OPPL-Galaxy, a Galaxy tool for enhancing ontology exploitation as part of bioinformatics workflows

Biomedical ontologies are key elements for building up the Life Sciences Semantic Web. Reusing and building biomedical ontologies requires flexible and versatile tools to manipulate them efficiently, in particular for enriching their axiomatic content. The Ontology Pre Processor Language (OPPL) is an OWL-based language for automating the changes to be performed in an ontology. OPPL augments the ontologists’ toolbox by providing a more efficient, and less error-prone, mechanism for enriching a biomedical ontology than that obtained by a manual treatment. Results We present OPPL-Galaxy, a wrapper for using OPPL within Galaxy. The functionality delivered by OPPL (i.e. automated ontology manipulation) can be combined with the tools and workflows devised within the Galaxy framework, resulting in an enhancement of OPPL. Use cases are provided in order to demonstrate OPPL-Galaxy’s capability for enriching, modifying and querying biomedical ontologies. Conclusions Coupling OPPL-Galaxy with other bioinformatics tools of the Galaxy framework results in a system that is more than the sum of its parts. OPPL-Galaxy opens a new dimension of analyses and exploitation of biomedical ontologies, including automated reasoning, paving the way towards advanced biological data analyses

Estudio de caso: Evaluación de impacto de la intervención del Proyecto INCOPA/ ADERS en Huánuco

El desafío de identificar y aprovechar nuevas oportunidades de mercado para los pequeños productores de papa peruana, articulándolos con otros actores de la cadena agro- alimentaria de este tubérculo, es asumido por el proyecto INCOPA – Promoción Competitiva de la Papa Peruana para Responder a Nuevas Oportunidades de Mercado1 – desde su origen en el año 2001. Este proyecto, que es financiado por la Agencia Suiza para la Cooperación y el Desarrollo (COSUDE) y coordinado por el Centro Internacional de la Papa (CIP), realizó en el año 2006 una evaluación de su segunda fase, en la cual se observaron algunos indicios sobre cambios positivos en cuanto a ingresos económicos y mejor relacionamiento con el mercado en las organizaciones y familias de productores participantes. Con el fin de complementar este estudio anterior, se decidió realizar un estudio de impacto para conocer la dimensión de estos y otros cambios en las familias de productores de una de sus sedes de operación, Huánuco, donde viene trabajando desde el año 2002, a través de su socio local ADERS. INCOPA y ADERS combinaron sus esfuerzos y capacidades en esta sede, en una intervención que no fue planificada del modo en que finalmente se implementó. Esta fue tomando forma en el camino, aprovechando la oportunidad que dio el proyecto PRO-PAPA, y bajo la influencia del Enfoque Participativo de Cadenas Productivas (EPCP), en pleno desarrollo durante la intervención. Se llegó a consolidar una forma de trabajar que tanto ADERS como INCOPA han sabido sacar provecho y extender a otros lugares

Optical Photometry of the Type Ia SN 1999ee and the Type Ib/c SN 1999ex in IC 5179

We present UBVRIz lightcurves of the Type Ia SN 1999ee and the Type Ib/c SN 1999ex, both located in the galaxy IC 5179. SN 1999ee has an extremely well sampled lightcurve spanning from 10 days before Bmax through 53 days after peak. Near maximum we find systematic differences ~0.05 mag in photometry measured with two different telescopes, even though the photometry is reduced to the same local standards around the supernova using the specific color terms for each instrumental system. We use models for our bandpasses and spectrophotometry of SN 1999ee to derive magnitude corrections (S-corrections) and remedy this problem. This exercise demonstrates the need of accurately characterizing the instrumental system before great photometric accuracies of Type Ia supernovae can be claimed. It also shows that this effect can have important astrophysical consequences since a small systematic shift of 0.02 mag in the B-V color can introduce a 0.08 mag error in the extinction corrected peak B magnitudes of a supernova and thus lead to biased cosmological parameters. The data for the Type Ib/c SN 1999ex present us with the first ever observed shock breakout of a supernova of this class. These observations show that shock breakout occurred 18 days before Bmax and support the idea that Type Ib/c supernovae are due to core collapse of massive stars rather than thermonuclear disruption of white dwarfs.Comment: 55 pages, 15 figures, accepted by the Astronomical Journa

The Distance to SN 1999em from the Expanding Photosphere Method

We present optical and IR spectroscopy of the first two months of evolution of the Type II SN 1999em. We combine these data with high-quality optical/IR photometry beginning only three days after shock breakout, in order to study the performance of the ``Expanding Photosphere Method'' (EPM) in the determination of distances. With this purpose we develop a technique to measure accurate photospheric velocities by cross-correlating observed and model spectra. The application of this technique to SN 1999em shows that we can reach an average uncertainty of 11% in velocity from an individual spectrum. Our analysis shows that EPM is quite robust to the effects of dust. In particular, the distances derived from the VI filters change by only 7% when the adopted visual extinction in the host galaxy is varied by 0.45 mag. The superb time sampling of the BVIZJHK light-curves of SN 1999em permits us to study the internal consistency of EPM and test the dilution factors computed from atmosphere models for Type II plateau supernovae. We find that, in the first week since explosion, the EPM distances are up to 50% lower than the average, possibly due the presence of circumstellar material. Over the following 65 days, on the other hand, our tests lend strong credence to the atmosphere models, and confirm previous claims that EPM can produce consistent distances without having to craft specific models to each supernova. This is particularly true for the VI filters which yield distances with an internal consistency of 4%. From the whole set of BVIZJHK photometry, we obtain an average distance of 7.5+/-0.5 Mpc, where the quoted uncertainty (7%) is a conservative estimate of the internal precision of the method obtained from the analysis of the first 70 days of the supernova evolution.Comment: 68 pages, 15 tables, 22 figures, to appear in Ap

