against Pawley refinement outputs generated using the TF12LS program [David, Ibberson & Matthewman (1992). Report RAL-92-032. Rutherford Appleton Laboratory, Chilton, Didcot, Oxon, UK]. Here, it is shown that ExtSym can be used successfully with many well known powder diffraction analysis packages, namely DASH [David, Shankland, van de Streek, Pidcock, Motherwell & Cole (2006). J. Appl. Cryst. 39, 910-915], FullProf [Rodriguez-Carvajal (1993). Physica B, 192, 55-69], GSAS [Larson & Von Dreele (1994). Report LAUR 86-748. Los Alamos National Laboratory, New Mexico, USA], PRODD [Wright (2004). Z. Kristallogr. 219, 1-11] and TOPAS [Coelho (2003). Bruker AXS GmbH, Karlsruhe, Germany]. In addition, a precise description of the optimal input for ExtSym is given to enable other software packages to interface with ExtSym and to allow the improvement/modification of existing interfacing scripts. ExtSym takes as input the powder data in the form of integrated intensities and error estimates for these intensities. The output returned by ExtSym is demonstrated to be strongly dependent on the accuracy of these error estimates and the reason for this is explained. ExtSym is tested against a wide range of data sets, confirming the algorithm to be very successful at ranking the published extinction symbol as the most likely. (C) 2008 International Union of Crystallography Printed in Singapore - all rights reserved.

Coriolis interactions about x-y axes in symmetric tops

Selection rules and matrix elements are derived for Coriolis interactions between vibrational levels due to rotation about (x, y) axes in symmetric top molecules. The theory is developed in detail for the case of interaction between an A1 and an E species vibrational level in a C3v molecule; perturbations to both the positions and the intensities of the rovibration transitions in the spectrum are considered. A computer program has been written which calculates exactly the perturbed spectrum of two interacting rovibration bands according to this model, the results being presented directly by a graph plotter connected to the computer. This has been used to interpret perturbations observed in two pairs of interacting fundamentals in the spectrum of CH3F (ν2 - ν5 and ν3 - ν6) and one pair in CD3Cl (ν2 - ν5). The resulting analysis of the observed spectrum leads to new values for some vibration-rotation interaction constants and also leads to a unique determination of the sign relationship between the dipole moment derivatives in each pair of interacting normal vibrations. These sign relations are summarized in Figs. 8, 12, and 15.

Second order Coriolis resonance in the v2, v5 Raman bands of CH3F

The vibration-rotation Raman spectrum of the ν2 and ν5 fundamentals of CH3F is reported, from 1320 to 1640 cm−1, with a resolution of about 0.3 cm−1. The Coriolis resonance between the two bands leads to many perturbation-allowed transitions. Where the resonance is still sufficiently weak that the quantum number K′ retains its meaning, perturbation-allowed transitions are observed for all values of ΔK from +4 to −4; in regions of strong resonance, however, we can only say that the observed transitions obey the selection rule Δ(k−l) = 0 or ±3. The spectrum has been analyzed by band contour simulation using a computer program based on exact diagonalization of the Hamiltonian within the ν2, ν5 vibrational levels, and improved vibration-rotation constants for these bands are reported. The relative magnitudes and relative sings of polarizability derivatives involved in these vibrations are also reported.

Inferring population history with DIY ABC: a user-friendly approach to approximate Bayesian computation

Genetic data obtained on population samples convey information about their evolutionary history. Inference methods can extract part of this information but they require sophisticated statistical techniques that have been made available to the biologist community (through computer programs) only for simple and standard situations typically involving a small number of samples. We propose here a computer program (DIY ABC) for inference based on approximate Bayesian computation (ABC), in which scenarios can be customized by the user to fit many complex situations involving any number of populations and samples. Such scenarios involve any combination of population divergences, admixtures and population size changes. DIY ABC can be used to compare competing scenarios, estimate parameters for one or more scenarios and compute bias and precision measures for a given scenario and known values of parameters (the current version applies to unlinked microsatellite data). This article describes key methods used in the program and provides its main features. The analysis of one simulated and one real dataset, both with complex evolutionary scenarios, illustrates the main possibilities of DIY ABC.

A phylogenetic mixture model for detecting pattern-heterogeneity in gene sequence or character-state data

We describe a general likelihood-based 'mixture model' for inferring phylogenetic trees from gene-sequence or other character-state data. The model accommodates cases in which different sites in the alignment evolve in qualitatively distinct ways, but does not require prior knowledge of these patterns or partitioning of the data. We call this qualitative variability in the pattern of evolution across sites "pattern-heterogeneity" to distinguish it from both a homogenous process of evolution and from one characterized principally by differences in rates of evolution. We present studies to show that the model correctly retrieves the signals of pattern-heterogeneity from simulated gene-sequence data, and we apply the method to protein-coding genes and to a ribosomal 12S data set. The mixture model outperforms conventional partitioning in both these data sets. We implement the mixture model such that it can simultaneously detect rate- and pattern-heterogeneity. The model simplifies to a homogeneous model or a rate- variability model as special cases, and therefore always performs at least as well as these two approaches, and often considerably improves upon them. We make the model available within a Bayesian Markov-chain Monte Carlo framework for phylogenetic inference, as an easy-to-use computer program.

