105,397 research outputs found
Log::ProgramInfo: A Perl module to collect and log data for bioinformatics pipelines.
Get PDFBackgroundTo 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)
Get PDFThe 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
Get PDFOne 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
Get PDFErbium 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
Get PDFPattern 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
Get PDFThe 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
Get PDFInterdigitated 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
- …
