Integrated software application for management of Hepatitis C Virus data

描述（由申请人提供）：丙型肝炎病毒（HCV）在美国感染了大约400万人，在全球感染了1.7亿人。HCV的高突变率导致在日常实验室研究和临床试验中产生大量新的基因序列和相关的生物学数据，随之而来的是严重的数据管理问题。调查人员目前依靠内部开发的数据库、通用软件产品和公共网络存储库的工具来分类、组织和分析他们的基因组和生物数据。这些工具不是为HCV基因组量身定制的，并且将数据从一个程序转移到另一个程序是劳动密集型的，容易出错。我们正在开发一种基于网络（相对于仅限本地服务器）的软件产品，为快速、高效和灵活地管理HCV数据而量身定制。该产品由图形用户界面（GUI）工具和数据存储和检索系统组成，它们都是专门为HCV分析设计的。它还包括一个商业关系数据库引擎。最值得注意的技术创新是我们的注释工具，它简化了关键实验数据点的捕获，存储和管理，并将这些用户定义的数据点（注释）与那些固有的系统和结构化数据点带入相同的可搜索上下文。其他创新包括我们的比对、系统发育和突变分析工具，这些工具是专门为HCV复制率及其易出错聚合酶的数学计算量身定制的。在初步和第一阶段的工作中，我们设计、构建并成功地对一个原型软件系统进行了单元测试，该系统由3层组成；演示（GUI），中间件（Domain）和关系数据库管理系统（RDBMS），包括用于进行HCV定制对齐和配置组件的工具，这些工具与高度灵活的查询工具相关联，以及用于组装和查看系统发育树的工具，以及用于生成显示原始电泳数据（轨迹）的图形工具，以及用于组装线和柱状图以绘制最多两个变量的工具。在第二阶段的工作中，我们将开发用于突变跟踪、报告生成和熵测量的附加工具，并且我们将开发统计例程、安全和安装包。1 .软件平台向云计算和托管环境的过渡；目的二世。开发一套进行全突变分析的工具；第三目标。制定统计程序；目的四：对软件应用程序进行单元测试。我们正在寻求资金来建立我们的产品，用可销售的生物信息学方法解决科学需求。通过这种方式，我们将信息学与基础研究相结合，以实现快速发现。我们相信，我们的疾病专用软件产品将有助于快速发展的HCV研究市场。结果将是大大提高分析能力和减少数据处理时间的软件。这些目标完全符合美国国立卫生研究院促进生物信息学和信息科学领域基础研究的范围，并可能带来巨大的公共利益。

DESCRIPTION (provided by applicant): The hepatitis C virus (HCV) infects approximately 4 million people in the U.S, and 170 million people worldwide. The high mutation rate of HCV results in vast numbers of new genetic sequences and associated biological data in the daily conduct of laboratory research and clinical trials with attendant serious data management problems. Investigators currently rely upon in-house developed databases, generic software products, and tools from public web repositories to sort, organize and analyze their genomic and biological data. These tools are not tailored to the HCV genome, and moving data from one program to the next is labor intensive and vulnerable to error. We are developing a web-based (vs. local server only) software product tailored for the rapid, efficient and flexible management of HCV data. The product consists of graphical-user interface (GUI) tools and a data-storage and retrieval system that are both designed specifically for HCV analysis. It also includes a commercial relational data base engine. The most notable technical innovation is our annotation tool which simplifies the capture, storage and management of crucial experimental data points, and brings these user defined data points (annotations) into the same searchable context as those that are inherently systemic and structured. Other innovations include our alignment, phylogenetics and mutation analysis tools that are specifically tailored to the mathematics of the HCV replication rate and its error-prone polymerase. In preliminary and Phase I work we designed, built and successfully unit tested a prototype software system, consisting of 3 tiers; presentation (GUI), middleware (Domain), and a relational database management system (RDBMS), and including tools for conducting HCV- tailored alignments and contig assemblies that are linked to a highly flexible query tool, as well as tools for assembling and viewing phylogenic trees and for producing graphics tool that present the raw electropherogram data (traces), and assemble line and bar graphs to plot up to two variables. In this Phase II work, we will develop additional tools for mutation tracking, report generation and entropy measurement, and we will develop statistical routines and security and installation packages. Specific Aims: Aim I. Transition the software platform to cloud computing and hosting environment; Aim II. Develop a suite of tools for conducting full mutation analysis; Aim III. Develop statistical routines; Aim IV. Unit test the software application. We are seeking funds to build our product, addressing a scientific need with a marketable bioinformatics approach. In this way, we will merge informatics with basic research for rapid discovery. We believe that our disease-specific software products will aid in the rapidly developing market of HCV research. The result will be software that greatly improves analysis capabilities and reduces data processing time. These goals fall well within the scope of the NIH to promote basic research in the field of bioinformatics and information sciences, and could lead to enormous public benefit.