Continued Development and Maintenance of the Systems Biology Workbench

描述(由申请人提供)：本申请旨在提供编程支持，以支持系统生物学工作台(SBW)和相关软件库的持续维护和开发。SBW是一个大型软件工具集合，用于模拟和分析蜂窝网络的动力学模型。事实证明，这个软件在研究与生物医学研究有关的问题方面最有用，特别是我们在DNA损伤的p53/MDM2反应方面的工作，如果没有这个资源，我们的干细胞分化模型是不可能的。SBW中的许多工具可以用作独立的应用程序，但当连接到SBW通信主干时，这些工具可以无缝地一起使用。这允许以不同的语言编写软件应用程序，潜在地，运行在不同平台上的软件应用程序协同工作。所有符合SBW标准的应用程序都可以读取和写入标准的SBML Level 2。这使得计算模型可以在SBW和任何其他符合SBML标准的工具集之间轻松共享。在此应用程序中，我们希望请求资源以继续维护软件并进一步改进其功能。维护SBW需要确保不同的工具可以在三个主要平台-Mac、Linux和Windows-上运行，特别是在它们更新时。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基本工具。除了保持当前的软件外，我们还希望扩展某些领域的功能。我们希望提出四个重点发展的范畴，包括： A)可用于确定模型中单位一致性的便携程序库； B)可移植的库，用于SBML和CellML之间的转换；c)开发合成框架和软件库，以便能够从其他子模型构建模型；d)将我们成功的视觉设计编辑器JDesigner移植到Mac和Linux平台。这些发展中的许多都将直接影响计算社区。将许多计划中的功能放入可移植库中，将使其他开发人员能够在他们自己的项目中重复使用这些工作。所有代码都将是开源的，并托管在SourceForge上。

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.