High Performance Biological Pairwise Sequence Alignment: FPGA versus GPU versus Cell BE versus GPP

This paper explores the pros and cons of reconfigurable computing in the form of FPGAs for high performance efficient computing. In particular, the paper presents the results of a comparative study between three different acceleration technologies, namely, Field Programmable Gate Arrays (FPGAs), Graphics Processor Units (GPUs), and IBM’s Cell Broadband Engine (Cell BE), in the design and implementation of the widely-used Smith-Waterman pairwise sequence alignment algorithm, with general purpose processors as a base reference implementation. Comparison criteria include speed, energy consumption, and purchase and development costs. The study shows that FPGAs largely outperform all other implementation platforms on performance per watt criterion and perform better than all other platforms on performance per dollar criterion, although by a much smaller margin. Cell BE and GPU come second and third, respectively, on both performance per watt and performance per dollar criteria. In general, in order to outperform other technologies on performance per dollar criterion (using currently available hardware and development tools), FPGAs need to achieve at least two orders of magnitude speed-up compared to general-purpose processors and one order of magnitude speed-up compared to domain-specific technologies such as GPUs

Human-Centered Approaches in Geovisualization Design: Investigating Multiple Methods Through a Long-Term Case Study

Working with three domain specialists we investigate human-centered approaches to geovisualization following an ISO13407 taxonomy covering context of use, requirements and early stages of design. Our case study, undertaken over three years, draws attention to repeating trends: that generic approaches fail to elicit adequate requirements for geovis application design; that the use of real data is key to understanding needs and possibilities; that trust and knowledge must be built and developed with collaborators. These processes take time but modified human-centred approaches can be effective. A scenario developed through contextual inquiry but supplemented with domain data and graphics is useful to geovis designers. Wireframe, paper and digital prototypes enable successful communication between specialist and geovis domains when incorporating real and interesting data, prompting exploratory behaviour and eliciting previously unconsidered requirements. Paper prototypes are particularly successful at eliciting suggestions, especially for novel visualization. Enabling specialists to explore their data freely with a digital prototype is as effective as using a structured task protocol and is easier to administer. Autoethnography has potential for framing the design process. We conclude that a common understanding of context of use, domain data and visualization possibilities are essential to successful geovis design and develop as this progresses. HC approaches can make a significant contribution here. However, modified approaches, applied with flexibility, are most promising. We advise early, collaborative engagement with data – through simple, transient visual artefacts supported by data sketches and existing designs – before moving to successively more sophisticated data wireframes and data prototypes

Agile Requirements Engineering: A systematic literature review

Nowadays, Agile Software Development (ASD) is used to cope with increasing complexity in system development. Hybrid development models, with the integration of User-Centered Design (UCD), are applied with the aim to deliver competitive products with a suitable User Experience (UX). Therefore, stakeholder and user involvement during Requirements Engineering (RE) are essential in order to establish a collaborative environment with constant feedback loops. The aim of this study is to capture the current state of the art of the literature related to Agile RE with focus on stakeholder and user involvement. In particular, we investigate what approaches exist to involve stakeholder in the process, which methodologies are commonly used to present the user perspective and how requirements management is been carried out. We conduct a Systematic Literature Review (SLR) with an extensive quality assessment of the included studies. We identified 27 relevant papers. After analyzing them in detail, we derive deep insights to the following aspects of Agile RE: stakeholder and user involvement, data gathering, user perspective, integrated methodologies, shared understanding, artifacts, documentation and Non-Functional Requirements (NFR). Agile RE is a complex research field with cross-functional influences. This study will contribute to the software development body of knowledge by assessing the involvement of stakeholder and user in Agile RE, providing methodologies that make ASD more human-centric and giving an overview of requirements management in ASD.Ministerio de Economía y Competitividad TIN2013-46928-C3-3-RMinisterio de Economía y Competitividad TIN2015-71938-RED

Assessment and Evaluation of Sand Control Methods for a North Sea Field

Imperial Users onl

Bioconductor: open software development for computational biology and bioinformatics.

The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. The goals of the project include: fostering collaborative development and widespread use of innovative software, reducing barriers to entry into interdisciplinary scientific research, and promoting the achievement of remote reproducibility of research results. We describe details of our aims and methods, identify current challenges, compare Bioconductor to other open bioinformatics projects, and provide working examples

Quick Screening of Well Survivability in a Producing Reservoir

Imperial Users onl

Relevance, benefits, and problems of software modelling and model driven techniques—A survey in the Italian industry

Context Claimed benefits of software modelling and model driven techniques are improvements in productivity, portability, maintainability and interoperability. However, little effort has been devoted at collecting evidence to evaluate their actual relevance, benefits and usage complications. Goal The main goals of this paper are: (1) assess the diffusion and relevance of software modelling and MD techniques in the Italian industry, (2) understand the expected and achieved benefits, and (3) identify which problems limit/prevent their diffusion. Method We conducted an exploratory personal opinion survey with a sample of 155 Italian software professionals by means of a Web-based questionnaire on-line from February to April 2011. Results Software modelling and MD techniques are very relevant in the Italian industry. The adoption of simple modelling brings common benefits (better design support, documentation improvement, better maintenance, and higher software quality), while MD techniques make it easier to achieve: improved standardization, higher productivity, and platform independence. We identified problems, some hindering adoption (too much effort required and limited usefulness) others preventing it (lack of competencies and supporting tools). Conclusions The relevance represents an important objective motivation for researchers in this area. The relationship between techniques and attainable benefits represents an instrument for practitioners planning the adoption of such techniques. In addition the findings may provide hints for companies and universitie

Determinants of firm-size

Overzicht van theoretische factoren die belangrijk zijn bij het verklaren van schaalgrootte van bedrijven en verschillen in schaalgrootte tussen vergelijkbare bedrijven. Naast de theoretische factoren worden enkele relevante trends beschreven en wordt gekeken naar de impact van deze trends op de mechanismen die schaalgrootte beïnvloeden. Terwijl het aantal overnames en fusies de laatste jaren sterk is toegenomen, is ook het aantal startende bedrijven sterk gegroeid. Per saldo is het gemiddelde bedrijf in Nederland licht in omvang afgenomen. De mechanismen die schaalgrootte en verdeling van schaalgrootte beïnvloeden, zijn bekeken op het niveau van de bedrijven zelf en op het niveau van sectoren. Bij het bedrijfsniveau gaat het bijvoorbeeld om schaal- en scopevoordelen, transactiekosten, ?agency-costs? en de levenscyclus van bedrijven. Mechanismen die belangrijk zijn op het niveau van sectoren of clusters zijn bijvoorbeeld externe schaal- en scope-effecten en netwerkeffecten. Overigens is er veel overlap tussen al deze mechanismen. Trends die belangrijk zijn voor schaalgrootte zijn met name globalisering, technologische ontwikkeling en deregulering.

Proceedings of the Salford Postgraduate Annual Research Conference (SPARC) 2011

These proceedings bring together a selection of papers from the 2011 Salford Postgraduate Annual Research Conference(SPARC). It includes papers from PhD students in the arts and social sciences, business, computing, science and engineering, education, environment, built environment and health sciences. Contributions from Salford researchers are published here alongside papers from students at the Universities of Anglia Ruskin, Birmingham City, Chester,De Montfort, Exeter, Leeds, Liverpool, Liverpool John Moores and Manchester