Continued Development and Maintenance of the Systems Biology Workbench

系统生物学工作台的持续开发和维护

• 批准号: 7681630
• 负责人: HERBERT M. SAURO
• 金额: $ 19.5万
• 依托单位: UNIVERSITY OF WASHINGTON
• 依托单位国家: 美国
• 财政年份: 2007
• 资助国家: 美国
• 起止时间: 2007-08-02 至 2011-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7681630
• 关键词: Affect; Area; Biomedical Research; Breast Cancer Cell; Cell model; Code; Collection; Communication; Communities; Computer Simulation; Computer software; DNA Damage; Databases; Decision Making; Development; Documentation; Ensure; Equation; Event; Glues; Growth; Kinetics; Language; Laws; Libraries; Linux; Maintenance; Modeling; Names; Noise; Operating System; Pathway interactions; Process; Property; Reaction; Reading; Research; Resources; Running; Sampling; Site; Software Tools; Systems Biology; Techniques; Testing; Translating; Translations; Update; Variant; Vertebral column; Visual; Work; Writing; base; biological systems; design; feeding; open source; predictive modeling; programs; response; simulation; stem cell differentiation; tool; wiki

DESCRIPTION (provided by applicant): This application is to provide programming support to enable the continued maintenance and development of the Systems Biology Workbench (SBW) and related software libraries. SBW is a large collection of software tools for enabling the simulation and analysis of kinetic models of cellular networks. This software have proved most useful in the study of problems related to biomedical research, in particular our work on the p53/Mdm2 response to DNA damage and our stem cell differentiation model would not have been possible without this resource. Many of the tools in SBW can be used as standalone applications but when connected to the SBW communications backbone, the tools may be used seamlessly together. This permits software applications to be written in different languages, potentially, running on different platforms to work together. All SBW compliant applications can read and, often write, standard SBML Level 2. This enables computational models to be easily shared between SBW and any other SBML compliant tool set. In this application we wish to request resources to continue to maintain the software and to contribute further improvements to its functionality. Maintenance of SBW requires ensuring that the different tools can run on the three main platforms - Mac, Linux and Windows - particularly as they are updated. In addition we need to continue to maintain and assist in the growth of the SBML ODE and stochastic test suite which are essential tools that we use in our development process. In addition to maintaining the current software we also wish to extent functionality in certain areas. We wish to propose four focus areas for further development, these include: a) A portable library that can be used to determine unit consistency in a model; b) A portable library for translation between SBML and CellML; c) Develop a composition framework and software libraries to enable models to be constructed from other submodels; d) To port our successful visual design editor, JDesigner, to the Mac and Linux platforms. Many of these developments will directly affect the computational community. Placing much of the planned functionality into portable libraries will enable other developers to reuse this work in their own projects. All code will be open source and hosted on sourceforge.

描述（由申请人提供）：此应用程序是为了提供编程支持，以启用系统生物学工作台（SBW）和相关软件库的持续维护和开发。 SBW是大量软件工具，用于启用细胞网络动力学模型的模拟和分析。事实证明，该软件在研究与生物医学研究有关的问题中最有用，特别是我们在p53/MDM2对DNA损伤的响应方面的工作，如果没有此资源，我们的干细胞分化模型将是不可能的。 SBW中的许多工具都可以用作独立应用程序，但是当连接到SBW通信骨架时，这些工具可以无缝使用。这允许软件应用程序以不同的语言编写，可能会在不同的平台上运行以合作。所有符合SBW的应用程序都可以读取并经常编写标准SBML级别2。这使得可以在SBW和任何其他符合SBML的工具集之间轻松共享计算模型。在此应用程序中，我们希望请求资源继续维护该软件，并为其功能做出进一步的改进。 SBW的维护需要确保不同工具可以在三个主要平台上运行 - Mac，Linux和Windows - 尤其是在更新时。此外，我们需要继续维护和协助SBML ODE和随机测试套件的增长，这是我们在开发过程中使用的重要工具。除了维护当前软件外，我们还希望在某些领域的功能。我们希望为进一步发展提出四个重点领域，其中包括： a）可用于确定模型中单元一致性的便携式库； b）用于SBML和CellML之间翻译的便携式库； c）开发一个组成框架和软件库，以使模型可以从其他子模型构建； d）将我们成功的视觉设计编辑器将JDesigner移植到Mac和Linux平台。这些发展中的许多将直接影响计算界。将许多计划的功能放入便携式库中，将使其他开发人员能够在自己的项目中重新使用这项工作。所有代码将是开源的，并在SourceForge上托管。