386,182 research outputs found

    Cerulean: A hybrid assembly using high throughput short and long reads

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    Genome assembly using high throughput data with short reads, arguably, remains an unresolvable task in repetitive genomes, since when the length of a repeat exceeds the read length, it becomes difficult to unambiguously connect the flanking regions. The emergence of third generation sequencing (Pacific Biosciences) with long reads enables the opportunity to resolve complicated repeats that could not be resolved by the short read data. However, these long reads have high error rate and it is an uphill task to assemble the genome without using additional high quality short reads. Recently, Koren et al. 2012 proposed an approach to use high quality short reads data to correct these long reads and, thus, make the assembly from long reads possible. However, due to the large size of both dataset (short and long reads), error-correction of these long reads requires excessively high computational resources, even on small bacterial genomes. In this work, instead of error correction of long reads, we first assemble the short reads and later map these long reads on the assembly graph to resolve repeats. Contribution: We present a hybrid assembly approach that is both computationally effective and produces high quality assemblies. Our algorithm first operates with a simplified version of the assembly graph consisting only of long contigs and gradually improves the assembly by adding smaller contigs in each iteration. In contrast to the state-of-the-art long reads error correction technique, which requires high computational resources and long running time on a supercomputer even for bacterial genome datasets, our software can produce comparable assembly using only a standard desktop in a short running time.Comment: Peer-reviewed and presented as part of the 13th Workshop on Algorithms in Bioinformatics (WABI2013

    Workshop time management system

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    The Workshop Time Management System is a web-based application that is specially built for the third party logistics provider and workshops, with the goals to improve efficiency and shortening processing time by automating all processes and workflows involved in a central application. This project will focus more on human resources planning and efficiency such as pending job assignment, mechanic job log, task efficiency, evaluation of mechanic performance and mechanic duty shift control. By implementing the new solutions to the system, the maintenance staff will be better informed of pending jobs or faults at the workshop whereas the mechanics will be able to access the necessary information instantly to rectify the problem. A number of improvements on the existing features will also be included, such as urgent task handling, vehicle quality inspection and job activation to ensure more accurate time estimation and further improve the flexibility of the system in handling the various situations. The project will be carried out systematically with the waterfall model of Software Development Life Cycle and Structured System Analysis and Design Methodology. The business process and environment is analyzed to enable a more thorough understanding of the problems, opportunities and directives that triggered the project. Overall, this project is expected to deliver a range of mission-critical applications, including a proprietary environmental compliance database for its corporate administrative staff, and a fleet management application for its vehicle maintenance crew at the workshop

    Software Sustainability: The Modern Tower of Babel

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    <p>The aim of this paper is to explore the emerging definitions of software sustainability from the field of software engineering in order to contribute to the question, what is software sustainability?</p

    Improving Practices in a Small Software Firm: An Ambidextrous Perspective

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    Despite documented best practices and specialized tools, software organizations struggle to deliver quality software that is on time, within budget, and meets customer requirements. Managers seeking improved software project outcomes face two dominant software paradigms which differ in their emphasis on upfront planning, customer collaboration, and product documentation: plan-driven and agile. Rather than promoting one approach over the other, this research advocates improving software management practices by developing the organization’s ambidextrous capability. Ambidextrous organizations have the ability to simultaneously succeed at two seemingly contradictory capabilities (e.g. discipline and agility) which leads to enhanced organizational performance. Overall, this study asks the question: How can an ambidextrous perspective facilitate improvement in software practices? Driven by this question, and based on a two year action research study at a small software firm, TelSoft, the objectives of this research are to: 1. Identify dualities involved in improving software practices 2. Design interventions based on these dualities to improve software practices 3. Explore the process of becoming an ambidextrous software organization The resulting dissertation consists of a summary and four papers that each identify and address particular dualities encountered during software process improvement. The first paper asserts that both process-driven and perception-driven inquiry should be used during assessment of software practices, presents a model that shows how this combination can occur, and demonstrates the use of this model at TelSoft. The second paper explicates two theories for understanding and resolving issues in requirements engineering practice – repeat-ability and response-ability – and argues for the need to negotiate between the two. The third paper identifies a tension between managing legacy and current processes and proposes a model for software process reengineering, a systematic process for leveraging legacy processes created during prior SPI efforts. Finally, the fourth paper applies the theoretical lens of ambidexterity to understand the overall change initiative in terms of the tension between alignment and adaptability. The study used a variety of data sources to diagnose software practices, including semi-structured interviews, software process documents, meeting interactions, and workshop discussions. Subsequently, we established, facilitated, and tracked focused improvement teams in the areas of customer relations, requirements management, quality assurance, project portfolio management, and process management. Furthermore, we created and trained two management teams with responsibility for ongoing management of SPI and project portfolio management respectively. We argue that these activities improved software practices at TelSoft and provided a stronger foundation for continuous improvement. Keywords: Ambidexterity, software process improvement (SPI), action research, requirements engineering assessment, action planning, software process reengineering, software management

