Biana: a software framework for compiling biological interactions and analyzing networks

Background: The analysis and usage of biological data is hindered by the spread of information across multiple repositories and the difficulties posed by different nomenclature systems and storage formats. In particular, there is an important need for data unification in the study and use of protein-protein interactions. Without good integration strategies, it is difficult to analyze the whole set of available data and its properties.Results: We introduce BIANA (Biologic Interactions and Network Analysis), a tool for biological information integration and network management. BIANA is a Python framework designed to achieve two major goals: i) the integration of multiple sources of biological information, including biological entities and their relationships, and ii) the management of biological information as a network where entities are nodes and relationships are edges. Moreover, BIANA uses properties of proteins and genes to infer latent biomolecular relationships by transferring edges to entities sharing similar properties. BIANA is also provided as a plugin for Cytoscape, which allows users to visualize and interactively manage the data. A web interface to BIANA providing basic functionalities is also available. The software can be downloaded under GNU GPL license from http://sbi.imim.es/web/BIANA.php.Conclusions: BIANA's approach to data unification solves many of the nomenclature issues common to systems dealing with biological data. BIANA can easily be extended to handle new specific data repositories and new specific data types. The unification protocol allows BIANA to be a flexible tool suitable for different user requirements: non-expert users can use a suggested unification protocol while expert users can define their own specific unification rules.

Análise de riscos e dificuldades no desenvolvimento de software

O trabalho que ora apresentamos tem como tema “ O Ensino da Expressão e Educação Físico-Motora nas Escolas do Ensino Básico de São Lourenço dos Órgãos – Pós – Reforma.” O mesmo tem como horizonte temporal o ano lectivo 2006/07 e abarca as Escolas Básicas do novel Município de São Lourenço dos Órgãos. O ensino da Expressão e Educação Físico – Motora (E.E.F.M.) reveste-se de enorme importância e, nos últimos anos, tem-se emprestado muita atenção a esta área, quer seja a nível planetário, quer seja a nível nacional. Hoje, muitos estudiosos preocupam-se com o ensino desta área e, em consequência procuram fazer algo que permita a promoção da mesma e seja vista como as outras ditas académicas, isto porque todos estão cientes da sua importância e pertinência dentro do sistema escolar. Diante de tudo o que já foi dito e na possibilidade de poder dar um contributo a bem da educação no nosso pais, em geral, e no Município de São Lourenço dos Órgãos, em particular, pretendemos compreender, entretanto, porque é que muitos professores não leccionam ou raras vezes leccionam a área da Expressão e Educação Físico – Motora.

ZNRD1 (zinc ribbon domain-containing 1) is a host cellular factor that influences HIV-1 replication and disease progression.

BACKGROUND: Human immunodeficiency virus (HIV) takes advantage of multiple host proteins to support its own replication. The gene ZNRD1 (zinc ribbon domain-containing 1) has been identified as encoding a potential host factor that influenced disease progression in HIV-positive individuals in a genomewide association study and also significantly affected HIV replication in a large-scale in vitro short interfering RNA (siRNA) screen. Genes and polymorphisms identified by large-scale analysis need to be followed up by means of functional assays and resequencing efforts to more precisely map causal genes. METHODS: Genotyping and ZNRD1 gene resequencing for 208 HIV-positive subjects (119 who experienced long-term nonprogression [LTNP] and 89 who experienced normal disease progression) was done by either TaqMan genotyping assays or direct sequencing. Genetic association analysis was performed with the SNPassoc package and Haploview software. siRNA and short hairpin RNA (shRNA) specifically targeting ZNRD1 were used to transiently or stably down-regulate ZNRD1 expression in both lymphoid and nonlymphoid cells. Cells were infected with X4 and R5 HIV strains, and efficiency of infection was assessed by reporter gene assay or p24 assay. RESULTS: Genetic association analysis found a strong statistically significant correlation with the LTNP phenotype (single-nucleotide polymorphism rs1048412; [Formula: see text]), independently of HLA-A10 influence. siRNA-based functional analysis showed that ZNRD1 down-regulation by siRNA or shRNA impaired HIV-1 replication at the transcription level in both lymphoid and nonlymphoid cells. CONCLUSION: Genetic association analysis unequivocally identified ZNRD1 as an independent marker of LTNP to AIDS. Moreover, in vitro experiments pointed to viral transcription as the inhibited step. Thus, our data strongly suggest that ZNRD1 is a host cellular factor that influences HIV-1 replication and disease progression in HIV-positive individuals.

