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.

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.

GYGAX: Multi-Sensor Software Platform API

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

3D modeling of high-T c superconductors by finite element software

A three-dimensional (3D) numerical model is proposed to solve the electromagnetic problems involving transport current and background field of a high-T c superconducting (HTS) system. The model is characterized by the E-J power law and H-formulation, and is successfully implemented using finite element software. We first discuss the model in detail, including the mesh methods, boundary conditions and computing time. To validate the 3D model, we calculate the ac loss and trapped field solution for a bulk material and compare the results with the previously verified 2D solutions and an analytical solution. We then apply our model to test some typical problems such as superconducting bulk array and twisted conductors, which cannot be tackled by the 2D models. The new 3D model could be a powerful tool for researchers and engineers to investigate problems with a greater level of complicity.

Quality practices and problems in free software projects

Free software and open source projects are often perceived to be of high quality. It has been suggested that the high level of quality found in some free software projects is related to the open development model which promotes peer review. While the quality of some free software projects is comparable to, if not better than, that of closed source software, not all free software projects are successful and of high quality. Even mature and successful projects face quality problems; some of these are related to the unique characteristics of free software and open source as a distributed development model led primarily by volunteers. In exploratory interviews performed with free software and open source developers, several common quality practices as well as actual quality problems have been identified. The results of these interviews are presented in this paper in order to take stock of the current status of quality in free software projects and to act as a starting point for the implementation of quality process improvement strategies.

Enhancing and developing the practical optimisation capabilities and intelligence of automatic design software

In the modern engineering design cycle the use of computational tools becomes a neces- sity. The complexity of the engineering systems under consideration for design increases dramatically as the demands for advanced and innovative design concepts and engineering products is expanding. At the same time the advancements in the available technology in terms of computational resources and power, as well as the intelligence of the design software, accommodate these demands and make them a viable approach towards the chal- lenge of real-world engineering problems. This class of design optimisation problems is by nature multi-disciplinary. In the present work we establish enhanced optimisation capabil- ities within the Nimrod/O tool for massively distributed execution of computational tasks through cluster and computational grid resources, and develop the potential to combine and benefit from all the possible available technological advancements, both software and hardware. We develop the interface between a Free Form Deformation geometry manage- ment in-house code with the 2D airfoil aerodynamic efficiency evaluation tool XFoil, and the well established multi-objective heuristic optimisation algorithm NSGA-II. A simple airfoil design problem has been defined to demonstrate the functionality of the design sys- tem, but also to accommodate a framework for future developments and testing with other state-of-the-art optimisation algorithms such as the Multi-Objective Genetic Algorithm (MOGA) and the Multi-Objective Tabu Search (MOTS) techniques. Ultimately, heav- ily computationally expensive industrial design cases can be realised within the presented framework that could not be investigated before. © 2012 by the authors. Published by the American Institute of Aeronautics and Astronautics, Inc.

Enhancing and developing the practical optimisation capabilities and intelligence of automatic design software

In the modern engineering design cycle the use of computational tools becomes a necessity. The complexity of the engineering systems under consideration for design increases dramatically as the demands for advanced and innovative design concepts and engineering products is expanding. At the same time the advancements in the available technology in terms of computational resources and power, as well as the intelligence of the design software, accommodate these demands and make them a viable approach towards the challenge of real-world engineering problems. This class of design optimisation problems is by nature multi-disciplinary. In the present work we establish enhanced optimisation capabilities within the Nimrod/O tool for massively distributed execution of computational tasks through cluster and computational grid resources, and develop the potential to combine and benefit from all the possible available technological advancements, both software and hardware. We develop the interface between a Free Form Deformation geometry management in-house code with the 2D airfoil aerodynamic efficiency evaluation tool XFoil, and the well established multi-objective heuristic optimisation algorithm NSGA-II. A simple airfoil design problem has been defined to demonstrate the functionality of the design system, but also to accommodate a framework for future developments and testing with other state-of-the-art optimisation algorithms such as the Multi-Objective Genetic Algorithm (MOGA) and the Multi-Objective Tabu Search (MOTS) techniques. Ultimately, heavily computationally expensive industrial design cases can be realised within the presented framework that could not be investigated before. ©2012 AIAA.

Manopt, a matlab toolbox for optimization on manifolds

Optimization on manifolds is a rapidly developing branch of nonlinear optimization. Its focus is on problems where the smooth geometry of the search space can be leveraged to design effcient numerical algorithms. In particular, optimization on manifolds is well-suited to deal with rank and orthogonality constraints. Such structured constraints appear pervasively in machine learning applications, including low-rank matrix completion, sensor network localization, camera network registration, independent component analysis, metric learning, dimensionality reduction and so on. The Manopt toolbox, available at www.manopt.org, is a user-friendly, documented piece of software dedicated to simplify experimenting with state of the art Riemannian optimization algorithms. By dealing internally with most of the differential geometry, the package aims particularly at lowering the entrance barrier. © 2014 Nicolas Boumal.