Database Software for Complex Cell Biological Pathways

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所必需的。这个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。这一点意义重大，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进程实验数据中提取机械的因果信息方面发挥着越来越重要的作用。在第一阶段SBIR的支持下，集成生物信息公司开发了一个原型，并成功地证明了ProcessDB的可行性。ProcessDB是一种快速、灵活和可扩展的软件产品，其长期目标是更快、更有效地测试涉及数百甚至数千个相互作用分子的复杂细胞生物学理论。该第二阶段SBIR项目有两个具体目标：1)将ProcessDB原型扩展为商业版本，成功地将数据库技术与动力学建模相结合，并将受到学术研究、生物技术公司和药物研发领域的广泛分子细胞生物学家的欢迎；2)在涵盖当前广泛细胞生物学问题的多种研究环境中成功应用ProcessDB软件产品。为了实现这些目标，将增加新的功能，以扩展已经强大的ProcessDB原型的功能和可用性：1)灵活的基于标准的可视化用户界面，允许用户选择绘制而不是使用表格输入他们的假设；2)基于标准的互操作性，与30多个系统生物学软件工具和与两个关键求解器应用程序的完整本地界面；3)包括已发布模型的经过测试和验证的ProcessDB版本；以及4)与公共领域路径和信号数据库的互操作性。这项工作将使用我们在第一阶段成功测试的方法进行：1)使用现代计算机辅助软件工程(CASE*方法)方法来分析、设计、构建、测试、记录和生产ProcessDB；以及2)与专业细胞生物学家建立广泛的咨询、合作和客户关系，他们为我们提供关于每个软件版本的持续反馈和对新功能的知识请求，这些新功能将帮助ProcessDB成为现代分子细胞生物学以及最终也是其他学科综合工作的基本工具。

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.