An Energy-Aware Bioinformatics Application for Assembling Short Reads in High Performance Computing Systems

Current biomedical technologies are producing massive amounts of data on an unprecedented scale. The increasing complexity and growth rate of biological data has made bioinformatics data processing and analysis a key and computationally intensive task. High performance computing (HPC) has been successfully applied to major bioinformatics applications to reduce computational burden. However, a naïve approach for developing parallel bioinformatics applications may achieve a high degree of parallelism while unnecessarily expending computational resources and consuming high levels of energy. As the wealth of biological data and associated computational burden continues to increase, there has become a need for the development of energy efficient computational approaches in the bioinformatics domain. To address this issue, we have developed an energy-aware scheduling (EAS) model to run computationally intensive applications that takes both deadline requirements and energy factors into consideration. An example of a computationally demanding process that would benefit from our scheduling model is the assembly of short sequencing reads produced by next generation sequencing technologies. Next generation sequencing produces a very large number of short DNA reads from a biological sample. Multiple overlapping fragments must be aligned and merged into long stretches of contiguous sequence before any useful information can be gathered. The assembly problem is extremely difficult due to the complex nature of underlying genome structure and inherent biological error present in current sequencing technologies. We apply our EAS model to a newly proposed assembly algorithm called Merge and Traverse, giving us the ability to generate speed up profiles. Our EAS model was also able to dynamically adjust the number of nodes needed to meet given deadlines for different sets of reads

Energy Awareness and Scheduling in Mobile Devices and High End Computing

In the context of the big picture as energy demands rise due to growing economies and growing populations, there will be greater emphasis on sustainable supply, conservation, and efficient usage of this vital resource. Even at a smaller level, the need for minimizing energy consumption continues to be compelling in embedded, mobile, and server systems such as handheld devices, robots, spaceships, laptops, cluster servers, sensors, etc. This is due to the direct impact of constrained energy sources such as battery size and weight, as well as cooling expenses in cluster-based systems to reduce heat dissipation. Energy management therefore plays a paramount role in not only hardware design but also in user-application, middleware and operating system design. At a higher level Datacenters are sprouting everywhere due to the exponential growth of Big Data in every aspect of human life, the buzz word these days is Cloud computing. This dissertation, focuses on techniques, specifically algorithmic ones to scale down energy needs whenever the system performance can be relaxed. We examine the significance and relevance of this research and develop a methodology to study this phenomenon. Specifically, the research will study energy-aware resource reservations algorithms to satisfy both performance needs and energy constraints. Many energy management schemes focus on a single resource that is dedicated to real-time or nonreal-time processing. Unfortunately, in many practical systems the combination of hard and soft real-time periodic tasks, a-periodic real-time tasks, interactive tasks and batch tasks must be supported. Each task may also require access to multiple resources. Therefore, this research will tackle the NP-hard problem of providing timely and simultaneous access to multiple resources by the use of practical abstractions and near optimal heuristics aided by cooperative scheduling. We provide an elegant EAS model which works across the spectrum which uses a run-profile based approach to scheduling. We apply this model to significant applications such as BLAT and Assembly of gene sequences in the Bioinformatics domain. We also provide a simulation for extending this model to cloud computing to answers “what if” scenario questions for consumers and operators of cloud resources to help answers questions of deadlines, single v/s distributed cluster use and impact analysis of energy-index and availability against revenue and ROI

Focus: A Graph Approach for Data-Mining and Domain-Specific Assembly of Next Generation Sequencing Data

