1,767 research outputs found

    Workflow Management Systems and ERP Systems: Differences, Commonalities, and Applications

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    Two important classes of information systems, Workflow Management Systems(WfMSs) and Enterprise Resource Planning (ERP) systems, have been used to support e-business process redesign, integration, and management. While both technologies can help with business process automation, data transfer, and information sharing, the technological approach and features of solutions provided by WfMS and ERP are different. Currently, there is a lack of understanding of these two classes of information systems in the industry and academia, thus hindering their effective applications. In this paper, we present a comprehensive comparison between these two classes of systems. We discuss how the two types of systems can be used independently or together to develop intra- and inter-organizational application solutions. In particular, we also explore the roles of WfMS and ERP in the next generation of IT architecture based on web services. Our findings should help businesses make better decisions in the adoption of both WfMS and ERP in their e-business strategies

    Multithreaded variant calling in elPrep 5

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    We present elPrep 5, which updates the elPrep framework for processing sequencing alignment/map files with variant calling. elPrep 5 can now execute the full pipeline described by the GATK Best Practices for variant calling, which consists of PCR and optical duplicate marking, sorting by coordinate order, base quality score recalibration, and variant calling using the haplotype caller algorithm. elPrep 5 produces identical BAM and VCF output as GATK4 while significantly reducing the runtime by parallelizing and merging the execution of the pipeline steps. Our benchmarks show that elPrep 5 speeds up the runtime of the variant calling pipeline by a factor 8-16x on both whole-exome and whole-genome data while using the same hardware resources as GATK4. This makes elPrep 5 a suitable drop-in replacement for GATK4 when faster execution times are needed

    An efficient and accurate framework for large-scale sequences of DNA barcodes

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    Dissertação de mestrado integrado em Engenharia InformáticaDNA barcodes are short sequences of pre-defined gene regions that contain a sufficient amount of intra- and inter-species genetic information. High-throughput sequencing techniques are currently used to identify large sequences of DNA barcodes in a species genome, in a relatively short time. Domain experts require adequate self-contained tools to accurately and efficiently process DNA barcode data in a reasonable time, taking advantage of current parallel and heterogeneous computing systems. They also expect to use these tools on different computing platforms, from laptops to high-performance servers, without requiring a broad knowledge in software engineering to develop efficient computational applications. The main goal of this project was to develop a framework and associated user-friendly tools for domain experts to efficiently support DNA barcoding studies, providing an abstraction of the performance issues. 4SpecID is the key outcome of this work: an application software that integrates a semi-automated auditing and annotation tool for reference libraries, to ensure the quality standards of the compiled data, aiming to enable a grounded decision when identifying species from DNA barcodes. Its graphics interface aids the end user to specify the operations and it also simplifies data filtering and remote file handling. The C++ ported version (from MATLAB) was fully tested and is more robust than the original version. Architecture features common to laptop and compute servers were exploited, namely parallel programming techniques and memory models. The presented validation and performance results show significant improvements on execution times, not only on the sequential version, but also by using the available parallel capabilities of the underlying computing platforms.Os códigos de barras de ADN são pequenas sequência de regiões genéticas predefinidas que contêm uma quantidade suficiente de informação genética intra e interespécies. Técnicas de sequenciamento de alto desempenho são usadas na identificação de grandes sequências de códigos de barras de ADN no genoma de uma espécie. No entanto, é necessário que sejam desenvolvidas ferramentas adequadas para que os especialistas de domínio processem dados de código de barras de ADN de forma precisa e num intervalo de tempo viável, utilizando os sistemas de computação paralelos e heterogêneos que existem. Destas ferramentas é esperado que possam ser utilizadas recorrendo a diferentes plataformas de computação, de laptops a servidores de alto desempenho, sem exigir um amplo conhecimento em engenharia de software para serem utilizadas ou usadas para a criação de outras ferramentas. O objetivo principal deste projeto é desenvolver uma estrutura que forneça uma abstração dos possíveis desafios de desempenho e permitir que especialistas no domínio tenham uma forma computacional eficiente para realizar um estudo de código de barras de DNA. Neste projecto desenvolveu-se uma ferramenta, 4SpecID, que visa permitir uma decisão fundamentada na identificação de espécies através de códigos de barras de DNA: uma auditoria semi-automática e ferramenta de anotação para bibliotecas de referência, para garantir os padrões de qualidade dos dados compilados. Este projeto também explorou as vantagens das arquiteturas de servidores de computação e laptops mais comuns, como técnicas de programação paralela e modelos de memória. Os resultados de validação e desempenho apresentados mostram que é possível obter melhores tempos de execução utilizando as características disponíveis das plataformas subjacentes

    A Survey of Languages for Specifying Dynamics: A Knowledge Engineering Perspective

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    A number of formal specification languages for knowledge-based systems has been developed. Characteristics for knowledge-based systems are a complex knowledge base and an inference engine which uses this knowledge to solve a given problem. Specification languages for knowledge-based systems have to cover both aspects. They have to provide the means to specify a complex and large amount of knowledge and they have to provide the means to specify the dynamic reasoning behavior of a knowledge-based system. We focus on the second aspect. For this purpose, we survey existing approaches for specifying dynamic behavior in related areas of research. In fact, we have taken approaches for the specification of information systems (Language for Conceptual Modeling and TROLL), approaches for the specification of database updates and logic programming (Transaction Logic and Dynamic Database Logic) and the generic specification framework of abstract state machine

    Automatic Verification of Erlang-Style Concurrency

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    This paper presents an approach to verify safety properties of Erlang-style, higher-order concurrent programs automatically. Inspired by Core Erlang, we introduce Lambda-Actor, a prototypical functional language with pattern-matching algebraic data types, augmented with process creation and asynchronous message-passing primitives. We formalise an abstract model of Lambda-Actor programs called Actor Communicating System (ACS) which has a natural interpretation as a vector addition system, for which some verification problems are decidable. We give a parametric abstract interpretation framework for Lambda-Actor and use it to build a polytime computable, flow-based, abstract semantics of Lambda-Actor programs, which we then use to bootstrap the ACS construction, thus deriving a more accurate abstract model of the input program. We have constructed Soter, a tool implementation of the verification method, thereby obtaining the first fully-automatic, infinite-state model checker for a core fragment of Erlang. We find that in practice our abstraction technique is accurate enough to verify an interesting range of safety properties. Though the ACS coverability problem is Expspace-complete, Soter can analyse these verification problems surprisingly efficiently.Comment: 12 pages plus appendix, 4 figures, 1 table. The tool is available at http://mjolnir.cs.ox.ac.uk/soter
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