CC* Compute: BioBurst

该项目的目标是部署BioBurst系统，以增强加州大学圣地亚哥分校的高性能计算能力，采用旨在加速生物和生命科学研究的技术。在过去的几年里，用于破译脱氧核糖核酸(DNA)和核糖核酸(RNA)等遗传物质的测序仪器取得了革命性的进展。DNA和RNA携带着遗传密码，控制着生命所必需蛋白质的生产。这场DNA/RNA测序技术革命的一个副产品是产生了大量数据，为了实现科学进步，必须存储和分析这些数据。进行这些分析的方式强调必须克服的现有研究计算系统，以便扩大调查范围和缩短得出结果的时间。BioBurst系统旨在用创新技术增强校园研究计算系统，以加快DNA/RNA序列数据的数据访问和计算。更好地了解DNA和RNA有可能促进我们国家的健康和福祉，使对致病生物机制的新见解以及新生物燃料和农产品的开发等应用成为可能。该项目的技术目标是实施现有校园研究计算系统的单独计划分区，其技术旨在解决重要的生物信息学计算类别，包括基因组学、转录组学和免疫受体谱系分析。BioBurst系统将包括以下主要组件：(1)具有40 TB非易失性存储器的I/O加速器，以及旨在缓解许多生物信息学代码所特有的小块/小文件I/O问题的软件；(2)基于FPGA的计算加速器节点，已被证明在22分钟内执行完整人类基因组的多路分解、读取映射和变体调用；(3)将访问I/O加速器并为运行生物信息学应用程序提供单独调度资源的672个商用计算核心；(4)与大规模并行文件系统的集成，该文件系统支持流I/O并具有存放与许多生物信息学研究相关的大量数据的能力；以及5)对作业调度程序进行定制以适应生物信息学工作流，该工作流可由单个用户一次提交的数百到数千个作业组成。这些组件将被整合为现有生产研究计算系统的一个分区，为校园内的研究人员提供独特且高度可用的资源。一个关键目标是提供大量计算能力，每年进行大约8,000次全基因组分析，外加快速周转(60分钟)的能力。单基因组分析，以及用于暂存相关工作集的足够固态硬盘(SSD)容量(200 GB-1TB)。

The goal of the project is to deploy the BioBurst system to enhance the high performance computing capabilities at the University of California, San Diego, with technology designed to accelerate biological and life sciences research. The last few years have seen revolutionary advances in sequencing instruments for decoding genetic materials such as deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA and RNA carry the genetic code and control the production of proteins essential to life. A byproduct of this revolution in DNA/RNA sequencing technology is the production of vast amounts of data that must be stored and analyzed in order to achieve scientific progress. The manner of conducting these analysis stresses existing research computing systems in ways that must be overcome in order to expand the scope of investigations and reduce the time to results. The BioBurst system aims to augment the campus research computing system with innovative technology to speed up both data access and computation on DNA/RNA sequence data. A better understanding of DNA and RNA has the potential for advancing our Nation's health and well-being, enabling applications such as new insights into the biological mechanisms causing disease, and the development of new biofuels and agriculture products. The technical goal of the project is to implement a separately scheduled partition of the existing campus research computing system with technology designed to address important classes of bioinformatics computing including genomics, transcriptomics, and immune receptor repertoire analysis. The BioBurst system will incorporate the following major components: (1) I/O acceleration appliance with 40 terabytes of non-volatile memory and software designed to alleviate the small-block/small-file I/O problem characteristic of many bioinformatics codes; (2) An FPGA-based computational accelerator node that has been demonstrated to perform demultiplexing, read mapping, and variant calling of complete human genomes in 22 minutes; (3) 672 commodity computing cores which will access the I/O accelerator and provide a separately scheduled resource for running bioinformatics applications; (4) integration with a large scale parallel file system, which supports streaming I/O and has the capacity to stage large amounts of data associated with many bioinformatics studies; and 5) customization to the job scheduler to accommodate bioinformatics workflows, which can consist of hundreds to thousands of jobs submitted by a single user at one time. These components will be integrated as a partition of the existing production research computing system, providing a unique and highly usable resource by researchers across campus. A key objective is to provide bulk computing capacity to conduct in the order of 8,000 whole-genome analyses per year plus the ability for quick turnaround ( 60 min.) single-genome analyses, and sufficient solid state disk (SSD) capacity for staging associated working sets (200GB - 1TB).