BioHDF - Open Binary File Standards for Bioinformatics

BioHDF - 生物信息学开放二进制文件标准

• 批准号: 6992995
• 负责人: TODD M SMITH
• 金额: $ 14.28万
• 依托单位: GEOSPIZA, INC.
• 依托单位国家: 美国
• 财政年份: 2005
• 资助国家: 美国
• 起止时间: 2005-09-05 至 2006-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6992995
• 关键词: DNA; artificial intelligence; bioengineering /biomedical engineering; bioinformatics; computational biology; computer program /software; computer system design /evaluation; functional /structural genomics; genetic mapping; genetic polymorphism; mathematics; molecular biology information system; nucleic acid sequence; single nucleotide polymorphism; virus genetics

DESCRIPTION (provided by applicant): Geospiza Inc. and the National Center for Supercomputing Applications (NCSA) are creating a standards based software framework around NCSA's Heirarchical Data Format (HDF5). The envisioned framework will integrate algorithms important in DNA and protein sequence analysis to create scalable high throughput software systems which will be accessed using new graphical user interfaces (GUIs) to provide researchers with new views of their data to finish sequencing projects in large-scale genome sequencing, microbial genome sequencing, viral epidemiology, polymorphism detection, phylogenetic analysis, multi-locus sequence typing, confirmatory sequencing, and EST analysis. In our vision, algorithms will be either integrated into the system to directly read and write from HDF5 project files, or they will communicate with project files via filter programs that produce standardized XML formatted data. Through this model, a scalable solution will support different applications of DNA sequencing, fulfilling the many needs and requirements expressed by the medical research community now and into the future. As the first step in this process we will, define requirements for editing and versioning data in DNA sequencing, research and propose data models for the computational phases of DNA sequencing and annotating DNA sequence data using existing standards, create a prototype application for DNA sequencing based SNP discovery, and engage the bioinformatics community for BioHDF adoption. In the past ten years the cost of sequencing DNA has dropped over 1000 fold and the amount of raw sequence data, entering our national repositories is doubling every 12 months. DNA sequencing is fundamental to biological research activities such as genomics, systems biology, and clinical medicine. Proposals are being sought to decrease sequencing costs by two orders of magnitude through technology refinements with an ultimate vision of developing technology to sequence human genome equivalents for $1000 each. The amount of data that will be produced through these endeavors is unimaginable. However, the $1,000 genome will not advance medical research unless we integrate all phases of the DNA sequencing process and treat the creation, management, finishing, analysis, and sharing of the data as common goals.

描述（由申请人提供）：Geospiza Inc. 和国家超级计算应用中心 (NCSA) 正在围绕 NCSA 的分层数据格式 (HDF5) 创建基于标准的软件框架。设想的框架将集成DNA和蛋白质序列分析中重要的算法，以创建可扩展的高通量软件系统，该系统将使用新的图形用户界面（GUI）进行访问，为研究人员提供数据的新视图，以完成大规模基因组测序、微生物基因组测序、病毒流行病学、多态性检测、系统发育分析、多位点序列分型、 验证性测序和 EST 分析。 在我们的愿景中，算法要么集成到系统中以直接读取和写入 HDF5 项目文件，要么通过生成标准化 XML 格式数据的过滤程序与项目文件进行通信。通过该模型，可扩展的解决方案将支持 DNA 测序的不同应用，满足医学研究界现在和未来表达的许多需求和要求。作为此过程的第一步，我们将定义 DNA 测序中编辑和版本控制数据的要求，研究并提出 DNA 测序计算阶段的数据模型，并使用现有标准注释 DNA 序列数据，创建基于 SNP 发现的 DNA 测序原型应用程序，并让生物信息学社区参与 BioHDF 的采用。 在过去十年中，DNA 测序的成本下降了 1000 多倍，进入我们国家存储库的原始序列数据量每 12 个月就会翻一番。 DNA 测序是基因组学、系统生物学和临床医学等生物学研究活动的基础。目前正在寻求通过技术改进将测序成本降低两个数量级的提案，最终愿景是开发以每个 1000 美元的价格对人类基因组等价物进行测序的技术。通过这些努力将产生的数据量是难以想象的。然而，除非我们整合 DNA 测序过程的所有阶段，并将数据的创建、管理、整理、分析和共享视为共同目标，否则 1,000 美元的基因组不会推动医学研究。