Next Generation Sequencing (NGS) has emerged as a key technology leading to revolutionary breakthroughs in numerous biomedical research areas. These technologies produce millions to billions of short DNA reads that represent a small fraction of the original target DNA sequence. These short reads contain little information individually but are produced at a high coverage of the original sequence such that many reads overlap. Overlap relationships allow for the reads to be linearly ordered and merged by computational programs called assemblers into long stretches of contiguous sequence called contigs that can be used for research applications. Although the assembly of the reads produced by NGS remains a difficult task, it is the process of extracting useful knowledge from these relatively short sequences that has become one of the most exciting and challenging problems in Bioinformatics. The assembly of short reads is an aggregative process where critical information is lost as reads are merged into contigs. In addition, the assembly process is treated as a black box, with generic assembler tools that do not adapt to input data set characteristics. Finally, as NGS data throughput continues to increase, there is an increasing need for smart parallel assembler implementations. In this dissertation, a new assembly approach called Focus is proposed. Unlike previous assemblers, Focus relies on a novel hybrid graph constructed from multiple graphs at different levels of granularity to represent the assembly problem, facilitating information capture and dynamic adjustment to input data set characteristics. This work is composed of four specific aims: 1) The implementation of a robust assembly and analysis tool built on the hybrid graph platform 2) The development and application of graph mining to extract biologically relevant features in NGS data sets 3) The integration of domain specific knowledge to improve the assembly and analysis process. 4) The construction of smart parallel computing approaches, including the application of energy-aware computing for NGS assembly and knowledge integration to improve algorithm performance. In conclusion, this dissertation presents a complete parallel assembler called Focus that is capable of extracting biologically relevant features directly from its hybrid assembly graph

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

A Dynamic Run-Profile Energy-Aware Approach for Scheduling Computationally Intensive Bioinformatics Applications

High Performance Computing (HPC) resources are housed in large datacenters, which consume exorbitant amounts of energy and are quickly demanding attention from businesses as they result in high operating costs. On the other hand HPC environments have been very useful to researchers in many emerging areas in life sciences such as Bioinformatics and Medical Informatics. In an earlier work, we introduced a dynamic model for energy aware scheduling (EAS) in a HPC environment; the model is domain agnostic and incorporates both the deadline parameter as well as energy parameters for computationally intensive applications. Our proposed EAS model incorporates 2-phases. In the Offline Phase, we use a run profile based approach to generate the initial schedule. In the Online Phase a feedback mechanism is incorporated between the EAS Engine and the master scheduling process. As scheduled tasks are completed, actual execution times are used to adjust the resources required for scheduling remaining tasks using the least number of nodes while meeting a given deadline. In this paper we study the impact of the quality of initial schedule using different run profiles which is the starting point for the EAS algorithm on the number of adjustments which is critical to the overall energy optimization as every adjustment made has an overhead. The conducted experiments show that the proposed approach succeeded in meeting preset deadlines while minimizing the number of nodes; thus reducing overall energy utilized and that choosing the right profile in the Offline phase has an impact on the energy optimization achieved by the EAS algorithm

\u3ci\u3eBioinformatics and Biomedical Engineering\u3c/i\u3e

Editors: Francisco Ortuño, Ignacio Rojas Chapter, Identification of Biologically Significant Elements Using Correlation Networks in High Performance Computing Environments, co-authored by Kathryn Dempsey Cooper, Sachin Pawaskar, and Hesham Ali, UNO faculty members. The two volume set LNCS 9043 and 9044 constitutes the refereed proceedings of the Third International Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2015, held in Granada, Spain in April 2015. The 134 papers presented were carefully reviewed and selected from 268 submissions. The scope of the conference spans the following areas: bioinformatics for healthcare and diseases, biomedical engineering, biomedical image analysis, biomedical signal analysis, computational genomics, computational proteomics, computational systems for modelling biological processes, eHealth, next generation sequencing and sequence analysis, quantitative and systems pharmacology, Hidden Markov Model (HMM) for biological sequence modeling, advances in computational intelligence for bioinformatics and biomedicine, tools for next generation sequencing data analysis, dynamics networks in system medicine, interdisciplinary puzzles of measurements in biological systems, biological networks, high performance computing in bioinformatics, computational biology and computational chemistry, advances in drug discovery and ambient intelligence for bio emotional computing.https://digitalcommons.unomaha.edu/facultybooks/1323/thumbnail.jp

