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

Solution oriented partnerships - A new business model for integrating global-production efficiencies with sustainability

A business model for integrating global-production efficiencies with sustainability is discussed. Two trends that emulate some of the aspects of the wealthy are the increasing willingness of many to pay extra for customization such as clothes, of kitchens and the increasing acceptance of purchasing a service as a product substitute. Two final trends that are also based in the attitudes of people is an increased awareness of the value of local culture and an increased concern with issues of sustainability. The results show that the goal congruence between for-profit and not-for-profit organizations puts emphasis on value and belief of the organization.

BarraCUDA - a fast short read sequence aligner using graphics processing units.

BACKGROUND: With the maturation of next-generation DNA sequencing (NGS) technologies, the throughput of DNA sequencing reads has soared to over 600 gigabases from a single instrument run. General purpose computing on graphics processing units (GPGPU), extracts the computing power from hundreds of parallel stream processors within graphics processing cores and provides a cost-effective and energy efficient alternative to traditional high-performance computing (HPC) clusters. In this article, we describe the implementation of BarraCUDA, a GPGPU sequence alignment software that is based on BWA, to accelerate the alignment of sequencing reads generated by these instruments to a reference DNA sequence. FINDINGS: Using the NVIDIA Compute Unified Device Architecture (CUDA) software development environment, we ported the most computational-intensive alignment component of BWA to GPU to take advantage of the massive parallelism. As a result, BarraCUDA offers a magnitude of performance boost in alignment throughput when compared to a CPU core while delivering the same level of alignment fidelity. The software is also capable of supporting multiple CUDA devices in parallel to further accelerate the alignment throughput. CONCLUSIONS: BarraCUDA is designed to take advantage of the parallelism of GPU to accelerate the alignment of millions of sequencing reads generated by NGS 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 from http://seqbarracuda.sf.net.

IS/IT resources and business value: Operationalization of an information oriented framework

Several studies have highlighted the importance of information and information quality in organisations and thus information is regarded as key determinant for the success and organisational performance. In this paper, we review selected contributions and introduce a model that shows how IS/IT resources and capabilities could be interlinked with IS/IT utilization, organizational performance and business value. Complementing other models and frameworks, we explicitly consider information from a management maturity, quality and risk perspective and show how the new framework can be operationalized with existing assessment approaches by using empirical data from four industrial case studies. © 2012 Springer-Verlag.

An information oriented framework for relating IS/IT resources and business value

Several studies have highlighted the importance of information and information quality in organisations and thus information is regarded as key determinant for the success and organisational performance. At the same time, there are numerous studies, frameworks and case studies examining the impact of information technology and systems to business value. Recently, several studies have proposed maturity models for information management capabilities in the literature, which claim that a higher maturity results in a higher organizational performance. Although these studies provide valuable information about the underlying relations, most are limited in specifying the relationship in more detail. Furthermore, most prominent approaches do not or at least not explicitly consider information as important influencing factor for organisational performance. In this paper, we aim to review selected contributions and introduce a model that shows how IS/IT resources and capabilties could be interlinked with IS/IT utilization, organizational performance and business value. Complementing other models and frameworks, we explicitly consider information from a management maturity, quality and risk perspective. Moreover, the paper discusses how each part of the model can be assessed in order to validate the model in future studies.

IPLR: An online resource for Greek word-level and sublexical information

We present a new online psycholinguistic resource for Greek based on analyses of written corpora combined with text processing technologies developed at the Institute for Language & Speech Processing (ILSP), Greece. The "ILSP PsychoLinguistic Resource" (IPLR) is a freely accessible service via a dedicated web page, at http://speech.ilsp.gr/iplr. IPLR provides analyses of user-submitted letter strings (words and nonwords) as well as frequency tables for important units and conditions such as syllables, bigrams, and neighbors, calculated over two word lists based on printed text corpora and their phonetic transcription. Online tools allow retrieval of words matching user-specified orthographic or phonetic patterns. All results and processing code (in the Python programming language) are freely available for noncommercial educational or research use. © 2010 Springer Science+Business Media B.V.