Integrated Desktop Software for Management of Hepatitic C Data

用于管理丙型肝炎数据的集成桌面软件

• 批准号: 8103362
• 负责人: Johanna C Craig
• 金额: $ 3.4万
• 依托单位: GATACA, LLC
• 依托单位国家: 美国
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-07-19 至 2011-07-18
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8103362
• 关键词: Address; Architecture; Basic Science; Bioinformatics; Biological; Cause of Death; Chronic; Cirrhosis; Clinical; Clinical Trials; Code; Color; Computer software; Data; Data Collection; Data Storage and Retrieval; Database Management Systems; Databases; Development; Disease; Entropy; Face; Fibrosis; Funding; Generations; Generic Drugs; Genetic; Genome; Genomics; Goals; Graph; HIV Seropositivity; Hepatitis C virus; Infection; Informatics; Information Sciences; Internet; Laboratory Research; Lead; Link; Liver diseases; Marketing; Mathematics; Measurement; Mutation; Mutation Analysis; Pathology; Patients; Pharmaceutical Preparations; Phase; Phylogenetic Analysis; Phylogeny; Polymerase; Primary carcinoma of the liver cells; Reporting; Research; Research Personnel; Scientist; Security; Sorting - Cell Movement; Staging; Structure; System; Testing; Time; Trees; United States National Institutes of Health; Viral; Virus; Virus Replication; Work; computerized data processing; data management; design; falls; flexibility; graphical user interface; improved; innovation; middleware; programs; prototype; public health relevance; repository; software systems; tool

DESCRIPTION (provided by applicant): The hepatitis C virus (HCV) infects approximately 4 million people in the U.S. 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 homespun 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 desktop 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 work we designed, built and successfully unit- tested a prototype software system. The software architecture for that product consists of 3 tiers; presentation (GUI), middleware (Domain), and a relational database management system (RDBMS). In Phase I we will develop an alignment tool which will be linked to the existent query tool and include a contig assembler (aim I) for analyzing complete and partial genomic sequences. We will also develop a phylogeny tool for assembling alignments into evolutionary trees that will color-code and time-stamp the input sequences (aim II), and a graphics tool that will present the raw electropherogram data (traces), and assemble line and bar graphs to plot up to two variables (aim III). In Phase II 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. Develop an alignment tool; Aim II Develop a phylogeny tool. Aim III. Develop a graphics tool; 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. PUBLIC HEALTH RELEVANCE: The hepatitis C virus is difficult to study and not effectively treated with anti-viral drugs, with fewer than 50% responding favorably to the current therapies. Efficacious options are years away. A major problem that investigators face is the rapid mutation rate of the virus and the related difficult data management problems that result from this rapid mutation rate. We are developing a powerful software product that will make it easier for scientists to overcome these data management problems. Moreover, our design will streamline the serious bottleneck of data management, significantly compressing the time between data collection and cure discovery.

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。HCV的高突变率导致在实验室研究和临床试验的日常进行中产生大量新的基因序列和相关的生物学数据，伴随着严重的数据管理问题。研究人员目前依赖于自制的数据库，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。这些工具并不适合HCV基因组，并且将数据从一个程序转移到下一个程序是劳动密集型的，并且容易出错。我们正在开发一种桌面软件产品，用于快速，高效和灵活地管理HCV数据。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，两者都是专为HCV分析而设计的。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）带入与那些固有的系统和结构化数据点相同的可搜索上下文。其他创新包括我们的比对，遗传学和突变分析工具，这些工具专门针对HCV复制率及其易错聚合酶的数学计算。在前期工作中，我们设计、构建了一个原型软件系统，并成功地对其进行了单元测试.该产品的软件体系结构由3层组成：表示（GUI）、中间件（域）和关系数据库管理系统（RDBMS）。在第一阶段，我们将开发一个比对工具，它将连接到现有的查询工具，并包括一个重叠群组装器（目的I），用于分析完整和部分基因组序列。我们还将开发一种用于将比对组装成进化树的遗传学工具，该进化树将对输入序列进行颜色编码和时间戳（目标II），以及一种图形工具，该图形工具将呈现原始电泳图数据（痕迹），并组装线条图和条形图以绘制多达两个变量（目标III）。在第二阶段，我们将开发用于突变跟踪、报告生成和熵测量的其他工具，并将开发统计例程、安全和安装包。具体目标：目标一。开发一个对齐工具;目标II开发一个对齐工具。Aim III.开发一个图形工具;目标四。对软件应用程序进行单元测试。我们正在寻求资金来构建我们的产品，以可销售的生物信息学方法解决科学需求。通过这种方式，我们将把信息学与基础研究结合起来，以便快速发现。我们相信，我们的疾病特异性软件产品将有助于快速发展的HCV研究市场。其结果将是软件，大大提高分析能力，减少数据处理时间。这些目标完全属于NIH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。 公共卫生关系：丙型肝炎病毒很难研究，也不能用抗病毒药物有效治疗，只有不到50%的人对目前的治疗有良好的反应。有效的选择还需要几年时间。研究人员面临的一个主要问题是病毒的快速突变率以及由此导致的相关数据管理困难问题。我们正在开发一种功能强大的软件产品，使科学家更容易克服这些数据管理问题。此外，我们的设计将简化数据管理的严重瓶颈，显着压缩数据收集和治愈发现之间的时间。