A new chance-constrained maximum capture location problem

The paper presents a new model based on the basic Maximum Capture model,MAXCAP. The New Chance Constrained Maximum Capture modelintroduces astochastic threshold constraint, which recognises the fact that a facilitycan be open only if a minimum level of demand is captured. A metaheuristicbased on MAX MIN ANT system and TABU search procedure is presented tosolve the model. This is the first time that the MAX MIN ANT system isadapted to solve a location problem. Computational experience and anapplication to 55 node network are also presented.

Aplicación de software de interpolación en las evaluaciones hidroacústicas de la biomasa y distribución de recursos pelágicos

Propone una alternativa para el procesamiento de datos de ecointegración acústica cuando se pretende obtener la distribución y el nivel de biomasa de recursos marinos, mediante la aplicación de un software de interpolación de datos.

Surviving in a competitive spatial market: The threshold capture model

Most facility location decision models ignore the fact that for a facility to survive it needs a minimum demand level to cover costs. In this paper we present a decision model for a firm thatwishes to enter a spatial market where there are several competitors already located. This market is such that for each outlet there is a demand threshold level that has to be achievedin order to survive. The firm wishes to know where to locate itsoutlets so as to maximize its market share taking into account the threshold level. It may happen that due to this new entrance, some competitors will not be able to meet the threshold and therefore will disappear. A formulation is presented together with a heuristic solution method and computational experience.

KemapMobile: una adaptación de la herramienta software KeMap a la plataforma Android

Este trabajo describe el proceso de creación de la herramienta de software KemapMobile para la plataforma Android. El artefacto es una adaptación del software de escritorio KeMap que se integra en la plataforma educativa VerilUOC y permite a los estudiantes conectarse a ella para descargar, en la aplicación, ejercicios con los que poner a prueba y afianzar sus conocimientos sobre la simplificación de funciones lógicas booleanas con mapas de Karnaugh y tablas de verdad. La arquitectura cliente-servidor de la aplicación permite a los estudiantes disponer de ejercicios personalizados y al profesorado obtener datos sobre el uso de la herramienta y sobre la progresión del alumnado.

Projecto de Software Utilizando a UML Caso Prático: Modelação do Subsistema de Secretaria Digital – Universidade Jean Piaget

O presente trabalho demonstra a utilização da linguagem UML na modelação (também se aplica à projecção e desenvolvimento) de sistemas. Incorpora um estudo de caso que consiste na modelação (também, propostas de implementação, sobretudo ao nível do modelo de dados) de um subsistema que faz parte do Sistema de Gestão Académico (SIAC) na Universidade Jean Piaget de Cabo Verde (Unipiaget).O trabalho surge após a percepção das dificuldades em que os alunos e não só, se enfrentam para terem acessos aos dados académicos, principalmente nos períodos em que estes se encontram de férias, daí a necessidade de implementação da Universidade Digital. Assim, aproveitando as boas práticas do desenvolvimento de sistemas, iniciou-se o processo da subdivisão do problema maior (Universidade Digital) em subproblemas (vários subsistemas), cujo projecto se concentra na análise e modelação do subsistema de secretaria digital. A metodologia adoptada foi a do diálogo directo programado e não programado, aplicação de questionários e entrevistas, assim como a da proposta de melhorias.Sendo assim, o trabalho iniciou-se com o levantamento de requisitos e avaliado face ao comportamento de subsistema no seu modo presencial (estado actual). E, por fim foram efectuadas propostas de melhorias, as quais permitirão alcançar a satisfação dos potênciais actores (utilizador do sistema).

