Squid – a simple bioinformatics grid

BACKGROUND: BLAST is a widely used genetic research tool for analysis of similarity between nucleotide and protein sequences. This paper presents a software application entitled "Squid" that makes use of grid technology. The current version, as an example, is configured for BLAST applications, but adaptation for other computing intensive repetitive tasks can be easily accomplished in the open source version. This enables the allocation of remote resources to perform distributed computing, making large BLAST queries viable without the need of high-end computers. RESULTS: Most distributed computing / grid solutions have complex installation procedures requiring a computer specialist, or have limitations regarding operating systems. Squid is a multi-platform, open-source program designed to "keep things simple" while offering high-end computing power for large scale applications. Squid also has an efficient fault tolerance and crash recovery system against data loss, being able to re-route jobs upon node failure and recover even if the master machine fails. Our results show that a Squid application, working with N nodes and proper network resources, can process BLAST queries almost N times faster than if working with only one computer. CONCLUSION: Squid offers high-end computing, even for the non-specialist, and is freely available at the project web site. Its open-source and binary Windows distributions contain detailed instructions and a "plug-n-play" instalation containing a pre-configured example

Image Segmentation by Image Foresting Transform with Non-smooth Connectivity Functions

Abstract-Image segmentation, such as to extract an object from a background, is very useful for medical and biological image analysis. In this work, we propose new methods for interactive segmentation of multidimensional images, based on the Image Foresting Transform (IFT), by exploiting for the first time non-smooth connectivity functions (NSCF) with a strong theoretical background. The new algorithms provide global optimum solutions according to an energy function of graph cut, subject to high-level boundary constraints (polarity and shape), or consist in a sequence of paths' optimization in residual graphs. Our experimental results indicate substantial improvements in accuracy in relation to other state-of-the-art methods, by allowing the customization of the segmentation to a given target object

Sistema de alvenaria com incorporação de resíduos: blocos de terra compactada com ligante geopolimérico

A produção de resíduos é um problema comum a todas as sociedades, que importa gerir de forma adequada para proteger o meio ambiente do impacto que atividade do Homem lhe provoca. O setor da construção civil é responsável por uma percentagem muito importante dos resíduos produzidos anualmente a nível Mundial. Como tal, exige-se que os agentes ligados a este setor desenvolvam soluções construtivas que promovam a valorização dos resíduos, com base na sua reciclagem em novos materiais de construção. Estes materiais, ao entrarem no mercado e ao serem integrados nas construções, permitiram substituir parte dos materiais correntes por materiais reciclados. Da execução de uma construção resultam resíduos compostos por diversas fileiras de materiais, de onde se destacam os solos resultantes de trabalhos de escavação, que podem ser reutilizados em trabalhos de aterro/enchimento necessários em obra, mas os solos excedentes constituem um problema a gerir. Estes solos podem ser reutilizados em outras obras ou transportados para uma bolsa de solos, onde aguardam reutilização. Contudo, os solos excedentes podem constitur um recurso que pode ser valorizado através da promoção de um uso alternativo em obra. No presente artigo pretende-se caracterizar o desempenho mecânico de um sistema de alvenaria à base de blocos de terra compactada (BTC). Estes BTC foram desenvolvidos com base na incorporação de solo residual granítico (SRG), típico do Norte de Portugal, estabilizado com um ligante geopolimérico. Este ligante é obtido por ativação alcalina de um outro resíduo, proveniente da indústria energética, nomeadamente as cinzas volantes. O desempenho do sistema de alvenaria de BTC foi avaliado através de um programa experimental, constatando-se um bom desempenho mecânico da solução.Este trabalho foi financiado por fundos do FEDER através do Programa Operacional Fatores de Competitividade – COMPETE e por fundos nacionais, através da Fundação para Ciência e a Tecnologia - FCT no âmbito do projeto POCI-01-0145-FEDER-007633 e da bolsa de pósdoutoramento FRH/BPD/97082/2013. Os autores agradecem ao Pedro Esteves o seu contributo na execução do programa experimental e ao Eng.º Jorge Henriques, em representação da PEGOP – Energia Elétrica SA, pela disponibilização da cinza volante

