JEnsembl: a version-aware Java API to Ensembl data systems

Motivation: The Ensembl Project provides release-specific Perl APIs for efficient high-level programmatic access to data stored in various Ensembl database schema. Although Perl scripts are perfectly suited for processing large volumes of text-based data, Perl is not ideal for developing large-scale software applications nor embedding in graphical interfaces. The provision of a novel Java API would facilitate type-safe, modular, object-orientated development of new Bioinformatics tools with which to access, analyse and visualize Ensembl data. Results: The JEnsembl API implementation provides basic data retrieval and manipulation functionality from the Core, Compara and Variation databases for all species in Ensembl and EnsemblGenomes and is a platform for the development of a richer API to Ensembl datasources. The JEnsembl architecture uses a text-based configuration module to provide evolving, versioned mappings from database schema to code objects. A single installation of the JEnsembl API can therefore simultaneously and transparently connect to current and previous database instances (such as those in the public archive) thus facilitating better analysis repeatability and allowing ‘through time’ comparative analyses to be performed. Availability: Project development, released code libraries, Maven repository and documentation are hosted at SourceForge (http://jensembl.sourceforge.net). Contact: [email protected], [email protected], [email protected]

N-Body Simulations of Alternate Gravity Models

Theories in which gravity is weaker on cosmological scales have been proposed to explain the observed acceleration of the universe. The nonlinear regime in such theories is not well studied, though it is likely that observational tests of structure formation will lie in this regime. A class of alternate gravity theories may be approximated by modifying Poisson's equation. We have run N-body simulations of a set of such models to study the nonlinear clustering of matter on 1-100 Mpc scales. We find that nonlinear gravity enhances the deviations of the power spectrum of these models from standard gravity. This occurs due to mode-coupling, so that models with an excess or deficit of large-scale power (at k < 0.2/Mpc) lead to deviations in the power spectrum at smaller scales as well (up to k ~ 1/Mpc), even though the linear spectra match very closely on the smaller scales. This makes it easier to distinguish such models from general relativity using the three-dimensional power spectrum probed by galaxy surveys and the weak lensing power spectrum. If the potential for light deflection is modified in the same way as the potential that affects the dark matter, then weak lensing constrains deviations from gravity even more strongly. Our simulations show that even with a modified potential, gravitational evolution is approximately universal. Based on this, the Peacock-Dodds approach can be adapted to get an analytical fit for the nonlinear power spectra of alternate gravity models, though the recent Smith et al formula is less successful. Our conclusions extend to models with modifications of gravity on scales of 1-20 Mpc. We also use a way of measuring projected power spectra from simulations that lowers the sample variance, so that fewer realizations are needed to reach a desired level of accuracy.Comment: 26 pages, 10 figures, matches published versio

Quantifying Florida Bay Habitat Suitability for Fishes and Invertebrates Under Climate Change Scenarios

The Florida Bay ecosystem supports a number of economically important ecosystem services, including several recreational fisheries, which may be affected by changing salinity and temperature due toclimate change. In this paper, we use a combination of physical models and habitat suitability index models to quantify the effects of potential climate change scenarios on a variety of juvenile fish and lobster species in Florida Bay. The climate scenarios include alterations in sea level, evaporation and precipitation rates, coastal runoff, and water temperature. We find that the changes in habitat suitability vary in both magnitude and direction across the scenarios and species, but are on average small. Only one of the seven species we investigate (Lagodon rhomboides, i.e., pinfish) sees a sizable decrease in optimal habitat under any of the scenarios. This suggests that the estuarine fauna of Florida Bay may not be as vulnerable to climate change as other components of the ecosystem, such as those in the marine/terrestrial ecotone. However, these models are relatively simplistic, looking only at single species effects of physical drivers without considering the many interspecific interactions that may play a key role in the adjustment of the ecosystem as a whole. More complex models that capture the mechanistic links between physics and biology, as well as the complex dynamics of the estuarine food web, may be necessary to further understand the potential effects of climate change on the Florida Bay ecosystem

