879 research outputs found
Analyzing large-scale DNA Sequences on Multi-core Architectures
Rapid analysis of DNA sequences is important in preventing the evolution of
different viruses and bacteria during an early phase, early diagnosis of
genetic predispositions to certain diseases (cancer, cardiovascular diseases),
and in DNA forensics. However, real-world DNA sequences may comprise several
Gigabytes and the process of DNA analysis demands adequate computational
resources to be completed within a reasonable time. In this paper we present a
scalable approach for parallel DNA analysis that is based on Finite Automata,
and which is suitable for analyzing very large DNA segments. We evaluate our
approach for real-world DNA segments of mouse (2.7GB), cat (2.4GB), dog
(2.4GB), chicken (1GB), human (3.2GB) and turkey (0.2GB). Experimental results
on a dual-socket shared-memory system with 24 physical cores show speed-ups of
up to 17.6x. Our approach is up to 3x faster than a pattern-based parallel
approach that uses the RE2 library.Comment: The 18th IEEE International Conference on Computational Science and
Engineering (CSE 2015), Porto, Portugal, 20 - 23 October 201
Characterizing and Accelerating Bioinformatics Workloads on Modern Microarchitectures
Bioinformatics, the use of computer techniques to analyze biological data, has been a particularly active research field in the last two decades. Advances in this field have contributed to the collection of enormous amounts of data, and the sheer amount of available data has started to overtake the processing capability possible with current computer systems. Clearly, computer architects need to have a better understanding of how bioinformatics applications work and what kind of architectural techniques could be used to accelerate these important scientific workloads on future processors. In this dissertation, we develop a bioinformatic benchmark suite and provide a detailed characterization of these applications in common use today from a computer architect's point of view. We analyze a wide range of detailed execution characteristics including instruction mix, IPC measurements, L1 and L2 cache misses on a real architecture; and proceed to analyze the workloads' memory access characteristics. We then concentrate on accelerating a particularly computationally intensive bioinformatics workload on the novel Cell Broadband Engine multiprocessor architecture. The HMMER workload is used for protein profile searching using hidden Markov models, and most of its execution time is spent running the Viterbi algorithm. We parallelize and partition the HMMER application to implement it on the Cell Broadband Engine. In order to run the Viterbi algorithm on the 256KB local stores of the Cell BE synergistic processing units (SPEs), we present a method to develop a fast SIMD implementation of the Viterbi algorithm that reduces the storage requirements significantly. Our HMMER implementation for the Cell BE architecture, Cell-HMMER, exploits the multiple levels of parallelism inherent in this application, and can run protein profile searches up to 27.98 times faster than a modern dual-core x86 microprocessor
Efficient similarity search on multimedia databases
Manipulating and retrieving multimedia data has received increasing attention with the advent of cloud storage facilities. The ability of querying by similarity over large data collections is mandatory to improve storage and user interfaces. But, all of them are expensive operations to solve only in CPU; thus, it is convenient to take into account High Performance Computing (HPC) techniques in their solutions. The Graphics Processing Unit (GPU) as an alternative HPC device has been increasingly used to speedup certain computing processes. This work introduces a pure GPU architecture to build the Permutation Index and to solve approximate similarity queries on multimedia databases. The empirical results of each implementation have achieved different level of speedup which are related with characteristics of GPU and the particular database used.Eje: Workshop Bases de datos y minerĂa de datos (WBDDM)Red de Universidades con Carreras en Informática (RedUNCI
Efficient similarity search on multimedia databases
Manipulating and retrieving multimedia data has received increasing attention with the advent of cloud storage facilities. The ability of querying by similarity over large data collections is mandatory to improve storage and user interfaces. But, all of them are expensive operations to solve only in CPU; thus, it is convenient to take into account High Performance Computing (HPC) techniques in their solutions. The Graphics Processing Unit (GPU) as an alternative HPC device has been increasingly used to speedup certain computing processes. This work introduces a pure GPU architecture to build the Permutation Index and to solve approximate similarity queries on multimedia databases. The empirical results of each implementation have achieved different level of speedup which are related with characteristics of GPU and the particular database used.Eje: Workshop Bases de datos y minerĂa de datos (WBDDM)Red de Universidades con Carreras en Informática (RedUNCI
MR-CUDASW - GPU accelerated Smith-Waterman algorithm for medium-length (meta)genomic data
The idea of using a graphics processing unit (GPU) for more than simply graphic output purposes has been around for quite some time in scientific communities. However, it is only recently that its benefits for a range
of bioinformatics and life sciences compute-intensive tasks has been recognized. This thesis investigates the possibility of improving the performance of the overlap determination stage of an Overlap Layout Consensus
(OLC)-based assembler by using a GPU-based implementation of the Smith-Waterman algorithm.