Algorithm-Hardware Co-Design for Performance-driven Embedded Genomics

PhD ThesisGenomics includes development of techniques for diagnosis, prognosis and therapy of over 6000 known genetic disorders. It is a major driver in the transformation of medicine from the reactive form to the personalized, predictive, preventive and participatory (P4) form. The availability of genome is an essential prerequisite to genomics and is obtained from the sequencing and analysis pipelines of the whole genome sequencing (WGS). The advent of second generation sequencing (SGS), significantly, reduced the sequencing costs leading to voluminous research in genomics. SGS technologies, however, generate massive volumes of data in the form of reads, which are fragmentations of the real genome. The performance requirements associated with mapping reads to the reference genome (RG), in order to reassemble the original genome, now, stands disproportionate to the available computational capabilities. Conventionally, the hardware resources used are made of homogeneous many-core architecture employing complex general-purpose CPU cores. Although these cores provide high-performance, a data-centric approach is required to identify alternate hardware systems more suitable for affordable and sustainable genome analysis. Most state-of-the-art genomic tools are performance oriented and do not address the crucial aspect of energy consumption. Although algorithmic innovations have reduced runtime on conventional hardware, the energy consumption has scaled poorly. The associated monetary and environmental costs have made it a major bottleneck to translational genomics. This thesis is concerned with the development and validation of read mappers for embedded genomics paradigm, aiming to provide a portable and energy-efficient hardware solution to the reassembly pipeline. It applies the algorithmhardware co-design approach to bridge the saturation point arrived in algorithmic innovations with emerging low-power/energy heterogeneous embedded platforms. Essential to embedded paradigm is the ability to use heterogeneous hardware resources. Graphical processing units (GPU) are, often, available in most modern devices alongside CPU but, conventionally, state-of-the-art read mappers are not tuned to use both together. The first part of the thesis develops a Cross-platfOrm Read mApper using opencL (CORAL) that can distribute workload on all available devices for high performance. OpenCL framework mitigates the need for designing separate kernels for CPU and GPU. It implements a verification-aware filtration algorithm for rapid pruning and identification of candidate locations for mapping reads to the RG. Mapping reads on embedded platforms decreases performance due to architectural differences such as limited on-chip/off-chip memory, smaller bandwidths and simpler cores. To mitigate performance degradation, in second part of the thesis, we propose a REad maPper for heterogeneoUs sysTEms (REPUTE) which uses an efficient dynamic programming (DP) based filtration methodology. Using algorithm-hardware co-design and kernel level optimizations to reduce its memory footprint, REPUTE demonstrated significant energy savings on HiKey970 embedded platform with acceptable performance. The third part of the thesis concentrates on mapping the whole genome on an embedded platform. We propose a Pyopencl based tooL for gEnomic workloaDs tarGeting Embedded platfoRms (PLEDGER) which includes two novel contributions. The first one proposes a novel preprocessing strategy to generate low-memory footprint (LMF) data structure to fit all human chromosomes at the cost of performance. Second contribution is LMF DP-based filtration method to work in conjunction with the proposed data structures. To mitigate performance degradation, the kernel employs several optimisations including extensive usage of bit-vector operations. Extensive experiments using real human reads were carried out with state-of-the-art read mappers on 5 different platforms for CORAL, REPUTE and PLEDGER. The results show that embedded genomics provides significant energy savings with similar performance compared to conventional CPU-based platforms

Practical Data Processing Approach for RNA Sequencing of Microorganisms

The rapid evolvement of sequencing technology has generated huge amounts of DNA/RNA sequences, even with the continuous performance acceleration. Due to the wide variety of basic studies and applications derived from the huge number of species and the microorganism diversity, the targets to be sequenced are also expanding. The huge amounts of data generated by recently developed high-throughput sequencers have required highly efficient data analysis algorithms using recently developed high-performance computers. We have developed a highly accurate and cost-effective mapping strategy that includes the exclusion of unreliable base calls and correction of the reference sequence through provisional mapping of RNA sequencing reads. The use of mapping software tools, such as HISAT and STAR, precisely aligned RNA-Seq reads to the genome of a filamentous fungus considering exon-intron boundaries. The accuracy of the expression analysis through the refinement of gene models was achieved by the results of mapped RNA-Seq reads in combination with ab initio gene finding tools using generalized hidden Markov models (GHMMs). Visualization of the mapping results greatly helps evaluate and improve the entire analysis in terms of both wet experiment and data processing. We believe that at least a portion of our approach is useful and applicable to the analysis of any microorganism