Genome-wide DNA polymorphism analyses using VariScan

BACKGROUND: DNA sequence polymorphisms analysis can provide valuable information on the evolutionary forces shaping nucleotide variation, and provides an insight into the functional significance of genomic regions. The recent ongoing genome projects will radically improve our capabilities to detect specific genomic regions shaped by natural selection. Current available methods and software, however, are unsatisfactory for such genome-wide analysis. RESULTS: We have developed methods for the analysis of DNA sequence polymorphisms at the genome-wide scale. These methods, which have been tested on a coalescent-simulated and actual data files from mouse and human, have been implemented in the VariScan software package version 2.0. Additionally, we have also incorporated a graphical-user interface. The main features of this software are: i) exhaustive population-genetic analyses including those based on the coalescent theory; ii) analysis adapted to the shallow data generated by the high-throughput genome projects; iii) use of genome annotations to conduct a comprehensive analyses separately for different functional regions; iv) identification of relevant genomic regions by the sliding-window and wavelet-multiresolution approaches; v) visualization of the results integrated with current genome annotations in commonly available genome browsers. CONCLUSION: VariScan is a powerful and flexible suite of software for the analysis of DNA polymorphisms. The current version implements new algorithms, methods, and capabilities, providing an important tool for an exhaustive exploratory analysis of genome-wide DNA polymorphism data

Proposal of a simulation model and design of an alternative storage system for AndaSol I solar plant

The storage system in a concentrated solar plant is considered an important concern to increase the capacity factor of the plant by producing power during the night or in cloudy days. This paper presents different storage materials, and introduces several storage systems available. Moreover, the paper is focused on the analysis of a thermocline system, which consists on a single tank that typically works with molten salt and quartzite rock as storage media. A simulation model of heat charging and discharging process is designed with the numerical solution of non dimensional Schumann equations. These equations describe the heat transfer between the thermal fluid and the filler material. The model has been validated with experimental data, and the results have been compared with other models. Then, the proposed model is then used to design an alternative storage system for the solar plant AndaSol I. Moreover, the model has been used analyze the influence of the ratio between height and diameter of the tank in the energy storage efficiency. Finally, a comparison between three thermal storage fluids has been made in order to find out which Heat Transfer Fluid is better for the designed thermal storage tank.Outgoin

Considerations for the inclusion of 2x mammalian genomes in phylogenetic analyses

Comment on Milinkovitch et al.: http://genomebiology.com/2010/11/2/R1

Cultura y matemáticas a la vista de todos secretos guardados en piedra superficies regladas en la Sagrada familia de Antoni Gaudí

Las matemáticas ayudan a interpretar, comprender y valorar nuestro entorno. Cualquier edificio (incluso restos arqueológicos) nos permite trabajar matemáticas próximas al alumno y contextualizadas. Mostraremos ejemplos centrados en la Sagrada Familia de Barcelona y alrededores para ilustrar cómo aprovechar un edificio singular para observar el entorno con mirada matemática y aprender matemáticas. Hay mucha matemática en las fachadas de las catedrales. En la fachada de la Pasión de la Sagrada Familia de Barcelona aparece un cuadrado mágico de 4x4, similar al del grabado de Alberto Durero (la melancolía) pero algo modificado. Nos preguntamos el por qué del cambio y constataremos la relación entre cultura y matemáticas. Por otro lado, Antoni Gaudí estudió las superficies regladas y fue pionero a la hora de utilizarlas en sus construcciones, tanto por su belleza estética como por sus propiedades físicas y facilidad de construcción. Mostramos cómo estas superficies aparecen en la naturaleza, en el arte, en la arquitectura y en la tecnología; Gaudí las utiliza en la Sagrada Familia y construimos algunos modelos

VariScan Software

Linux / Mac OS X : The package includes executables for linux (variscan) and Mac OS X (variscan). For other Unix-based platforms you will have to compile it from the source files included in the VariScan package. Windows: The package includes (src directory), the source code, the project (variscan.dev) and makefile (variscan.win) files to be used, for instance, for the Dev-C++ (a free Integrated Development Environment for the C/C++ programming language)Podeu consultar l'article relacionat a: http://hdl.handle.net/2445/7384Podeu consultar la pàgina de desenvolupament del programari: http://www.ub.edu/softevol/VariScan is a software package for the analysis of DNA sequence polymorphisms at the whole genome scale. Among other features, the software: (1) can conduct many population genetic analyses; (2) incorporates a multiresolution wavelet transform-based method that allows capturing relevant information from DNA polymorphism data; and (3) it facilitates the visualization of the results in the most commonly used genome browsers

