Log::ProgramInfo: A Perl module to collect and log data for bioinformatics pipelines.

BackgroundTo reproduce and report a bioinformatics analysis, it is important to be able to determine the environment in which a program was run. It can also be valuable when trying to debug why different executions are giving unexpectedly different results.ResultsLog::ProgramInfo is a Perl module that writes a log file at the termination of execution of the enclosing program, to document useful execution characteristics. This log file can be used to re-create the environment in order to reproduce an earlier execution. It can also be used to compare the environments of two executions to determine whether there were any differences that might affect (or explain) their operation.AvailabilityThe source is available on CPAN (Macdonald and Boutros, Log-ProgramInfo. http://search.cpan.org/~boutroslb/Log-ProgramInfo/).ConclusionUsing Log::ProgramInfo in programs creating result data for publishable research, and including the Log::ProgramInfo output log as part of the publication of that research is a valuable method to assist others to duplicate the programming environment as a precursor to validating and/or extending that research

An Analysis of the Shore Beetle Communities of Some Channelized Streams in Northwest Ohio (Coleoptera)

The present shore beetle communities of some northwest Ohio streams channelized between 1937 and 1973 were studied. Quantitative and qualitative analyses were made to determine the effects of channelization on the community and the results are discussed. Ninety species, chiefly Carabidae, Heteroceridae and Staphylinidae, were collected; at least 20 not previously reported from Ohio. In addition, some species associations are noted

Metastability in a stochastic neural network modeled as a velocity jump Markov process

One of the major challenges in neuroscience is to determine how noise that is present at the molecular and cellular levels affects dynamics and information processing at the macroscopic level of synaptically coupled neuronal populations. Often noise is incorprated into deterministic network models using extrinsic noise sources. An alternative approach is to assume that noise arises intrinsically as a collective population effect, which has led to a master equation formulation of stochastic neural networks. In this paper we extend the master equation formulation by introducing a stochastic model of neural population dynamics in the form of a velocity jump Markov process. The latter has the advantage of keeping track of synaptic processing as well as spiking activity, and reduces to the neural master equation in a particular limit. The population synaptic variables evolve according to piecewise deterministic dynamics, which depends on population spiking activity. The latter is characterised by a set of discrete stochastic variables evolving according to a jump Markov process, with transition rates that depend on the synaptic variables. We consider the particular problem of rare transitions between metastable states of a network operating in a bistable regime in the deterministic limit. Assuming that the synaptic dynamics is much slower than the transitions between discrete spiking states, we use a WKB approximation and singular perturbation theory to determine the mean first passage time to cross the separatrix between the two metastable states. Such an analysis can also be applied to other velocity jump Markov processes, including stochastic voltage-gated ion channels and stochastic gene networks

Er doped oxide nanoparticles in silica based optical fibres

Erbium doped materials are of great interest in optical telecommunications due to the Er3+ intra-4f emission at 1.54 ?m. Erbium doped fibre amplifiers (EDFA) were developed in silica glass because of the low losses at this wavelength and the reliability of this glass. Developments of new rare earth doped fibre amplifiers aim to control their spectroscopic properties including shape and width of the gain curve and optical quantum efficiency. Standard silica glass modifiers, such as aluminium, result in very good properties in current EDFA. However, for more drastic spectroscopic changes, more important modifications of the rare earth ions local environment are required. To address this aim, we present a fibre fabrication route creating rare earth doped calcia?silica or calcia?phosphosilica nanoparticles embedded in silica glass. By adding alkaline earth elements such as calcium, in low concentration, one can obtain a glass with an immisci- bility gap so that phase separation occurs with an appropriate heat treatment. We investigated the role of two elements: calcium and phosphorus (a standard silica modifier). Scanning electron microscopy shows that nanoparticles are only observed when calcium is incorporated. The size of the particles is determined to be around 50 nm in preform samples. The nature of these particles depends on phosphorus content: without P, electron diffraction shows that the particles are amorphous whilst they are partially crystalline when phosphorus is added. In addition through use of energy dispersive x-ray techniques, we have shown that erbium ions are located in the nanoparticles

Rayleigh-Benard Convection with a Radial Ramp in Plate Separation

Pattern formation in Rayleigh-Benard convection in a large-aspect-ratio cylinder with a radial ramp in the plate separation is studied analytically and numerically by performing numerical simulations of the Boussinesq equations. A horizontal mean flow and a vertical large scale counterflow are quantified and used to understand the pattern wavenumber. Our results suggest that the mean flow, generated by amplitude gradients, plays an important role in the roll compression observed as the control parameter is increased. Near threshold the mean flow has a quadrupole dependence with a single vortex in each quadrant while away from threshold the mean flow exhibits an octupole dependence with a counter-rotating pair of vortices in each quadrant. This is confirmed analytically using the amplitude equation and Cross-Newell mean flow equation. By performing numerical experiments the large scale counterflow is also found to aid in the roll compression away from threshold but to a much lesser degree. Our results yield an understanding of the pattern wavenumbers observed in experiment away from threshold and suggest that near threshold the mean flow and large scale counterflow are not responsible for the observed shift to smaller than critical wavenumbers.Comment: 10 pages, 13 figure

The stochastic dynamics of nanoscale mechanical oscillators immersed in a viscous fluid

The stochastic response of nanoscale oscillators of arbitrary geometry immersed in a viscous fluid is studied. Using the fluctuation-dissipation theorem it is shown that deterministic calculations of the governing fluid and solid equations can be used in a straightforward manner to directly calculate the stochastic response that would be measured in experiment. We use this approach to investigate the fluid coupled motion of single and multiple cantilevers with experimentally motivated geometries.Comment: 5 pages, 5 figure

Microwave characteristics of interdigitated photoconductors on a HEMT structure

Interdigitated photoconductive detectors of various geometries were fabricated on AlGaAs/GaAs heterostructure material. The processes used in the fabrication of these devices are described, and the results of a study of their optical and electrical characteristics are presented