Database Software for Complex Cell Biological Pathways

描述(申请人提供)：复杂性是21世纪生物研究和药物发现的巨大挑战。解决这一挑战的一种方法是计算细胞生物学的新领域，它是在细胞生物学、化学动力学和计算机科学的交汇下出现的。它的潜力在于开发新的软件工具，即使正在研究的系统变得越来越复杂，也能促进细胞生物学研究。这一阶段的SBIR提案融合了数据库技术和动力学建模来构建一个这样的工具。旨在论证将数据库技术与建模软件相结合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。第一个目标是完成一个名为ProcessDB的原型软件应用程序，它具有一组健壮的功能，支持对大型模型进行高效的制定、量化、比较和测试。ProcessDB建立在分子、复合体、细胞位置、状态和过程等细胞和分子生物学原语的数据库上，并将允许细胞生物学家将他们的图表、工作假设和实验方案翻译和输出到第三方建模和优化软件，以进行模拟和参数估计。该项目的第二个目标是可行性测试。一个由三位专业细胞和分子生物学家组成的小组将使用我们的软件应用程序来构建和测试他们的生物系统的多个工作模型。如果原型软件1)具有所述的特征，2)可以通过互联网获得，以及3)允许细胞生物学家轻松地输入他们的理论并根据他们自己的动态实验数据对其进行定量测试，则可行性将被证明。没有一个现有的软件包使用分子、络合物、位置和过程的数据库来管理多个大型机械模型的制定和测试。对我们的用户的好处是更快地从机械上理解复杂的细胞生物学途径。

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.