Empowering real-time, web-based genomic big data analysis at commercial scale.

实现商业规模的实时、基于网络的基因组大数据分析。

• 批准号: 9379482
• 负责人: Gabor T Marth
• 金额: $ 5万
• 依托单位: FRAMESHIFT LABS, INC.
• 依托单位国家: 美国
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-09-22 至 2017-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9379482
• 关键词: Back; Big Data; Bioinformatics; Chromosomes; Communities; Computer Analysis; Computer Hardware; Computer software; Computers; Core Facility; Custom; DNA; DNA Sequencing Facility; DNA sequencing; Data; Data Analyses; Data Quality; Data Set; Databases; Development; Disease; Drops; Effectiveness; Ensure; Equilibrium; Family; Fees; Funding; Galaxy; Generations; Genes; Genetic; Genome; Genomics; Goals; Grant; Human Genome; Imagery; Institution; Internet; Intuition; Large-Scale Sequencing; Lead; Libraries; Licensing; Metagenomics; Methods; Modeling; Online Systems; Performance; Phase; Population; Positioning Attribute; Preparation; Quality Control; Reporting; Research; Research Infrastructure; Resolution; Resources; Sampling; Sequence Alignment; Software Tools; Techniques; Text; Time; Variant; Work; base; commercial application; computer infrastructure; computing resources; cost; empowered; experience; genetic counselor; genetic pedigree; genetic variant; genome wide association study; genome-wide; genomic data; improved; infrastructure development; interest; next generation sequencing; open source; operation; public health relevance; scale up; statistics; task analysis; tool; trend; tumor; web app; whole genome

 DESCRIPTION (provided by applicant): The academic iobio project delivers web-based applications that visualize and provide real-time interactive analysis with multiple different data types generated as part of next-generation sequencing projects. These applications are open-source and provided for free. This proposal aims to develop critical computational infrastructure to enable the iobio project to offer commercial applications, providing more power and functionality than is possible for the academic project. In particular, it is necessary to build multiple components that will facilitate management of large computational resources in an on-demand, scalable and robust manner and provide mechanisms for remote file storage. Additionally, functionality to seamlessly combine real-time analysis which is the mainstay of the academic developments with large scale analysis undertaken by commercial applications will empower all users of sequencing data from clinicians / genetic counsellors to large scale sequencing centres and institutions. The long-term objective of the proposal is to position Frameshift labs to rapidly and easily build new commercially viable web-based applications to tackle current bioinformatics analysis problems. This proposal also includes the development of a commercial application called multibam.iobio that will provide producers and consumers of large scale sequencing studies the means to evaluate the quality of their massive data sets. In order to perform population level genome wide association studies (GWAS) or more focused Mendelian studies on small family pedigrees, the quality of the data must be understood prior to expending large amounts of time and resources on analysis. The multibam.iobio application will visualize high-level statistics allowing outlier samples or data trends to be rapidly identified. More focused real-time analysis will be accessible for all samples. The effectiveness of sequencing projects, from focused somatic variant identification in tumor / normal pairs to population scale GWAS demands consistently high data quality, whether this is the underlying sequence alignments or genetic variants. Multibam.iobio will ensure that all interested parties, regardless of computational experience and resource limitations, can interrogate and fully understand their data.

 描述（由申请人提供）：学术iobio项目提供基于Web的应用程序，可视化并提供实时交互式分析多种不同的数据 作为下一代测序项目的一部分生成的类型。这些应用程序是开源的，免费提供。该提案旨在开发关键的计算基础设施，使iobio项目能够提供商业应用，提供比学术项目更多的功能。特别是，有必要建立多个组件，这将有助于管理大型计算资源的按需，可扩展和强大的方式，并提供远程文件存储机制。此外，将联合收割机实时分析（学术发展的支柱）与商业应用进行的大规模分析无缝结合的功能将使从临床医生/遗传咨询师到大规模测序中心和机构的测序数据的所有用户都能够使用。该提案的长期目标是使Frameshift实验室能够快速轻松地构建新的商业上可行的基于Web的应用程序，以解决当前的生物信息学分析问题。该提案还包括开发一个名为multibam.iobio的商业应用程序，该应用程序将为大规模测序研究的生产者和消费者提供评估其海量数据集质量的方法。为了进行群体水平的全基因组关联研究（GWAS）或更集中的孟德尔小家族谱系研究，必须在花费大量时间和资源进行分析之前了解数据的质量。multibam.iobio应用程序将可视化高级统计数据，允许快速识别离群样本或数据趋势。所有样品都可以进行更集中的实时分析。测序项目的有效性，从肿瘤/正常对中的集中体细胞变异识别到群体规模GWAS，都要求始终如一的高数据质量，无论是潜在的序列比对还是遗传变异。Multibam.iobio将确保所有相关方，无论计算经验和资源限制如何，都可以询问并充分理解他们的数据。