Spherical Collapse and Cluster Counts in Modified Gravity Models

Modifications to the gravitational potential affect the nonlinear gravitational evolution of large scale structures in the Universe. To illustrate some generic features of such changes, we study the evolution of spherically symmetric perturbations when the modification is of Yukawa type; this is non-trivial, because we should not and do not assume that Birkhoff's theorem applies. We then show how to estimate the abundance of virialized objects in such models. Comparison with numerical simulations shows reasonable agreement: When normalized to have the same fluctuations at early times, weaker large scale gravity produces fewer massive halos. However, the opposite can be true for models that are normalized to have the same linear theory power spectrum today, so the abundance of rich clusters potentially places interesting constraints on such models. Our analysis also indicates that the formation histories and abundances of sufficiently low mass objects are unchanged from standard gravity. This explains why simulations have found that the nonlinear power-spectrum at large k is unaffected by such modifications to the gravitational potential. In addition, the most massive objects in CMB-normalized models with weaker gravity are expected to be similar to the high-redshift progenitors of the most massive objects in models with stronger gravity. Thus, the difference between the cluster and field galaxy populations is expected to be larger in models with stronger large-scale gravity.Comment: 9 pages, 8 figures Accepted by Phys. Rev.

The number density of superdense early-type galaxies at 1<z<2 and the local cluster galaxies

Many of the early-type galaxies observed so far at z>1 turned out to have smaller radii with respect to that of a typical present-day early-type galaxy with comparable mass. This has generated the conviction that in the past early-type galaxies were more compact, hence denser, and that as a consequence, they should have increased their radius across the time to reconcile with the present-day ones. However, observations have not yet established whether the population of early-types in the early Universe was fully represented by compact galaxies nor if they were so much more numerous than in the present-day Universe to require an evolution of their sizes. Here we report the results of a study based on a complete sample of 34 early-type galaxies at 0.9<z_{spec}<1.92. We find a majority (62 per cent) of normal early-type galaxies similar to typical local ones, co-existing with compact early-types from ~2 to ~6 times smaller in spite of the same mass and redshift. The co-existence of normal and compact early-type galaxies at ~1.5 suggests that their build-up taken place in the first 3-4 Gyr, followed distinct paths. Also, we find that the number density of compact early-types at ~1.5 is consistent with the lower limits of the local number density of compact early-types derived from local clusters of galaxies. The similar number of compact early-types found in the early and in the present day Universe frustrates the hypothesized effective radius evolution while provides evidence that also compact ETGs were as we see them today 9-10 Gyr ago. Finally, the fact that (at least) most of the compact ETGs at high-z are accounted for by compact early-types in local cluster of galaxies implies that the former are the direct progenitors of the compact early-type cluster galaxies establishing a direct link between environment and early phases of assembly of ETGs.Comment: Published on MNRAS Letters (5 pages, 2 figures, 1 table

BLAST Observations of the South Ecliptic Pole field: Number Counts and Source Catalogs

We present results from a survey carried out by the Balloon-borne Large Aperture Submillimeter Telescope (BLAST) on a 9 deg^2 field near the South Ecliptic Pole at 250, 350 and 500 {\mu}m. The median 1{\sigma} depths of the maps are 36.0, 26.4 and 18.4 mJy, respectively. We apply a statistical method to estimate submillimeter galaxy number counts and find that they are in agreement with other measurements made with the same instrument and with the more recent results from Herschel/SPIRE. Thanks to the large field observed, the new measurements give additional constraints on the bright end of the counts. We identify 132, 89 and 61 sources with S/N>4 at 250, 350, 500 {\mu}m, respectively and provide a multi-wavelength combined catalog of 232 sources with a significance >4{\sigma} in at least one BLAST band. The new BLAST maps and catalogs are available publicly at http://blastexperiment.info.Comment: 25 pages, 6 figures, 4 tables, Accepted by ApJS. Maps and catalogs available at http://blastexperiment.info

Crossing the Phantom Divide: Theoretical Implications and Observational Status

If the dark energy equation of state parameter w(z) crosses the phantom divide line w=-1 (or equivalently if the expression d(H^2(z))/dz - 3\Omega_m H_0^2 (1+z)^2 changes sign) at recent redshifts, then there are two possible cosmological implications: Either the dark energy consists of multiple components with at least one non-canonical phantom component or general relativity needs to be extended to a more general theory on cosmological scales. The former possibility requires the existence of a phantom component which has been shown to suffer from serious theoretical problems and instabilities. Therefore, the later possibility is the simplest realistic theoretical framework in which such a crossing can be realized. After providing a pedagogical description of various dark energy observational probes, we use a set of such probes (including the Gold SnIa sample, the first year SNLS dataset, the 3-year WMAP CMB shift parameter, the SDSS baryon acoustic oscillations peak (BAO), the X-ray gas mass fraction in clusters and the linear growth rate of perturbations at z=0.15 as obtained from the 2dF galaxy redshift survey) to investigate the priors required for cosmological observations to favor crossing of the phantom divide. We find that a low \Omega_m prior (0.2<\Omega_m <0.25) leads, for most observational probes (except of the SNLS data), to an increased probability (mild trend) for phantom divide crossing. An interesting degeneracy of the ISW effect in the CMB perturbation spectrum is also pointed out.Comment: Accepted in JCAP (to appear). Comments added, typos corrected. 19 pages (revtex), 8 figures. The numerical analysis files (Mathematica + Fortran) with instructions are available at http://leandros.physics.uoi.gr/pdl-cross/pdl-cross.htm . The ppt file of a relevant talk may be downloaded from http://leandros.physics.uoi.gr/pdl-cross/pdl2006.pp

