Virtual Machines and Cloud Computing for automated and portable sequence analysis

在此输入文本，它是应用程序的新摘要信息。此部分不得超过30行文本。 越来越多的序列数据正在多个生物医学研究学科中产生，特别是通过将下一代测序技术应用于人类及其相关微生物组的基因组分析。然而，序列处理所需的生物信息学基础设施，需要苛刻的软件安装和访问强大的CPU，目前提出了一个戏剧性的瓶颈，进一步扩大在这一领域的研究。我们的提案旨在通过生成一个便携式的、独立的虚拟机（VM）软件包来解决这个问题，该软件包结合了所有必要的工具来执行基本的宏基因组、病毒和真核序列分析。该虚拟机将允许研究人员在本地或服务器网络上轻松实现整个软件管道，独立于正在使用的操作系统，并且无需进一步的安装步骤。此外，由于VM包的移动性，研究人员将有机会将计算密集型处理步骤外包给外部云计算网络，这些网络作为免费的学术和商业服务存在。作为拟议项目的一部分，我们将为宏基因组、病毒和真核基因组测序项目组装生物信息学分析管道，这些项目与人类微生物组和人类宿主的研究相关（目标1）。支持的应用将包括基于16 S rRNA的系统发育和群落比较，以及宏基因组HMP样本中病毒、细菌和真核序列的识别、组装、注释和功能表征。此外，将提供用于该领域中其他日益相关的应用的管道，用于从HMP样品中去除人类DNA，真核和原核DNA和RNA序列作图，包括SNP和剪接位点鉴定以及从头序列组装和来自人类微生物组的真核微生物（例如真菌和原生生物）的注释。集成的分析管道将被打包到一个虚拟机中，创建一个独立的按钮序列分析包（目标2），该分析包将针对商业和学术云的性能进行优化（目标3）。将确定云对下一代序列分析的适用性的客观衡量标准，包括运行时性能指标，如执行时间和相对加速，对磁盘存储的要求，内存和数据传输吞吐量。与广泛的用户社区（包括利用云平台的关键合作者）的联系将促进云平台上进行序列分析的互操作性和标准的开发（目标4）。将提供大量文件，包括互动式在线培训研讨会（网络研讨会）。用户满意度，包括软件的易用性，文件的质量和教学研讨会的价值将进行调查。将设立一个咨询委员会，与项目官员一起审查所有用户统计数据、性能指标、技术发展和项目的总体成功情况。

Enter the text here that is the new abstract information for your application. This section must be no longer than 30 lines of text. Increasing amounts of sequence data are being generated in multiple biomedical research disciplines, particularly through the application of next-generation sequencing technologies to the genomic analysis of humans and their associated microbiome. However, the bioinformatic infrastructure necessary for sequence processing, requiring demanding software installations and access to powerful CPUs, currently presents a dramatic bottleneck for the further expansion of research in this field. Our proposal aims to address this problem through the generation of a portable, stand-alone Virtual Machine (VM) software package that combines all essential tools to perform basic Metagenomic, Viral and Eukaryotic sequence analysis. This VM will allow researchers to easily implement entire software pipelines locally or on server networks, independently of the operating system that is being used and without further installation steps. Furthermore, due to the mobility of the VM package, researchers will have the opportunity to outsource compute-intensive processing steps to external Cloud Computing networks that exist as free academic and commercial services. As part of the proposed project, we will assemble bioinformatics analysis pipelines for metagenomic, viral and eukaryotic genome sequencing projects with relevance to research on the human microbiome and the human host (Aim 1). Supported applications will include 16S rRNA-based phylogeny and community comparison, and identification, assembly, annotation and functional characterization of viral, bacterial and eukaryotic sequences from metagenomic HMP samples. In addition, pipelines for other increasingly relevant applications in this field will be provided for the removal of human DNA from HMP samples, eukaryotic and prokaryotic DNA and RNA sequence mapping, including SNP and splice site identification and de novo sequence assembly and annotation of eukaryotic microbes from the human microbiome, such as fungi and protists. Integrated analysis pipelines will be packaged into a VM, creating a stand-alone, push-button sequence analysis package (Aim 2), which will be optimized for performance on commercial and academic Clouds (Aim 3). Objective measures of the suitability of Clouds for next-generation sequence analysis will be determined and include runtime performance metrics, such as execution time and relative speedup, requirements on disk storage, memory, and data transfer throughput to and from Clouds. Outreach to the broad user community, including key collaborators utilizing Cloud platforms, will promote interoperability and development of standards for performing sequence analysis on Cloud platforms (Aim 4). Extensive documentation will be provided, including interactive online training seminars (webinars). User satisfaction, including software ease of use, quality of documentation, and value of instructional seminars will be surveyed. An advisory board will be established and used in reviewing all user statistics, performance metrics, technical developments and overall success of the project in conjunction with the Program Officer.