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，以实现系统生物学分析仪（SBW）和相关软件库的持续维护和开发。SBW是一个大型的软件工具集合，用于模拟和分析细胞网络的动力学模型。该软件已被证明在与生物医学研究有关的问题的研究中是最有用的，特别是我们在p53/Mdm 2对DNA损伤的反应方面的工作，如果没有这个资源，我们的干细胞分化模型就不可能实现。SBW中的许多工具可以作为独立的应用程序使用，但当连接到SBW通信骨干时，这些工具可以无缝地一起使用。这允许软件应用程序以不同的语言编写，可能在不同的平台上运行以一起工作。所有SBW兼容的应用程序都可以读取和写入标准SBML Level 2。这使得计算模型能够在SBW和任何其他SBML兼容工具集之间轻松共享。在本申请中，我们希望请求提供资源，以继续维护软件并进一步改进其功能。SBW的维护需要确保不同的工具可以在三个主要平台上运行- Mac，Linux和Windows -特别是当它们更新时。此外，我们需要继续维护和协助SBML ODE和随机测试套件的发展，这是我们在开发过程中使用的重要工具。除了维护当前的软件，我们还希望在某些领域扩展功能。我们建议进一步发展四个重点领域，包括： a）可用于确定模型中单元一致性的可移植库; B）一个用于SBML和CellML之间转换的可移植库; c）开发一个组合框架和软件库，使模型能够从其他子模型构建; d）将我们成功的可视化设计编辑器JDesigner移植到Mac和Linux平台。这些发展中的许多将直接影响计算社区。将许多计划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.