In this thesis an existing GPU-accelerated sequence alignment algorithm is adapted and expanded to reduce its completion time. A number of improvements and changes are made to the original software. Workload distribution, query profile construction, and thread scheduling techniques implemented by the original program are replaced by custom methods specifically designed to handle medium-length reads.
Accordingly, this algorithm is the first highly parallel solution that has been specifically optimized to process medium-length nucleotide reads (DNA/RNA) from modern sequencing machines (i.e. Ion Torrent).
Results show that the software reaches up to 82 GCUPS (Giga Cell Updates Per Second) on a single-GPU graphic card running on a commodity desktop hardware. As a result it is the fastest GPU-based implemen-
tation of the Smith-Waterman algorithm tailored for processing medium-length nucleotide reads. Despite being designed for performing the Smith-Waterman algorithm on medium-length nucleotide sequences, this
program also presents great potential for improving heterogeneous computing with CUDA-enabled GPUs in general and is expected to make contributions to other research problems that require sensitive pairwise alignment to be applied to a large number of reads. Our results show that it is possible to improve the performance of bioinformatics algorithms by taking full advantage of the compute resources of the underlying commodity hardware and further, these results are especially encouraging since GPU performance grows faster than multi-core CPUs
Castell: a heterogeneous cmp architecture scalable to hundreds of processors
Technology improvements and power constrains have taken multicore architectures to dominate
microprocessor designs over uniprocessors. At the same time, accelerator based architectures
have shown that heterogeneous multicores are very efficient and can provide high throughput for
parallel applications, but with a high-programming effort. We propose Castell a scalable chip
multiprocessor architecture that can be programmed as uniprocessors, and provides the high
throughput of accelerator-based architectures.
Castell relies on task-based programming models that simplify software development. These
models use a runtime system that dynamically finds, schedules, and adds hardware-specific features
to parallel tasks. One of these features is DMA transfers to overlap computation and data
movement, which is known as double buffering. This feature allows applications on Castell
to tolerate large memory latencies and lets us design the memory system focusing on memory
bandwidth.
In addition to provide programmability and the design of the memory system, we have used
a hierarchical NoC and added a synchronization module. The NoC design distributes memory
traffic efficiently to allow the architecture to scale. The synchronization module is a consequence
of the large performance degradation of application for large synchronization latencies.
Castell is mainly an architecture framework that enables the definition of domain-specific
implementations, fine-tuned to a particular problem or application. So far, Castell has been
successfully used to propose heterogeneous multicore architectures for scientific kernels, video
decoding (using H.264), and protein sequence alignment (using Smith-Waterman and clustalW).
It has also been used to explore a number of architecture optimizations such as enhanced DMA
controllers, and architecture support for task-based programming models.
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PhyloGibbs-MP: Module Prediction and Discriminative Motif-Finding by Gibbs Sampling
PhyloGibbs, our recent Gibbs-sampling motif-finder, takes phylogeny into account in detecting binding sites for transcription factors in DNA and assigns posterior probabilities to its predictions obtained by sampling the entire configuration space. Here, in an extension called PhyloGibbs-MP, we widen the scope of the program, addressing two major problems in computational regulatory genomics. First, PhyloGibbs-MP can localise predictions to small, undetermined regions of a large input sequence, thus effectively predicting cis-regulatory modules (CRMs) ab initio while simultaneously predicting binding sites in those modules—tasks that are usually done by two separate programs. PhyloGibbs-MP's performance at such ab initio CRM prediction is comparable with or superior to dedicated module-prediction software that use prior knowledge of previously characterised transcription factors. Second, PhyloGibbs-MP can predict motifs that differentiate between two (or more) different groups of regulatory regions, that is, motifs that occur preferentially in one group over the others. While other “discriminative motif-finders” have been published in the literature, PhyloGibbs-MP's implementation has some unique features and flexibility. Benchmarks on synthetic and actual genomic data show that this algorithm is successful at enhancing predictions of differentiating sites and suppressing predictions of common sites and compares with or outperforms other discriminative motif-finders on actual genomic data. Additional enhancements include significant performance and speed improvements, the ability to use “informative priors” on known transcription factors, and the ability to output annotations in a format that can be visualised with the Generic Genome Browser. In stand-alone motif-finding, PhyloGibbs-MP remains competitive, outperforming PhyloGibbs-1.0 and other programs on benchmark data
Bioinformatics
This book is divided into different research areas relevant in Bioinformatics such as biological networks, next generation sequencing, high performance computing, molecular modeling, structural bioinformatics, molecular modeling and intelligent data analysis. Each book section introduces the basic concepts and then explains its application to problems of great relevance, so both novice and expert readers can benefit from the information and research works presented here
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