    Model Based Development of Quality-Aware Software Services

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    Modelling languages and development frameworks give support for functional and structural description of software architectures. But quality-aware applications require languages which allow expressing QoS as a first-class concept during architecture design and service composition, and to extend existing tools and infrastructures adding support for modelling, evaluating, managing and monitoring QoS aspects. In addition to its functional behaviour and internal structure, the developer of each service must consider the fulfilment of its quality requirements. If the service is flexible, the output quality depends both on input quality and available resources (e.g., amounts of CPU execution time and memory). From the software engineering point of view, modelling of quality-aware requirements and architectures require modelling support for the description of quality concepts, support for the analysis of quality properties (e.g. model checking and consistencies of quality constraints, assembly of quality), tool support for the transition from quality requirements to quality-aware architectures, and from quality-aware architecture to service run-time infrastructures. Quality management in run-time service infrastructures must give support for handling quality concepts dynamically. QoS-aware modeling frameworks and QoS-aware runtime management infrastructures require a common evolution to get their integration

    Towards an Intellectual Property Rights Strategy for Innovation in Europe

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    On October 13, 2009 the Science and Technology Options Assessment Panel (STOA) together with Knowledge4Innovation/The Lisbon Forum, supported by Technopolis Consulting Group and TNO, organised a half-day workshop entitled ‘Towards an Intellectual Property Rights Strategy for Innovation in Europe’. This workshop was part of the 1st European Innovation Summit at the European Parliament which took place on 13 October and 14 October 2009. It addressed the topics of the evolution and current issues concerning the European Patent System as well as International Protection and Enforcement of IPR (with special consideration of issues pertaining to IP enforcement in the Digital Environment). Conclusions drawn point to the benefits of a comprehensive European IPR strategy, covering a broad range of IP instruments and topics

    Technical Debt Prioritization: State of the Art. A Systematic Literature Review

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    Background. Software companies need to manage and refactor Technical Debt issues. Therefore, it is necessary to understand if and when refactoring Technical Debt should be prioritized with respect to developing features or fixing bugs. Objective. The goal of this study is to investigate the existing body of knowledge in software engineering to understand what Technical Debt prioritization approaches have been proposed in research and industry. Method. We conducted a Systematic Literature Review among 384 unique papers published until 2018, following a consolidated methodology applied in Software Engineering. We included 38 primary studies. Results. Different approaches have been proposed for Technical Debt prioritization, all having different goals and optimizing on different criteria. The proposed measures capture only a small part of the plethora of factors used to prioritize Technical Debt qualitatively in practice. We report an impact map of such factors. However, there is a lack of empirical and validated set of tools. Conclusion. We observed that technical Debt prioritization research is preliminary and there is no consensus on what are the important factors and how to measure them. Consequently, we cannot consider current research conclusive and in this paper, we outline different directions for necessary future investigations
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