BioHDF - Open Binary File Standards for Bioinformatics

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（HDF 5）创建基于标准的软件框架。设想的框架将整合DNA和蛋白质序列分析中的重要算法，以创建可扩展的高通量软件系统，该软件系统将使用新的图形用户界面（GUI）访问，为研究人员提供新的数据视图，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。 在我们的设想中，算法将被集成到系统中，直接从HDF 5项目文件中读取和写入，或者它们将通过产生标准化XML格式数据的过滤程序与项目文件进行通信。通过这种模式，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的许多需求和要求。作为该过程的第一步，我们将定义DNA测序中编辑和版本化数据的要求，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DNA测序的SNP发现的原型应用程序，并让生物信息学社区参与BioHDF的采用。 在过去的十年中，DNA测序的成本下降了1000多倍，进入我们国家数据库的原始序列数据量每12个月翻一番。DNA测序是生物研究活动的基础，如基因组学，系统生物学和临床医学。正在寻求通过技术改进将测序成本降低两个数量级的建议，最终愿景是开发技术，以每个1000美元的价格对人类基因组等同物进行测序。通过这些努力将产生的数据量是不可想象的。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、分析和共享作为共同目标，否则1,000美元的基因组不会推动医学研究。

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.