11,128 research outputs found

    FAST: FAST Analysis of Sequences Toolbox.

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    FAST (FAST Analysis of Sequences Toolbox) provides simple, powerful open source command-line tools to filter, transform, annotate and analyze biological sequence data. Modeled after the GNU (GNU's Not Unix) Textutils such as grep, cut, and tr, FAST tools such as fasgrep, fascut, and fastr make it easy to rapidly prototype expressive bioinformatic workflows in a compact and generic command vocabulary. Compact combinatorial encoding of data workflows with FAST commands can simplify the documentation and reproducibility of bioinformatic protocols, supporting better transparency in biological data science. Interface self-consistency and conformity with conventions of GNU, Matlab, Perl, BioPerl, R, and GenBank help make FAST easy and rewarding to learn. FAST automates numerical, taxonomic, and text-based sorting, selection and transformation of sequence records and alignment sites based on content, index ranges, descriptive tags, annotated features, and in-line calculated analytics, including composition and codon usage. Automated content- and feature-based extraction of sites and support for molecular population genetic statistics make FAST useful for molecular evolutionary analysis. FAST is portable, easy to install and secure thanks to the relative maturity of its Perl and BioPerl foundations, with stable releases posted to CPAN. Development as well as a publicly accessible Cookbook and Wiki are available on the FAST GitHub repository at https://github.com/tlawrence3/FAST. The default data exchange format in FAST is Multi-FastA (specifically, a restriction of BioPerl FastA format). Sanger and Illumina 1.8+ FastQ formatted files are also supported. FAST makes it easier for non-programmer biologists to interactively investigate and control biological data at the speed of thought

    Index to NASA Tech Briefs, 1975

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    This index contains abstracts and four indexes--subject, personal author, originating Center, and Tech Brief number--for 1975 Tech Briefs

    A gearbox model for processing large volumes of data by using pipeline systems encapsulated into virtual containers

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    Software pipelines enable organizations to chain applications for adding value to contents (e.g., confidentially, reliability, and integrity) before either sharing them with partners or sending them to the cloud. However, the pipeline components add overhead when processing large volumes of data, which can become critical in real-world scenarios. This paper presents a gearbox model for processing large volumes of data by using pipeline systems encapsulated into virtual containers. In this model, the gears represent applications, whereas gearboxes represent software pipelines. This model was implemented as a collaborative system that automatically performs Gear up (by using parallel patterns) and/or Gear down (by using in-memory storage) until all gears produce uniform data processing velocities. This model reduces delays and bottlenecks produced by the heterogeneous performance of applications included in software pipelines. The new container tool has been designed to encapsulate both the collaborative system and the software pipelines into a virtual container and deploy it on IT infrastructures. We conducted case studies to evaluate the performance of when processing medical images and PDF repositories. The incorporation of a capsule to a cloud storage service for pre-processing medical imagery was also studied. The experimental evaluation revealed the feasibility of applying the gearbox model to the deployment of software pipelines in real-world scenarios as it can significantly improve the end-user service experience when pre-processing large-scale data in comparison with state-of-the-art solutions such as Sacbe and Parsl.This work has been partially supported by the “Spanish Ministerio de Economia y Competitividad ” under the project grant TIN2016-79637-P “Towards Unification of HPC and Big Data paradigms”

    Status description and evaluation of the complete water supply system of Hinnerup

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    El trabajo realizado evalúa el estado de la planta de abastecimiento de agua de Hinnerup en todas sus fases: abstracción (incluyendo una evaluación del estado de los acuíferos), tratamiento, almacenamiento y distribución. Además, se espera un crecimiento de la zona urbana en los próximos años, con lo que se evalúa la posibilidad de mantener el suministro de calidad para la nueva cantidad que hay que abastecer, de nuevo en todas las fases del proceso. Para ello, se realiza una pertinente estimación del consumo en esta nueva zona urbana; así como una evaluación del punto de conexión de la misma y de la compatibilidad con el sistema existente. Por último, se realiza una evaluación de riesgos con el fin de determinar la vulnerabilidad del suministro de agua potable de la zona abastecida por esta planta, concluyendo en que el riesgo es bajo.The conducted report assesses the status of the Hinnerup water supply plant in all its phases: abstraction (including an assessment of the state of the aquifers), treatment, storage and distribution in the water supply area. Moreover, an urban area growth is expected in the upcoming years. Hence, the quality provided must still accomplish certain parameters in all the phases of the process. On this purpose, a justified estimation of the consumption in this new urban area is conducted, as well as an assessment of its connection point and compatibility with the existing system. Lastly, a risk assessment is performed in order to determine the vulnerability of the water supply system, concluding that the risk in general terms is low.Departamento de Construcciones Arquitectónicas, Ingeniería del Terreno y Mecánica de los Medios Continuos y Teoría de EstructurasGrado en Ingeniería Mecánic

    Analysing tactics in architectural patterns

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    We present an approach to analyse the application of tactics in architectural patterns. We define and illustrate the approach by resorting to Archery, a language for specifying, analysing and verifying architectural patterns. The approach consists of characterising the design principles of an architectural pattern as constraints, expressed in the language, and then, establishing a refinement relation based on their satisfaction. The application of tactics preserving refinement preserves the original design principles expressed themselves as constraints for the architectural pattern. The paper’s focus on fault-tolerance tactics, and identifies a set of requirements for a semantic framework characterising them. Model transformations to represent their application are discussed and illustrated through two case studies.FC

    Classifying and evaluating architecture design methods

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    The concept of software architecture has gained a wide popularity and is generally considered to play a fundamental role in coping with the inherent difficulties of the development of large-scale and complex software systems. This document first gives a definition of architectures. Second, a meta-model for architecture design methods is presented. This model is used for classifying and evaluating various architecture design approaches. The document concludes with the description of the identified problems
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