Calculation of converged rovibrational energies and partition function for methane using vibrational-rotational configuration interaction

The rovibration partition function of CH4 was calculated in the temperature range of 100-1000 K using well-converged energy levels that were calculated by vibrational-rotational configuration interaction using the Watson Hamiltonian for total angular momenta J=0-50 and the MULTIMODE computer program. The configuration state functions are products of ground-state occupied and virtual modals obtained using the vibrational self-consistent field method. The Gilbert and Jordan potential energy surface was used for the calculations. The resulting partition function was used to test the harmonic oscillator approximation and the separable-rotation approximation. The harmonic oscillator, rigid-rotator approximation is in error by a factor of 2.3 at 300 K, but we also propose a separable-rotation approximation that is accurate within 2% from 100 to 1000 K. (C) 2004 American Institute of Physics.

A policy model for secure information flow

When a computer program requires legitimate access to confidential data, the question arises whether such a program may illegally reveal sensitive information. This paper proposes a policy model to specify what information flow is permitted in a computational system. The security definition, which is based on a general notion of information lattices, allows various representations of information to be used in the enforcement of secure information flow in deterministic or nondeterministic systems. A flexible semantics-based analysis technique is presented, which uses the input-output relational model induced by an attacker's observational power, to compute the information released by the computational system. An illustrative attacker model demonstrates the use of the technique to develop a termination-sensitive analysis. The technique allows the development of various information flow analyses, parametrised by the attacker's observational power, which can be used to enforce what declassification policies.

Understanding cumulative risk

This paper summarizes the theory of simple cumulative risks—for example, the risk of food poisoning from the consumption of a series of portions of tainted food. Problems concerning such risks are extraordinarily difficult for naı¨ve individuals, and the paper explains the reasons for this difficulty. It describes how naı¨ve individuals usually attempt to estimate cumulative risks, and it outlines a computer program that models these methods. This account predicts that estimates can be improved if problems of cumulative risk are framed so that individuals can focus on the appropriate subset of cases. The paper reports two experiments that corroborated this prediction. They also showed that whether problems are stated in terms of frequencies (80 out of 100 people got food poisoning) or in terms of percentages (80% of people got food poisoning) did not reliably affect accuracy.

Predicting natural ventilation in a two-zone building driven by combined forces.

Natural ventilation relies on less controllable natural forces so that it needs more artificial control, and thus its prediction, design and analysis become more important. This paper presents both theoretical and numerical simulations for predicting the natural ventilation flow in a two-zone building with multiple openings which is subjected to the combined natural forces. To our knowledge, this is the first analytical solutions obtained so far for a building with more than one zones and in each zone with possibly more than 2 openings. The analytical solution offers a possibility for validating a multi-zone airflow program. A computer program MIX is employed to conduct the numerical simulation. Good agreement is achieved. Different airflow modes are identified and some design recommendations are also provided.

Eddy current testing program with scanning probe head having parallel and normal sensing coils

An eddy current testing system consists of a multi-sensor probe, computer and a special expansion card and software for data collection and analysis. The probe incorporates an excitation coil, and sensor coils; at least one sensor coil is a lateral current-normal coil and at least one is a current perturbation coil.

ASYM20: a program for force constant and normal coordinate calculations, with a critical review of the theory involved

The theory of harmonic force constant refinement calculations is reviewed, and a general-purpose program for force constant and normal coordinate calculations is described. The program, called ASYM20. is available through Quantum Chemistry Program Exchange. It will work on molecules of any symmetry containing up to 20 atoms and will produce results on a series of isotopomers as desired. The vibrational secular equations are solved in either nonredundant valence internal coordinates or symmetry coordinates. As well as calculating the (harmonic) vibrational wavenumbers and normal coordinates, the program will calculate centrifugal distortion constants, Coriolis zeta constants, harmonic contributions to the α′s. root-mean-square amplitudes of vibration, and other quantities related to gas electron-diffraction studies and thermodynamic properties. The program will work in either a predict mode, in which it calculates results from an input force field, or in a refine mode, in which it refines an input force field by least squares to fit observed data on the quantities mentioned above. Predicate values of the force constants may be included in the data set for a least-squares refinement. The program is written in FORTRAN for use on a PC or a mainframe computer. Operation is mainly controlled by steering indices in the input data file, but some interactive control is also implemented.

PopABC: a program to infer historical demographic parameters

PopABC is a computer package for inferring the pattern of demographic divergence of closely related populations and species. The software performs coalescent simulation in the framework of approximate Bayesian computation (ABC). PopABC can also be used to perform Bayesian model choice to discriminate between different demographic scenarios. The program can be used either for research or for education and teaching purposes.

Jpowder: a Java-based program for the display and examination of powder diffraction data

The ability to display and inspect powder diffraction data quickly and efficiently is a central part of the data analysis process. Whilst many computer programs are capable of displaying powder data, their focus is typically on advanced operations such as structure solution or Rietveld refinement. This article describes a lightweight software package, Jpowder, whose focus is fast and convenient visualization and comparison of powder data sets in a variety of formats from computers with network access. Jpowder is written in Java and uses its associated Web Start technology to allow ‘single-click deployment’ from a web page, http://www.jpowder.org. Jpowder is open source, free and available for use by anyone.