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程序中心（NCSA）正在围绕NCSA的继承人结构数据格式（HDF5）创建基于标准的软件框架。 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,确认性测序和EST分析。 在我们的愿景中，算法要么集成到系统中以直接从HDF5项目文件读取和写入，要么通过产生标准化的XML格式数据的过滤器程序与项目文件进行通信。通过此模型，可扩展的解决方案将支持DNA测序的不同应用，从而满足医学研究界和未来医学研究界表达的许多需求和要求。作为此过程的第一步，我们将在DNA测序中定义和使用现有标准的DNA测序和注释DNA序列数据的数据模型编辑和版本的数据模型，为基于DNA测序的SNP发现创建原型的DNA序列数据，并为BioInforms Communition提供了生物源性及其对生物HDF的生物学群体的应用。 在过去的十年中，测序DNA的成本下降了1000倍，而原始序列数据的量则下降了，进入我们的国家存储库每12个月增加一倍。 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。通过技术的改进，提出的提案通过两种数量级来降低测序成本，并具有开发技术的最终愿景，以每人1000美元的价格对人类基因组等效序列进行序列。通过这些努力产生的数据数量是不可想象的。但是，除非我们整合DNA测序过程的所有阶段并处理数据的创建，管理，分析，分析和共享数据作为共同目标，否则1,000美元的基因组将不会进步医学研究。