BarraCUDA – a Fast Sequence Mapping Software using Graphics Processing Units

High-throughput DNA sequencing (HTS) instruments today are capable of generating millions of sequencing reads in a short period of time, and this represents a serious challenge to current bioinformatics pipeline in processing such an enormous amount of data in a fast and economical fashion. Modern graphics cards are powerful processing units that consist of hundreds of scalar processors in parallel in order to handle the rendering of high-definition graphics in real-time. It is this computational capability that we propose to harness in order to accelerate some of the time-consuming steps in analyzing data generated by the HTS instruments. We have developed BarraCUDA, a novel sequence mapping software that utilizes the parallelism of NVIDIA CUDA graphics cards to map sequencing reads to a particular location on a reference genome. While delivering a similar mapping fidelity as other mainstream programs , BarraCUDA is a magnitude faster in mapping throughput compared to its CPU counterparts. The software is also capable of supporting multiple CUDA devices in parallel to further accelerate the mapping throughput. BarraCUDA is designed to take advantage of the parallelism of GPU to accelerate the mapping of millions of sequencing reads generated by HTS instruments. By doing this, we could, at least in part streamline the current bioinformatics pipeline such that the wider scientific community could benefit from the sequencing technology. BarraCUDA is currently available at http://seqbarracuda.sf.net

Customizing the technology roadmapping technique for software companies

Software importance keeps growing fast and consistently for many organizations. The growth of software functionality in manufactured products and the emergence of digital media, convergent spaces including digital content, software, and multi-channels to the market, are recent examples of organizational changes where software assumed a central position for the corporate strategy. This paper analyzes the alignment between strategic objectives and software development processes at software companies and proposes a methodology to ensure that development processes are aligned with the corporate capabilities required to exploit future market opportunities. The methodology includes the categorization of different software companies according to their core capabilities and the customization of the technology roadmapping technique for software companies. The research process included the realization of case studies and a survey. (c) 2006 PICMET.

Discussion: Widening engineering horizons: Addressing the complexity of sustainable development

The following discussion is from an Institution of Civil Engineers (ICE) prestige lecture based on the original paper and delivered by the authors at the ICE in London on 24 September 2008.1 The event was chaired by Engineering Sustainability editorial panel chair, Professor Chris Rogers from Birmingham University. It was attended by an audience of 130 people as well as being watched by a similar number over a live web-cast. The web-cast can be accessed from the ICE archive for online viewing at http://scenta. interwise.com/etechb/ OnDemand/TH6509.

Impacts of concurrency, iteration, design review, and problem complexity on design project lead time and error generation

A case study of an aircraft engine manufacturer is used to analyze the effects of management levers on the lead time and design errors generated in an iteration-intensive concurrent engineering process. The levers considered are amount of design-space exploration iteration, degree of process concurrency, and timing of design reviews. Simulation is used to show how the ideal combination of these levers can vary with changes in design problem complexity, which can increase, for instance, when novel technology is incorporated in a design. Results confirm that it is important to consider multiple iteration-influencing factors and their interdependencies to understand concurrent processes, because the factors can interact with confounding effects. The article also demonstrates a new approach to derive a system dynamics model from a process task network. The new approach could be applied to analyze other concurrent engineering scenarios. © The Author(s) 2012.

Everywhere and nowhere: nearshore software development in the context of globalisation

Offshore software development has been identified as one of the most striking manifestations of contemporary globalisation and as evidence of placelessness, the idea that information and communication technologies have rendered location irrelevant. Research in the International Business and Information Systems fields, in contrast, has suggested that all locations are not equal and has identified a number of characteristics that may influence the attractiveness of a location for multinational investment and offshoring, respectively. These literatures, however, focus almost exclusively on quantitative, economic characteristics that are seen as fixed and applying uniformly throughout a whole country. They therefore offer little guidance on the suitability of particular locations as offshoring destinations, especially in countries without a track record in offshore software development. Drawing on two cases of nearshore software development centres set up by offshore service providers in the Caribbean, this paper illustrates that, while the initial decision to establish the ventures reflected a logic of placelessness, characteristics of these particular locations affected their subsequent success. Through the findings, we therefore develop a typology of espoused, unanticipated and remediable locational characteristics, which illustrates that locational attractiveness may vary significantly within countries and that offshore service providers and government agencies can modify locational characteristics to their advantage.

Disentangling the Complexity of Early-Stage Technology Acquisitions

While tools have been developed to assist firms' decision making for bringing known products and components into the supply chain, fewer tools are available to guide the acquisition of earlier-stage technologies, which is a riskier proposition due to higher technological and market uncertainties. Through synthesis of literature in technology sourcing, open innovation, alliances, mergers and acquisitions, outsourcing, and technology and knowledge transfer and consultation with industry, this paper identifies critical issues that decision makers should consider before making an early-stage technology acquisition. Sixteen questions emerge to guide decision making, comprising internal, technology, and partner assessments. These questions allow a firm to disentangle the complexity of early-stage technology acquisitions and select the most appropriate targets.

GYGAX: Multi-Sensor Software Platform API

CLI .NET 4.0 research prototype platform coded in C# and Windows Presentation Foundation (WPF)