An Ontological Approach to Analyze the Data Required by a System Quality Scheme

According to IEEE, software quality is the degree to which software possesses a desired combination of attributes. Quality attributes have been of interest to the software community since 1970 and in the past few years this interest has increase. However, still is not clear how product quality should apply in the development process. The need to know what quality characteristics influence a specific entity and which is the information required to cover its measurement is the objective of this work. This paper presents an ontology to document a quality scheme with a specification based on ISO/IEC 25010. This contribution includes rules and queries that help to determine the data required to carry out the measurement process.Sociedad Argentina de Informática e Investigación Operativa (SADIO

Empirical codon substitution matrix

BACKGROUND: Codon substitution probabilities are used in many types of molecular evolution studies such as determining Ka/Ks ratios, creating ancestral DNA sequences or aligning coding DNA. Until the recent dramatic increase in genomic data enabled construction of empirical matrices, researchers relied on parameterized models of codon evolution. Here we present the first empirical codon substitution matrix entirely built from alignments of coding sequences from vertebrate DNA and thus provide an alternative to parameterized models of codon evolution. RESULTS: A set of 17,502 alignments of orthologous sequences from five vertebrate genomes yielded 8.3 million aligned codons from which the number of substitutions between codons were counted. From this data, both a probability matrix and a matrix of similarity scores were computed. They are 64 × 64 matrices describing the substitutions between all codons. Substitutions from sense codons to stop codons are not considered, resulting in block diagonal matrices consisting of 61 × 61 entries for the sense codons and 3 × 3 entries for the stop codons. CONCLUSION: The amount of genomic data currently available allowed for the construction of an empirical codon substitution matrix. However, more sequence data is still needed to construct matrices from different subsets of DNA, specific to kingdoms, evolutionary distance or different amount of synonymous change. Codon mutation matrices have advantages for alignments up to medium evolutionary distances and for usages that require DNA such as ancestral reconstruction of DNA sequences and the calculation of Ka/Ks ratios

A model for documenting architectural decisions

A software architecture is the result of architectural design decisions. Documenting a software architecture should not only describe the final model, but also why the architecture looks as it does. During the software architecture design process, several decisions are made, which need to be captured and documented in a systematic way to prevent knowledge vaporization and high architecture’ costs of change. In this work, a model for capturing, documenting and recovering architectural design processes and their underlying design rationale is proposed. The design process is envisioned under an operational perspective, where design decisions are represented as sequences of operations. Besides, the model is extensible to manage several design products types from different domains and views, including aspects of architectural rationale. Complementary, the proposal provides a semi-automatic mechanism for generating architectural rationale documents based on the use of templates.Sociedad Argentina de Informática e Investigación Operativa (SADIO

OMA 2011: orthology inference among 1000 complete genomes

OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genomes. Initiated in 2004, the project is at its 11th release. It now includes 1000 genomes, making it one of the largest resources of its kind. Here, we describe recent developments in terms of species covered; the algorithmic pipeline—in particular regarding the treatment of alternative splicing, and new features of the web (OMA Browser) and programming interface (SOAP API). In the second part, we review the various representations provided by OMA and their typical applications. The database is publicly accessible at http://omabrowser.or

Poly(ethylene) glycols and mechanochemistry for the preparation of bioactive 3,5-disubstituted hydantoins

International audienceMechanochemistry was effective for the preparation of 3,5-disubstituted hydantoins from a-amino methyl esters, using either 1,1 0-carbonyldiimidazole (CDI) or alkyl isocyanates. The preparation of the antimicrobial additives, 3-allyl-5,5 0-dimethyl hydantoin (ADMH) and 1-chloro-3-ethyl-5,5 0-dimethyl hydantoin (CEDMH) were performed by grinding. A chlorination reaction, never described before by mechanochemistry was achieved by Ca(ClO) 2 , while the preparation of the bioactive anticonvulsant marketed drug ethotoin was achieved by a novel approach based on poly(ethylene) glycol (PEGs) assisted grinding

New distributional records for the Crowned Eagle (<i>Harpyhaliaetus coronatus</i>) in Western Argentina

The Crowned Eagle, <i>Harpyhaliaetus coronatus</i>, is regarded as endangered because of its low population numbers, the destruction of potential habitat, and the scarcity of records. Ecological studies on this species are required to develop conservation plans. We present 15 new distributional records obtained in the last 11 years. Based on the frequency of observed individuals and groups, and on the continuity of the habitats where it was recorded, we propose a priority area for ecological research on this species

New distributional records for the Crowned Eagle (<i>Harpyhaliaetus coronatus</i>) in Western Argentina

The Crowned Eagle, <i>Harpyhaliaetus coronatus</i>, is regarded as endangered because of its low population numbers, the destruction of potential habitat, and the scarcity of records. Ecological studies on this species are required to develop conservation plans. We present 15 new distributional records obtained in the last 11 years. Based on the frequency of observed individuals and groups, and on the continuity of the habitats where it was recorded, we propose a priority area for ecological research on this species

An Alternative Model of Amino Acid Replacement

The observed correlations between pairs of homologous protein sequences are typically explained in terms of a Markovian dynamic of amino acid substitution. This model assumes that every location on the protein sequence has the same background distribution of amino acids, an assumption that is incompatible with the observed heterogeneity of protein amino acid profiles and with the success of profile multiple sequence alignment. We propose an alternative model of amino acid replacement during protein evolution based upon the assumption that the variation of the amino acid background distribution from one residue to the next is sufficient to explain the observed sequence correlations of homologs. The resulting dynamical model of independent replacements drawn from heterogeneous backgrounds is simple and consistent, and provides a unified homology match score for sequence-sequence, sequence-profile and profile-profile alignment.Comment: Minor improvements. Added figure and reference