SciCombinator

Discover the most talked about and latest scientific content & concepts.

Concept: Linux

170

Existing repositories for experimental datasets typically capture snapshots of data acquired using a single experimental technique and often require manual population and continual curation. We present a storage system for heterogeneous research data that performs dynamic automated indexing to provide powerful search, discovery and collaboration features without the restrictions of a structured repository. ADAM is able to index many commonly used file formats generated by laboratory assays and therefore offers specific advantages to the experimental biology community. However, it is not domain specific and can promote sharing and re-use of working data across scientific disciplines. Availability and implementation: ADAM is implemented using Java and supported on Linux. It is open source under the GNU General Public License v3.0. Installation instructions, binary code, a demo system and virtual machine image and are available at http://www.imperial.ac.uk/bioinfsupport/resources/software/adam. CONTACT: m.woodbridge@imperial.ac.uk.

Concepts: Computer program, Free software, Linux, Linux kernel, GNU General Public License, GNU, GNU Project, Virtual machine

169

We present Masai, a read mapper representing the state-of-the-art in terms of speed and accuracy. Our tool is an order of magnitude faster than RazerS 3 and mrFAST, 2-4 times faster and more accurate than Bowtie 2 and BWA. The novelties of our read mapper are filtration with approximate seeds and a method for multiple backtracking. Approximate seeds, compared with exact seeds, increase filtration specificity while preserving sensitivity. Multiple backtracking amortizes the cost of searching a large set of seeds by taking advantage of the repetitiveness of next-generation sequencing data. Combined together, these two methods significantly speed up approximate search on genomic data sets. Masai is implemented in C++ using the SeqAn library. The source code is distributed under the BSD license and binaries for Linux, Mac OS X and Windows can be freely downloaded from http://www.seqan.de/projects/masai.

Concepts: Java, Source code, Mac OS X, Operating system, Mac OS, Macintosh, Linux, FreeBSD

28

Bioinformatics is challenged by the fact that traditional analysis tools have difficulty in processing large-scale data from high-throughput sequencing. The open source Apache Hadoop project, which adopts the MapReduce framework and a distributed file system, has recently given bioinformatics researchers an opportunity to achieve scalable, efficient and reliable computing performance on Linux clusters and on cloud computing services. In this article, we present MapReduce frame-based applications that can be employed in the next-generation sequencing and other biological domains. In addition, we discuss the challenges faced by this field as well as the future works on parallel computing in bioinformatics.

Concepts: Future, Hadoop, Cloud computing, Grid computing, Linux, Google, File system, MapReduce

27

In situ one-pot rapid layer-by-layer assembly of polymeric films as an active layer of a photoactive device via alternation of reductive and oxidative electropolymerization has been demonstrated. This novel fabrication without moving or changing experimental gears would be a powerful strategy to develop automated layer-by-layer machines.

Concepts: Carcinoma in situ, In situ, Linux, Linux kernel

27

: The recent emphasis on shared decision-making has increased the role of the Internet as a readily accessible medical reference source for patients and families. However, the lack of professional review creates concern over the quality, accuracy, and readability of medical information available to patients on the Internet.

Concepts: Web search engine, World Wide Web, Internet, History of the Internet, Searching, Linux

26

DIYABC is a software package for a comprehensive analysis of population history using approximate Bayesian computation (ABC) on DNA polymorphism data. Version 2.0 implements a number of new features and analytical methods. It allows: (i) the analysis of single nucleotide polymorphism (SNP) data at large number of loci, apart from microsatellite and DNA sequence data; (ii) efficient Bayesian model choice using linear discriminant analysis on summary statistics; and (iii) the serial launching of multiple post-processing analyses. DIYABC v2.0 also includes a user-friendly graphical interface with various new options. It can be run on three operating systems: GNU/Linux, Microsoft Windows and Apple Os X.

Concepts: Mathematical analysis, Mac OS X, Apple Inc., Operating system, Microsoft, Microsoft Windows, Graphical user interface, Linux

23

We present the segmented corrosion method that uses hydrofluoric acid to etch the fiber of a fiber laser for removing high-power cladding light to improve stripping uniformity and power handling capability. For theoretical guidelines, we propose a simulation model of etched-fiber stripping to evaluate the relationship between the etched-fiber parameters and cladding light attenuation and to analyze the stripping uniformity achieved with segmented corrosion. A two-segment etched fiber is fabricated with cladding light attenuation of 19.8 dB and power handling capability up to 670 W. We find that the cladding light is stripped uniformly and the temperature distribution is uniform without the formation of hot spots.

Concepts: Light, Optical fiber, Laser, Java, HotSpot, Free software, Etching, Linux

22

To examine the motivations and circumstances of individuals seeking information about self-abortion on the Internet.

Concepts: Web search engine, World Wide Web, Internet, Usenet, Linux, MySpace, Instant messaging, Stanford University

18

Embedded systems control and monitor a great deal of our reality. While some “classic” features are intrinsically necessary, such as low power consumption, rugged operating ranges, fast response and low cost, these systems have evolved in the last few years to emphasize connectivity functions, thus contributing to the Internet of Things paradigm. A myriad of sensing/computing devices are being attached to everyday objects, each able to send and receive data and to act as a unique node in the Internet. Apart from the obvious necessity to process at least some data at the edge (to increase security and reduce power consumption and latency), a major breakthrough will arguably come when such devices are endowed with some level of autonomous “intelligence”. Intelligent computing aims to solve problems for which no efficient exact algorithm can exist or for which we cannot conceive an exact algorithm. Central to such intelligence is Computer Vision (CV), i.e., extracting meaning from images and video. While not everything needs CV, visual information is the richest source of information about the real world: people, places and things. The possibilities of embedded CV are endless if we consider new applications and technologies, such as deep learning, drones, home robotics, intelligent surveillance, intelligent toys, wearable cameras, etc. This paper describes the Eyes of Things (EoT) platform, a versatile computer vision platform tackling those challenges and opportunities.

Concepts: Learning, Computer, Intelligence, Problem solving, Microprocessor, The Real World, Linux, Information appliance

15

Medical students often struggle to engage in extra-curricular research and audit. The Student Audit and Research in Surgery (STARSurg) network is a novel student-led, national research collaborative. Student collaborators contribute data to national, clinical studies while gaining an understanding of audit and research methodology and ethical principles. This study aimed to evaluate the educational impact of participation.

Concepts: Scientific method, Cohort study, Medicine, Clinical trial, Education, Physician, Student, Linux