UBVRIz Light Curves of 51 Type II Supernovae

We present a compilation of UBV RIz light curves of 51 type II supernovae discovered during the course of four different surveys during 1986 to 2003: the Cerro Tololo Supernova Survey, the Calan/Tololo Supernova Program (C&T), the Supernova Optical and Infrared Survey (SOIRS), and the Carnegie Type II Supernova Survey (CATS). The photometry is based on template-subtracted images to eliminate any potential host galaxy light contamination, and calibrated from foreground stars. This work presents these photometric data, studies the color evolution using different bands, and explores the relation between the magnitude at maximum brightness and the brightness decline parameter (s) from maximum light through the end of the recombination phase. This parameter is found to be shallower for redder bands and appears to have the best correlation in the B band. In addition, it also correlates with the plateau duration, being thus shorter (longer) for larger (smaller) s values.Comment: 110 pages, 9 Figures, 6 Tables, accepted in A

Does codon bias have an evolutionary origin?

<p>Abstract</p> <p>Background</p> <p>There is a 3-fold redundancy in the Genetic Code; most amino acids are encoded by more than one codon. These synonymous codons are not used equally; there is a Codon Usage Bias (CUB). This article will provide novel information about the origin and evolution of this bias.</p> <p>Results</p> <p>Codon Usage Bias (CUB, defined here as deviation from equal usage of synonymous codons) was studied in 113 species. The average CUB was 29.3 ± 1.1% (S.E.M, n = 113) of the theoretical maximum and declined progressively with evolution and increasing genome complexity. A Pan-Genomic Codon Usage Frequency (CUF) Table was constructed to describe genome-wide relationships among codons. Significant correlations were found between the number of synonymous codons and (i) the frequency of the respective amino acids (ii) the size of CUB. Numerous, statistically highly significant, internal correlations were found among codons and the nucleic acids they comprise. These strong correlations made it possible to predict missing synonymous codons (wobble bases) reliably from the remaining codons or codon residues.</p> <p>Conclusion</p> <p>The results put the concept of "codon bias" into a novel perspective. The internal connectivity of codons indicates that all synonymous codons might be integrated parts of the Genetic Code with equal importance in maintaining its functional integrity.</p

Plan de negocios de servicios de entretenimiento para el adulto mayor - Club Tayta

El envejecimiento poblacional es un fen?meno demogr?fico mundial al cual el Per? no es ajeno. Conforme trascurren los a?os se observa que la pir?mide poblacional se va invirtiendo, entre otras cosas porque la esperanza de vida ha ido aumentando de manera sostenida y la tasa de natalidad ha ido disminuyendo. Sus consecuencias, unidas a las caracter?sticas sociales, econ?micas y culturales del pa?s, tienden a afectar la calidad de vida de la poblaci?n adulto mayor y al propio proceso de envejecimiento. Aunque el Estado ha establecido un marco normativo y ha dispuesto el despliegue de diversas instituciones que permitan que los adultos mayores disfruten de una vejez activa y participativa en la comunidad, el alcance real de estas iniciativas es que se prioriza el cuidado de la salud f?sica dejando de lado aspectos sociales importantes como el entretenimiento. En ese contexto se plantea el ?Plan de Negocios de Servicios de Entretenimiento para el Adulto Mayor - Club Tayta?, como una alternativa que brinda servicios de entretenimiento especialmente dise?ados para el adulto mayor, mediante el desarrollo de talleres y actividades que les haga sentirse ?tiles, importantes y parte activa de la sociedad, elevando as? su calidad de vida

Ontology Design Patterns for bio-ontologies: a case study on the Cell Cycle Ontology

<p>Abstract</p> <p>Background</p> <p>Bio-ontologies are key elements of knowledge management in bioinformatics. Rich and rigorous bio-ontologies should represent biological knowledge with high fidelity and robustness. The richness in bio-ontologies is a prior condition for diverse and efficient reasoning, and hence querying and hypothesis validation. Rigour allows a more consistent maintenance. Modelling such bio-ontologies is, however, a difficult task for bio-ontologists, because the necessary richness and rigour is difficult to achieve without extensive training.</p> <p>Results</p> <p>Analogous to design patterns in software engineering, Ontology Design Patterns are solutions to typical modelling problems that bio-ontologists can use when building bio-ontologies. They offer a means of creating rich and rigorous bio-ontologies with reduced effort. The concept of Ontology Design Patterns is described and documentation and application methodologies for Ontology Design Patterns are presented. Some real-world use cases of Ontology Design Patterns are provided and tested in the Cell Cycle Ontology. Ontology Design Patterns, including those tested in the Cell Cycle Ontology, can be explored in the Ontology Design Patterns public catalogue that has been created based on the documentation system presented (<url>http://odps.sourceforge.net/</url>).</p> <p>Conclusions</p> <p>Ontology Design Patterns provide a method for rich and rigorous modelling in bio-ontologies. They also offer advantages at different development levels (such as design, implementation and communication) enabling, if used, a more modular, well-founded and richer representation of the biological knowledge. This representation will produce a more efficient knowledge management in the long term.</p