Search results for "Workstation"
showing 8 items of 28 documents
RabbitMash: accelerating hash-based genome analysis on modern multi-core architectures
2020
Abstract Motivation Mash is a popular hash-based genome analysis toolkit with applications to important downstream analyses tasks such as clustering and assembly. However, Mash is currently not able to fully exploit the capabilities of modern multi-core architectures, which in turn leads to high runtimes for large-scale genomic datasets. Results We present RabbitMash, an efficient highly optimized implementation of Mash which can take full advantage of modern hardware including multi-threading, vectorization and fast I/O. We show that our approach achieves speedups of at least 1.3, 9.8, 8.5 and 4.4 compared to Mash for the operations sketch, dist, triangle and screen, respectively. Furtherm…
Biometric sensors rapid prototyping on field-programmable gate arrays
2015
AbstractBiometric user authentication in large-scale distributed systems involves passive scanners and networked workstations and databases for user data acquisition, processing, and encryption. Unfortunately, traditional biometric authentication systems are prone to several attacks, such as Replay Attacks, Communication Attacks, and Database Attacks. Embedded biometric sensors overcome security limits of conventional software recognition systems, hiding its common attack points. The availability of mature reconfigurable hardware technology, such as field-programmable gate arrays, allows the developers to design and prototype the whole embedded biometric sensors. In this work, two strong an…
RNACache: Fast Mapping of RNA-Seq Reads to Transcriptomes Using MinHashing
2021
The alignment of reads to a transcriptome is an important initial step in a variety of bioinformatics RNA-seq pipelines. As traditional alignment-based tools suffer from high runtimes, alternative, alignment-free methods have recently gained increasing importance. We present a novel approach to the detection of local similarities between transcriptomes and RNA-seq reads based on context-aware minhashing. We introduce RNACache, a three-step processing pipeline consisting of minhashing of k-mers, match-based (online) filtering, and coverage-based filtering in order to identify truly expressed transcript isoforms. Our performance evaluation shows that RNACache produces transcriptomic mappings …
FPGA-based Acceleration of Detecting Statistical Epistasis in GWAS
2014
Abstract Genotype-by-genotype interactions (epistasis) are believed to be a significant source of unexplained genetic variation causing complex chronic diseases but have been ignored in genome-wide association studies (GWAS) due to the computational burden of analysis. In this work we show how to benefit from FPGA technology for highly parallel creation of contingency tables in a systolic chain with a subsequent statistical test. We present the implementation for the FPGA-based hardware platform RIVYERA S6-LX150 containing 128 Xilinx Spartan6-LX150 FPGAs. For performance evaluation we compare against the method iLOCi[9]. iLOCi claims to outperform other available tools in terms of accuracy.…
Ergonomic Comparison of a Sit-Stand Workstation With a Traditional Workstation in Visual Display Unit Work
2013
Purpose: To compare ergonomics of an electrically adjustable sit-stand workstation with a traditional workstation in video display unit (VDU) work. Methods: Twelve female workers (aged 27-53 years) participated in this experimental study. Electromyography, wrist postures, subjective assessments, and productivity were used to make the ergonomic comparison. Results: The muscle activity of the right trapezius (p=0.01) and left wrist extensors (p=0.02), extension of the right (p=0.05) and left (p=0.002) wrist, and perceived strain of the arms (p=0.05) were lower and productivity was better (p=0.02) when the workers used a low-sitting, high-sitting, or standing posture at the sit-stand workstati…
Effects of Using Standing Versus Sitting Workstations on the Well-Being at Work of Software Professionals
2016
Although people admittedly are one of the most valuable assets of many software companies, relatively little academic research has been done from the well-being at work aspect of software professionals. This intervention study aims to address this gap in prior research by examining the potential effects of using standing instead of sitting workstations on the well-being at work of software professionals in terms of physical activity, mental alertness, and stress. The two measurements before and after the intervention were conducted in June and September 2015 for 29 employees of a local site of a large Finnish software company by using questionnaires and the Firstbeat Lifestyle Assessment se…
Muscle activity patterns and spinal shrinkage in office workers using a sit–stand workstation versus a sit workstation
2016
Reducing sitting time by means of sit–stand workstations is an emerging trend, but further evidence is needed regarding their health benefits. This cross-sectional study compared work time muscle activity patterns and spinal shrinkage between office workers (aged 24–62, 58.3% female) who used either a sit–stand workstation (Sit–Stand group, n = 10) or a traditional sit workstation (Sit group, n = 14) for at least the past three months. During one typical workday, muscle inactivity and activity from quadriceps and hamstrings were monitored using electromyography shorts, and spinal shrinkage was measured using stadiometry before and after the workday. Compared with the Sit group, the Sit–Stan…
Visualization in the integrated SimPhoNy multiscale simulation framework
2018
Abstract We describe three distinct approaches to visualization for multiscale materials modelling research. These have been developed with the framework of the SimPhoNy FP7 EU-project, and complement each other in their requirements and possibilities. All have been integrated via wrappers to one or more of the simulation approaches within the SimPhoNy project. In this manuscript we describe and contrast their features. Together they cover visualization needs from electronic to macroscopic scales and are suited to simulations made on personal computers, workstations or advanced High Performance parallel computers. Examples as well as recommendations for future calculations are presented.