Biological CO2-methanation: An approach to standardization

Power-to-Methane as one part of Power-to-Gas has been recognized globally as one of the key elements for the transition towards a sustainable energy system. While plants that produce methane catalytically have been in operation for a long time, biological methanation has just reached industrial pilot scale and near-term commercial application. The growing importance of the biological method is reflected by an increasing number of scientific articles describing novel approaches to improve this technology. However, these studies are diffcult to compare because they lack a coherent nomenclature. In this article, we present a comprehensive set of parameters allowing the characterization and comparison of various biological methanation processes. To identify relevant parameters needed for a proper description of this technology, we summarized existing literature and defined system boundaries for Power-to-Methane process steps. On this basis, we derive system parameters providing information on the methanation system, its performance, the biology and cost aspects. As a result, three different standards are provided as a blueprint matrix for use in academia and industry applicable to both, biological and catalytic methanation. Hence, this review attempts to set the standards for a comprehensive description of biological and chemical methanation processes

f(R) theories

Over the past decade, f(R) theories have been extensively studied as one of the simplest modifications to General Relativity. In this article we review various applications of f(R) theories to cosmology and gravity - such as inflation, dark energy, local gravity constraints, cosmological perturbations, and spherically symmetric solutions in weak and strong gravitational backgrounds. We present a number of ways to distinguish those theories from General Relativity observationally and experimentally. We also discuss the extension to other modified gravity theories such as Brans-Dicke theory and Gauss-Bonnet gravity, and address models that can satisfy both cosmological and local gravity constraints.Comment: 156 pages, 14 figures, Invited review article in Living Reviews in Relativity, Published version, Comments are welcom

Novel computational methods for increasing PCR primer design effectiveness in directed sequencing

<p>Abstract</p> <p>Background</p> <p>Polymerase chain reaction (PCR) is used in directed sequencing for the discovery of novel polymorphisms. As the first step in PCR directed sequencing, effective PCR primer design is crucial for obtaining high-quality sequence data for target regions. Since current computational primer design tools are not fully tuned with stable underlying laboratory protocols, researchers may still be forced to iteratively optimize protocols for failed amplifications after the primers have been ordered. Furthermore, potentially identifiable factors which contribute to PCR failures have yet to be elucidated. This inefficient approach to primer design is further intensified in a high-throughput laboratory, where hundreds of genes may be targeted in one experiment.</p> <p>Results</p> <p>We have developed a fully integrated computational PCR primer design pipeline that plays a key role in our high-throughput directed sequencing pipeline. Investigators may specify target regions defined through a rich set of descriptors, such as Ensembl accessions and arbitrary genomic coordinates. Primer pairs are then selected computationally to produce a minimal amplicon set capable of tiling across the specified target regions. As part of the tiling process, primer pairs are computationally screened to meet the criteria for success with one of two PCR amplification protocols. In the process of improving our sequencing success rate, which currently exceeds 95% for exons, we have discovered novel and accurate computational methods capable of identifying primers that may lead to PCR failures. We reveal the laboratory protocols and their associated, empirically determined computational parameters, as well as describe the novel computational methods which may benefit others in future primer design research.</p> <p>Conclusion</p> <p>The high-throughput PCR primer design pipeline has been very successful in providing the basis for high-quality directed sequencing results and for minimizing costs associated with labor and reprocessing. The modular architecture of the primer design software has made it possible to readily integrate additional primer critique tests based on iterative feedback from the laboratory. As a result, the primer design software, coupled with the laboratory protocols, serves as a powerful tool for low and high-throughput primer design to enable successful directed sequencing.</p