Database Software for Complex Cell Biological Pathways

复杂细胞生物途径的数据库软件

• 批准号: 6911724
• 负责人: ROBERT D PHAIR
• 金额: $ 36.99万
• 依托单位: INTEGRATIVE BIOINFORMATICS, INC.
• 依托单位国家: 美国
• 财政年份: 2003
• 资助国家: 美国
• 起止时间: 2003-04-01 至 2006-12-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6911724
• 关键词: bioengineering /biomedical engineering; cell biology; cell component structure /function; chemical kinetics; chemical models; computational biology; computer human interaction; computer program /software; computer simulation; computer system design /evaluation; molecular biology information system

DESCRIPTION (provided by applicant): Database technology is widely recognized as essential for managing and analyzing large-scale experimental datasets. The innovative idea of this SBIR project is to apply database technology to the corresponding problem of managing large-scale cell biological theories or models. This is significant because computational cell biology/systems biology is playing an increasingly important role in helping molecular cell biologists extract mechanistic, cause-and-effect information from time course experimental data. With Phase I SBIR support, Integrative Biolnformatics, Inc. has developed a prototype and successfully demonstrated feasibility for ProcessDB, a fast, flexible and scalable software product whose long term objective is faster, more efficient testing of complex cell biological theories involving hundreds or even thousands of interacting molecules. This Phase II SBIR project has two specific aims: 1) to expand the ProcessDB prototype into a commercial version that successfully integrates database technology with kinetic modeling in a way that will be embraced by a broad range of molecular cell biologists in academic research, biotechnology companies, and pharmaceutical R&D; and 2) to successfully apply the ProcessDB software product in multiple research environments covering a wide range of current cell biological problems. To achieve these aims, new features will be added to expand the functionality and the usability of the already powerful ProcessDB prototype: 1) a flexible standards-based visual user interface allowing users the option to draw rather than use forms to enter their hypotheses; 2) standards-based interoperability with more than 30 systems biology software tools and full native interfaces with two key solver applications; 3) inclusion of tested and verified ProcessDB versions of published models; and 4) interoperability with public domain pathway and signaling databases. This work will be carried out using methods that we successfully tested in Phase I: 1) a modern computer assisted software engineering (CASE*Method) approach to the analysis, design, building, testing, documentation, and production of ProcessDB; and 2) extensive consulting, collaboration, and client relationships with expert cell biologists who provide us with continuous feedback on each software release and knowledgeable requests for new features that will help ProcessDB become an essential tool for integrative work in modern molecular cell biology and ultimately in other disciplines as well.

描述（由申请人提供）： 数据库技术被广泛认为是管理和分析大规模实验数据集必不可少的。 SBIR项目的创新思想是将数据库技术应用于管理大规模细胞生物学理论或模型的相应问题。这很重要，因为计算细胞生物学/系统生物学在帮助分子细胞生物学家从时间过程实验数据中提取机械和效应信息方面起着越来越重要的作用。借助I期SBIR支持，Integrative Biolgonformatics，Inc。开发了一种原型，并成功证明了ProcessDB的可行性，ProcessDB是一种快速，灵活和可扩展的软件产品，其长期目标更快，对复杂细胞生物学理论的更有效测试涉及数百或数千种相互作用的分子。该II阶段SBIR项目具有两个具体的目的：1）将ProcessDB原型扩展到商业版本中，该商业版本将数据库技术与动力学建模成功整合在一起，这种方式将被广泛的分子细胞生物学家在学术研究，生物技术公司和药品R＆D中所包含。 2）在多种研究环境中成功应用ProcessDB软件产品，涵盖了各种当前细胞生物学问题。为了实现这些目标，将添加新功能，以扩展已经强大的ProcessDB原型的功能和可用性：1）基于标准的可视化用户界面，使用户可以选择绘制而不是使用表单来输入其假设； 2）基于标准的互操作性与30多个系统生物学软件工具和具有两个关键求解器应用程序的完整本地接口； 3）包括已公开模型的经过测试和验证的ProcessDB版本； 4）与公共域通路和信号数据库的互操作性。这项工作将使用我们在I阶段成功测试的方法进行，1）现代计算机辅助软件工程（案例*方法）方法，用于分析，设计，建筑，测试，文档和ProcessDB的生产； 2）与专家细胞生物学家的广泛咨询，协作以及客户关系，他们为我们提供了每个软件发布的持续反馈，并知识渊博的新功能请求将有助于ProcessDB成为现代分子细胞生物学中综合工作的重要工具，并最终在其他学科中。