Experimental investigation on the repair of rammed earth by means of injection of mud grouts

This paper assesses the adhesion capacity of unmodified mud grouts used to repair structural cracks on medium and large scale rammed earth specimens. Beam and wallet-specimens were manufactured using a soil from Alentejo (Portugal), whose particle size distribution had to be first corrected due to its high clay content. An “artificial” (composed by kaolin and limestone powder) and a “natural” (composed by sieved soil and limestone powder) mud grout were used to repair the specimens, which were previously tested under three-point bending and diagonal-compression and then retested. The grout injection shown to provide satisfactory results regarding the adhesion capacity, but only if it is performed with the “natural” mud grout.Fundação para a Ciência e a Tecnologia (FCT

Modelling the structural behaviour of rammed earth components

Proceedings of the Twelfth International Conference on Computational Structures Technology, B.H.V. Topping and P. Iványi, (Editors), Civil-Comp Press, Stirlingshire, Scotland.The rammed earth technique has a significant presence in the earthen built heritage, where was used to build from simple dwellings to fortresses. However, the high vulnerability of rammed earth construction to decay agents and to seismic events puts at risk their further existence and the lives of millions of people. With respect to the seismic behaviour of rammed earth walls, the understanding and modelling of their shear behaviour are topics rarely approached in literature. Nevertheless, these topics are of significant importance in the preservation and strengthening of rammed earth constructions. This paper presents experimental and numerical work where the shear behaviour of unstabilised rammed earth is analysed. The experimental program consisted in the testing of several unstabilised rammed earth wallets subject to diagonal compression, which allowed a better understanding of the shear behaviour of unstabilised rammed earth. The numerical work consists of the modelling, of the previous tests, using the finite element method and by considering both the macroand micro-modelling approaches. In general, the numerical models showed a good agreement with the experimental results.The authors would like to thank gratefully the funding provided by the Portuguese Science and Technology Foundation through project FCOMP-01-0124-FEDER-028864 (FCT-PTDC/ECM-EST/2396/2012). Furthermore, the authors wish to express their gratitude to Júlio Machado for his valuable help in the experimental program.info:eu-repo/semantics/publishedVersio

Shear behaviour characterization of dry-stack masonry made of compressed earth blocks

Como material de construção não normalizado, a terra é ainda associada à construção de subsistência dos países em desenvolvimento. Porém, as vantagens da construção em terra têm sido cada vez mais reconhecidas, nomeadamente a sua sustentabilidade. Esta mudança de paradigma tem levado ao desenvolvimento de técnicas modernas de construção em terra, particularmente a alvenaria de blocos de terra comprimida (BTC). A estabilização química tradicional do solo é um processo de melhoramento frequentemente utilizado, mas que também aumenta significativamente a energia incorporada dos BTC. Este artigo apresenta uma solução de estabilização alternativa para BTC, baseada na ativação alcalina de cinza volante. O comportamento mecânico dos BTC e da respetiva alvenaria de junta seca é estudado através de um programa experimental, que inclui a caraterização do comportamento ao corte da alvenaria.Raw earth, as a non-standard building material, is still associated to the poor construction from the developing countries. However, the advantages of earth construction have been increasingly recognized, namely its sustainability. This change of paradigm have been led to the development of modern earth construction techniques, in particular of the masonry made of compressed earth blocks (CEBs). The traditional chemical stabilization of the soil is an improvement process used frequently, but which increases significantly the embodied energy of the CEBs. This paper presents an alternative stabilisation technique for CEBs, based on the alkaline activation of fly ash. The mechanical behaviour of the CEBs and of the respective dry-stack masonry is investigated through an experimental program, which includes the characterization of the shear behaviour of the masonryFundação para a Ciência e a Tecnologia (FCT