Database Software for Complex Cell Biological Pathways

复杂细胞生物途径的数据库软件

• 批准号: 6631386
• 负责人: ROBERT D PHAIR
• 金额: $ 9.97万
• 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 2004-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6631386
• 关键词: cell biology; cell component structure /function; chemical kinetics; chemical models; computer program /software; computer simulation; computer system design /evaluation; molecular biology information system

DESCRIPTION (provided by applicant): Complexity is the great challenge of 21st century biological research and pharmaceutical discovery. One approach to this challenge is the new field of computational cell biology, which has emerged at the confluence of cell biology, chemical kinetics, and computer science. Its potential lies in the development of new software tools that facilitate cell biological investigations even as the systems being studied grow increasingly complex. This Phase I SBIR proposal meshes database technology and kinetic modeling to construct one such tool. It aims to demonstrate the feasibility of a software platform that integrates database technology with modeling software. This platform will support the testing of multiple large-scale hypotheses against multiple experimental data sets. The first aim is to complete a prototype software application, called ProcessDB, with a robust set of features supporting efficient formulation, quantification, comparison, and testing of large models. ProcessDB is built on a database of cell and molecular biology primitives such as molecules, complexes, cellular locations, states, and processes, and will permit cell biologists to translate and export their diagrams, working hypotheses and experimental protocols to third-party modeling and optimization software for simulation and parameter estimation. The second aim of this project is feasibility testing. A panel of three expert cell and molecular biologists will exercise our software application by using it to build and test multiple working models of their biological systems. Feasibility will be demonstrated if the prototype software 1) has the stated features, 2) is available via the Internet, and 3) allows cell biologists to enter their theories easily and test them quantitatively against their own dynamic experimental data. No existing software package uses a database of molecules, complexes, places, and processes to manage the formulation and testing of multiple large-scale mechanistic models. The benefit to our users is a faster path to mechanistic understanding of complex cell biological pathways.

描述（由申请人提供）：复杂性是21世纪生物学研究和药物发现的重大挑战。应对这一挑战的一种方法是新的计算细胞生物学领域，该领域已经出现在细胞生物学，化学动力学和计算机科学的汇合处。它的潜力在于开发新的软件工具，即使研究的系统越来越复杂，也可以促进细胞生物学研究。此阶段I SBIR提案网络数据库技术和动力学建模，以构建一种这样的工具。它旨在证明将数据库技术与建模软件集成的软件平台的可行性。该平台将支持针对多个实验数据集的多个大规模假设的测试。第一个目的是完成一个称为ProcessDB的原型软件应用程序，并具有一组强大的功能，以支持大型模型的有效公式，量化，比较和测试。 ProcessDB建立在细胞和分子生物学原始数据的数据库上，例如分子，复合物，细胞位置，状态和过程，并将允许细胞生物学家翻译和导出其图表，工作假设以及实验方案，以进行第三方建模和优化软件，以进行模拟和参数估计。该项目的第二个目的是可行性测试。由三个专家细胞和分子生物学家组成的小组将通过使用它来构建和测试其生物系统的多个工作模型来行使我们的软件应用。如果原型软件1）具有陈述的功能，则可以证明可行性，2）可通过Internet获得，3）允许细胞生物学家轻松输入其理论，并根据自己的动态实验数据进行定量测试。没有现有的软件包使用分子，复合物，地点和过程的数据库来管理多个大规模机械模型的公式和测试。对我们的用户的好处是对复杂细胞生物学途径的机械理解的更快途径。