11,001 research outputs found
Heterogeneous computing architecture for fast detection of SNP-SNP interactions
The extent of data in a typical genome-wide association study (GWAS) poses considerable computational challenges to software tools for gene-gene interaction discovery. Exhaustive evaluation of all interactions among hundreds of thousands to millions of single nucleotide polymorphisms (SNPs) may require weeks or even months of computation. Massively parallel hardware within a modern Graphic Processing Unit (GPU) and Many Integrated Core (MIC) coprocessors can shorten the run time considerably. While the utility of GPU-based implementations in bioinformatics has been well studied, MIC architecture has been introduced only recently and may provide a number of comparative advantages that have yet to be explored and tested. We have developed a heterogeneous, GPU and Intel MIC-accelerated software module for SNP-SNP interaction discovery to replace the previously single-threaded computational core in the interactive web-based data exploration program SNPsyn. We report on differences between these two modern massively parallel architectures and their software environments. Their utility resulted in an order of magnitude shorter execution times when compared to the single-threaded CPU implementation. GPU implementation on a single Nvidia Tesla K20 runs twice as fast as that for the MIC architecture-based Xeon Phi P5110 coprocessor, but also requires considerably more programming effort.
General purpose GPUs are a mature platform with large amounts of computing power capable of tackling inherently parallel problems, but can prove demanding for the programmer. On the other hand the new MIC architecture, albeit lacking in performance reduces the programming effort and makes it up with a more general architecture suitable for a wider range of problems
Heterogeneous computing architecture for fast detection of SNP-SNP interactions
The extent of data in a typical genome-wide association study (GWAS) poses considerable computational challenges to software tools for gene-gene interaction discovery. Exhaustive evaluation of all interactions among hundreds of thousands to millions of single nucleotide polymorphisms (SNPs) may require weeks or even months of computation. Massively parallel hardware within a modern Graphic Processing Unit (GPU) and Many Integrated Core (MIC) coprocessors can shorten the run time considerably. While the utility of GPU-based implementations in bioinformatics has been well studied, MIC architecture has been introduced only recently and may provide a number of comparative advantages that have yet to be explored and tested. We have developed a heterogeneous, GPU and Intel MIC-accelerated software module for SNP-SNP interaction discovery to replace the previously single-threaded computational core in the interactive web-based data exploration program SNPsyn. We report on differences between these two modern massively parallel architectures and their software environments. Their utility resulted in an order of magnitude shorter execution times when compared to the single-threaded CPU implementation. GPU implementation on a single Nvidia Tesla K20 runs twice as fast as that for the MIC architecture-based Xeon Phi P5110 coprocessor, but also requires considerably more programming effort.
General purpose GPUs are a mature platform with large amounts of computing power capable of tackling inherently parallel problems, but can prove demanding for the programmer. On the other hand the new MIC architecture, albeit lacking in performance reduces the programming effort and makes it up with a more general architecture suitable for a wider range of problems
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Computational Strategies for Scalable Genomics Analysis.
The revolution in next-generation DNA sequencing technologies is leading to explosive data growth in genomics, posing a significant challenge to the computing infrastructure and software algorithms for genomics analysis. Various big data technologies have been explored to scale up/out current bioinformatics solutions to mine the big genomics data. In this review, we survey some of these exciting developments in the applications of parallel distributed computing and special hardware to genomics. We comment on the pros and cons of each strategy in the context of ease of development, robustness, scalability, and efficiency. Although this review is written for an audience from the genomics and bioinformatics fields, it may also be informative for the audience of computer science with interests in genomics applications
STOCHSIMGPU Parallel stochastic simulation for the Systems\ud Biology Toolbox 2 for MATLAB
Motivation: The importance of stochasticity in biological systems is becoming increasingly recognised and the computational cost of biologically realistic stochastic simulations urgently requires development of efficient software. We present a new software tool STOCHSIMGPU which exploits graphics processing units (GPUs)for parallel stochastic simulations of biological/chemical reaction systems and show that significant gains in efficiency can be made. It is integrated into MATLAB and works with the Systems Biology Toolbox 2 (SBTOOLBOX2) for MATLAB.\ud
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Results: The GPU-based parallel implementation of the Gillespie stochastic simulation algorithm (SSA), the logarithmic direct method (LDM), and the next reaction method (NRM) is approximately 85 times faster than the sequential implementation of the NRM on a central processing unit (CPU). Using our software does not require any changes to the user’s models, since it acts as a direct replacement of the stochastic simulation software of the SBTOOLBOX2
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MPRAnalyze: statistical framework for massively parallel reporter assays.
Massively parallel reporter assays (MPRAs) can measure the regulatory function of thousands of DNA sequences in a single experiment. Despite growing popularity, MPRA studies are limited by a lack of a unified framework for analyzing the resulting data. Here we present MPRAnalyze: a statistical framework for analyzing MPRA count data. Our model leverages the unique structure of MPRA data to quantify the function of regulatory sequences, compare sequences' activity across different conditions, and provide necessary flexibility in an evolving field. We demonstrate the accuracy and applicability of MPRAnalyze on simulated and published data and compare it with existing methods
Benchmarking SciDB Data Import on HPC Systems
SciDB is a scalable, computational database management system that uses an
array model for data storage. The array data model of SciDB makes it ideally
suited for storing and managing large amounts of imaging data. SciDB is
designed to support advanced analytics in database, thus reducing the need for
extracting data for analysis. It is designed to be massively parallel and can
run on commodity hardware in a high performance computing (HPC) environment. In
this paper, we present the performance of SciDB using simulated image data. The
Dynamic Distributed Dimensional Data Model (D4M) software is used to implement
the benchmark on a cluster running the MIT SuperCloud software stack. A peak
performance of 2.2M database inserts per second was achieved on a single node
of this system. We also show that SciDB and the D4M toolbox provide more
efficient ways to access random sub-volumes of massive datasets compared to the
traditional approaches of reading volumetric data from individual files. This
work describes the D4M and SciDB tools we developed and presents the initial
performance results. This performance was achieved by using parallel inserts, a
in-database merging of arrays as well as supercomputing techniques, such as
distributed arrays and single-program-multiple-data programming.Comment: 5 pages, 4 figures, IEEE High Performance Extreme Computing (HPEC)
2016, best paper finalis
Design and evaluation of a genomics variant analysis pipeline using GATK Spark tools
Scalable and efficient processing of genome sequence data, i.e. for variant
discovery, is key to the mainstream adoption of High Throughput technology for
disease prevention and for clinical use. Achieving scalability, however,
requires a significant effort to enable the parallel execution of the analysis
tools that make up the pipelines. This is facilitated by the new Spark versions
of the well-known GATK toolkit, which offer a black-box approach by
transparently exploiting the underlying Map Reduce architecture. In this paper
we report on our experience implementing a standard variant discovery pipeline
using GATK 4.0 with Docker-based deployment over a cluster. We provide a
preliminary performance analysis, comparing the processing times and cost to
those of the new Microsoft Genomics Services
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