Laboratorio virtual de química en software libre para la preparación de disoluciones

Con este TFM se muestra un laboratorio virtual de química a través de diversos experimentos para la preparación de disoluciones en función de sus expresiones de concentración.

Is the capture success of orchid bees (Hymenoptera, Apoidea) influenced by different baited trap designs? A case study from southern Brazil

Orchid bees are increasingly applied on Neotropical biomonitoring and bioindication studies due to the relative easiness of sampling and identification when compared to other bee groups. A considerable number of orchid bee community studies have been adopting baited traps as a sampling method, especially for replication purposes. However, the trap attributes are variable, and hitherto no evaluation of different designs was carried out. Here, five attributes of baited traps were tested: trap volume, number of entrance holes, presence of landing platform, kind of landing platform, and fixation content. We use Mann-Whitney tests to access differences in richness and abundance capture rates for each trap design. We found that volume, number of entrance holes, and fixation content do not influence orchid bees capture. However, the design without landing platforms had a significantly higher capture rate for richness when compared with sanded landing platforms. On the other hand, analyzing the kind of landing platform, we detected a significantly higher richness and abundance for the trap with landing platforms glued with sand. Despite the fact that the effects of different designs tested here were very punctual, we consider that results from samples taken with different baited trap designs are comparable. Some adjustments on trap design can be done according to the particularities of future studies.

How many diagnosis fields are needed to capture safety events in administrative data? Findings and recommendations from the WHO ICD-11 Topic Advisory Group on Quality and Safety

OBJECTIVE: As part of the WHO ICD-11 development initiative, the Topic Advisory Group on Quality and Safety explores meta-features of morbidity data sets, such as the optimal number of secondary diagnosis fields. DESIGN: The Health Care Quality Indicators Project of the Organization for Economic Co-Operation and Development collected Patient Safety Indicator (PSI) information from administrative hospital data of 19-20 countries in 2009 and 2011. We investigated whether three countries that expanded their data systems to include more secondary diagnosis fields showed increased PSI rates compared with six countries that did not. Furthermore, administrative hospital data from six of these countries and two American states, California (2011) and Florida (2010), were analysed for distributions of coded patient safety events across diagnosis fields. RESULTS: Among the participating countries, increasing the number of diagnosis fields was not associated with any overall increase in PSI rates. However, high proportions of PSI-related diagnoses appeared beyond the sixth secondary diagnosis field. The distribution of three PSI-related ICD codes was similar in California and Florida: 89-90% of central venous catheter infections and 97-99% of retained foreign bodies and accidental punctures or lacerations were captured within 15 secondary diagnosis fields. CONCLUSIONS: Six to nine secondary diagnosis fields are inadequate for comparing complication rates using hospital administrative data; at least 15 (and perhaps more with ICD-11) are recommended to fully characterize clinical outcomes. Increasing the number of fields should improve the international and intra-national comparability of data for epidemiologic and health services research, utilization analyses and quality of care assessment.

Manual de uso del software Ocean Data View (ODV)

El presente manual de uso del software de visualización de datos “Ocean Data View” (ODV) describe la exploración, análisis y visualización de datos oceanográficos según el formato de la colección mundial de base de datos del océano “World Ocean Database” (WOD). El manual comprende 6 ejercicios prácticos donde se describe paso a paso la creación de las metavariables, la importación de los datos y su visualización mediante mapas de latitud, longitud y gráficos de dispersión, secciones verticales y series de tiempo. Se sugiere el uso extensivo del ODV para la visualización de datos oceanográficos por el personal científico del IMARPE.