Joining forces in the quest for orthologs

Building momentum to coordinate and leverage community orthology prediction resources

eHive: An Artificial Intelligence workflow system for genomic analysis

<p>Abstract</p> <p>Background</p> <p>The Ensembl project produces updates to its comparative genomics resources with each of its several releases per year. During each release cycle approximately two weeks are allocated to generate all the genomic alignments and the protein homology predictions. The number of calculations required for this task grows approximately quadratically with the number of species. We currently support 50 species in Ensembl and we expect the number to continue to grow in the future.</p> <p>Results</p> <p>We present eHive, a new fault tolerant distributed processing system initially designed to support comparative genomic analysis, based on blackboard systems, network distributed autonomous agents, dataflow graphs and block-branch diagrams. In the eHive system a MySQL database serves as the central blackboard and the autonomous agent, a Perl script, queries the system and runs jobs as required. The system allows us to define dataflow and branching rules to suit all our production pipelines. We describe the implementation of three pipelines: (1) pairwise whole genome alignments, (2) multiple whole genome alignments and (3) gene trees with protein homology inference. Finally, we show the efficiency of the system in real case scenarios.</p> <p>Conclusions</p> <p>eHive allows us to produce computationally demanding results in a reliable and efficient way with minimal supervision and high throughput. Further documentation is available at: <url>http://www.ensembl.org/info/docs/eHive/</url>.</p

Changes in REVEAL risk score in patients with pulmonary arterial hypertension treated with macitentan in clinical practice: results from the PRACMA study

Background: Macitentan is a dual endothelin receptor antagonist indicated for the long-term treatment of pulmonary arterial hypertension (PAH). We evaluated the change over time in REVEAL risk score in incident and prevalent patients receiving macitentan for the first time. Methods: Retrospective, observational study including adult patients with idiopathic/heritable PAH or PAH associated with connective tissue disorders or congenital heart disease treated with macitentan for ≥6-month follow-up in Spain. The REVEAL risk score and risk strata were computed at the start of macitentan and after ≥6-month in patients with ≥7 out of 12 valid REVEAL components. Results: Overall, 81 patients (57 for the REVEAL score) were analysed, 77.8% women. The mean age was 57.2 years and 50.6% of patients had idiopathic/heritable PAH. Prevalent patients were 59.3 and 40.7% were incident. Main therapies for PAH included macitentan monotherapy (42.0%) and macitentan in combination with phosphodiesterase type 5 inhibitor (44.4%). With a median time of macitentan treatment of 10.5 months, the mean REVEAL score was 8.7 points at baseline and was 7.2 points after ≥6-month follow-up. The mean change (95% CI) in REVEAL risk score was - 1.4 (- 2.0, - 0.9) points (p < 0.0001), being - 1.8 (- 3.0, - 0.7) points (p = 0.0040) and - 1.2 (- 1.8, - 0.5) points (p = 0.0010), in incident and prevalent patients, respectively. The reduction was also significant by risk stratum (36.8% of patients in the high-very high risk strata at baseline versus 14.0% after ≥6-month, p < 0.05) and therapy group. The REVEAL components that significantly improved were WHO functional class (FC) (63.9% FC III at macitentan initiation and 23.6% after ≥6-month, p < 0.0001), 6-min walk test (mean change: 41.8 m, p < 0.01), brain natriuretic peptide (BNP) or N-terminal proBNP (NT-proBNP) (mean change of - 157.6 pg/mL and - 530.0 pg/mL, respectively, p < 0.05 both), and pulmonary vascular resistance (PVR) (mean change: - 3.4 WU, p < 0.01). Conclusions: In this study, treatment with macitentan improved the REVEAL risk strata and score in both incident and prevalent PAH patients, and in all patients regardless of the therapy strategy. Macitentan significantly improved some of REVEAL components including WHO FC, BNP/NT-proBNP, PVR, and 6-min walk test after at least 6-month follow-up

Readout electronics for low dark count pixel detectors based on geiger mode avalanche photodiodes fabricated in conventional CMOS technologies for future linear colliders

The high sensitivity and excellent timing accuracy of Geiger mode avalanche photodiodes makes them ideal sensors as pixel detectors for particle tracking in high energy physics experiments to be performed in future linear colliders. Nevertheless, it is well known that these sensors suffer from dark counts and afterpulsing noise, which induce false hits (indistinguishable from event detection) as well as an increase of the necessary area of the readout system. In this work, we present a comparison between APDs fabricated in a high voltage 0.35 µm and a high integration 0.13 µm commercially available CMOS technologies that has been performed to determine which of them best fits the particle collider requirements. In addition, a readout circuit that allows low noise operation is introduced. Experimental characterization of the proposed pixel is also presented in this work

Accurate extension of multiple sequence alignments using a phylogeny-aware graph algorithm

Motivation: Accurate alignment of large numbers of sequences is demanding and the computational burden is further increased by downstream analyses depending on these alignments. With the abundance of sequence data, an integrative approach of adding new sequences to existing alignments without their full re-computation and maintaining the relative matching of existing sequences is an attractive option. Another current challenge is the extension of reference alignments with fragmented sequences, as those coming from next-generation metagenomics, that contain relatively little information. Widely used methods for alignment extension are based on profile representation of reference sequences. These do not incorporate and use phylogenetic information and are affected by the composition of the reference alignment and the phylogenetic positions of query sequences