12,426 research outputs found
The Parallelism Motifs of Genomic Data Analysis
Genomic data sets are growing dramatically as the cost of sequencing
continues to decline and small sequencing devices become available. Enormous
community databases store and share this data with the research community, but
some of these genomic data analysis problems require large scale computational
platforms to meet both the memory and computational requirements. These
applications differ from scientific simulations that dominate the workload on
high end parallel systems today and place different requirements on programming
support, software libraries, and parallel architectural design. For example,
they involve irregular communication patterns such as asynchronous updates to
shared data structures. We consider several problems in high performance
genomics analysis, including alignment, profiling, clustering, and assembly for
both single genomes and metagenomes. We identify some of the common
computational patterns or motifs that help inform parallelization strategies
and compare our motifs to some of the established lists, arguing that at least
two key patterns, sorting and hashing, are missing
An Introduction to Programming for Bioscientists: A Python-based Primer
Computing has revolutionized the biological sciences over the past several
decades, such that virtually all contemporary research in the biosciences
utilizes computer programs. The computational advances have come on many
fronts, spurred by fundamental developments in hardware, software, and
algorithms. These advances have influenced, and even engendered, a phenomenal
array of bioscience fields, including molecular evolution and bioinformatics;
genome-, proteome-, transcriptome- and metabolome-wide experimental studies;
structural genomics; and atomistic simulations of cellular-scale molecular
assemblies as large as ribosomes and intact viruses. In short, much of
post-genomic biology is increasingly becoming a form of computational biology.
The ability to design and write computer programs is among the most
indispensable skills that a modern researcher can cultivate. Python has become
a popular programming language in the biosciences, largely because (i) its
straightforward semantics and clean syntax make it a readily accessible first
language; (ii) it is expressive and well-suited to object-oriented programming,
as well as other modern paradigms; and (iii) the many available libraries and
third-party toolkits extend the functionality of the core language into
virtually every biological domain (sequence and structure analyses,
phylogenomics, workflow management systems, etc.). This primer offers a basic
introduction to coding, via Python, and it includes concrete examples and
exercises to illustrate the language's usage and capabilities; the main text
culminates with a final project in structural bioinformatics. A suite of
Supplemental Chapters is also provided. Starting with basic concepts, such as
that of a 'variable', the Chapters methodically advance the reader to the point
of writing a graphical user interface to compute the Hamming distance between
two DNA sequences.Comment: 65 pages total, including 45 pages text, 3 figures, 4 tables,
numerous exercises, and 19 pages of Supporting Information; currently in
press at PLOS Computational Biolog
Probabilistic Graphical Models on Multi-Core CPUs using Java 8
In this paper, we discuss software design issues related to the development
of parallel computational intelligence algorithms on multi-core CPUs, using the
new Java 8 functional programming features. In particular, we focus on
probabilistic graphical models (PGMs) and present the parallelisation of a
collection of algorithms that deal with inference and learning of PGMs from
data. Namely, maximum likelihood estimation, importance sampling, and greedy
search for solving combinatorial optimisation problems. Through these concrete
examples, we tackle the problem of defining efficient data structures for PGMs
and parallel processing of same-size batches of data sets using Java 8
features. We also provide straightforward techniques to code parallel
algorithms that seamlessly exploit multi-core processors. The experimental
analysis, carried out using our open source AMIDST (Analysis of MassIve Data
STreams) Java toolbox, shows the merits of the proposed solutions.Comment: Pre-print version of the paper presented in the special issue on
Computational Intelligence Software at IEEE Computational Intelligence
Magazine journa
A collaborative citizen science platform for real-time volunteer computing and games
Volunteer computing (VC) or distributed computing projects are common in the
citizen cyberscience (CCS) community and present extensive opportunities for
scientists to make use of computing power donated by volunteers to undertake
large-scale scientific computing tasks. Volunteer computing is generally a
non-interactive process for those contributing computing resources to a project
whereas volunteer thinking (VT) or distributed thinking, which allows
volunteers to participate interactively in citizen cyberscience projects to
solve human computation tasks. In this paper we describe the integration of
three tools, the Virtual Atom Smasher (VAS) game developed by CERN, LiveQ, a
job distribution middleware, and CitizenGrid, an online platform for hosting
and providing computation to CCS projects. This integration demonstrates the
combining of volunteer computing and volunteer thinking to help address the
scientific and educational goals of games like VAS. The paper introduces the
three tools and provides details of the integration process along with further
potential usage scenarios for the resulting platform.Comment: 12 pages, 13 figure
Robots, drugs, reality and education: how the future will change how we think
Emerging technologies for learning report - Article exploring various future trends and their potential impact on educatio
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