Continued Development and Support of Essential SBML Infrastructure Software

描述（由申请人提供）：系统生物学标记语言（SBML）是计算系统生物学中软件工具的机器可读模型表示语言。通过支持SBML作为输入/输出格式，不同的工具都可以对模型的相同表示进行操作，从而消除了翻译错误的可能性，并确保了分析和模拟的共同起点。以前在GM070923上的工作帮助SBML作为事实上的标准得到了广泛的支持；截至2009年10月，全球已知超过175个软件系统（包括开源和商业）支持它。今天，有许多国际组织致力于支持下一代SBML，并定义新的模块化包来扩展SBML Level 3的特性。要求甚至预测社区开发特定SBML特性的方向已经变得非常困难。系统生物学建模社区在未来几年需要的是在他们认为合适的时间尺度上探索解决方案的余地。然而，与此同时，将核心软件开发和维护的某些方面完全作为自我维持的开源软件项目留给社区的其余部分还不可能。因此，此应用程序是GM070923的更新建议，其范围很窄，仅关注SBML软件。为了SBML社区的利益，我们希望再进行三年的软件开发和某些关键软件资源的支持。软件目标包括维护和继续增强libSBML、SBML测试套件、SBML演示器、SBML编辑器和在线SBML验证器；此外，我们将继续开发libSBML插件扩展，以支持SBML Level 3语言包，并开发SBML测试套件结果的在线数据库；最后，我们将开发新的软件资源，特别是libSBML的Java版本，以及SBML Level 3的正式模式。1

DESCRIPTION (provided by applicant): The Systems Biology Markup Language (SBML) is a machine-readable model representation language for software tools in computational systems biology. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations. Previous work on GM070923 helped make SBML widely supported as a de facto standard; as of October, 2009, over 175 software systems (both open-source and commercial) are known to support it worldwide. Today, there are a number of international groups working on supporting the next generation of SBML and defining new modular packages to extend the features of SBML Level 3. It has become difficult to mandate or even predict the direction in which specific SBML features are de- veloped by the community. What the systems biology modeling community needs for the next few years is leeway to explore solutions at the timescales they deem appropriate. However, at the same time, it not yet possible to leave certain aspects of core software development and maintenance entirely to the rest of the community as self-sustaining open-source software projects. Consequently, this application is a renewal proposal for GM070923 with a narrow scope focused on SBML software only. We wish to perform additional software development and support of certain crucial software resources for the benefit of the SBML commu- nity for three more years. The software goals include maintaining and continuing to enhance libSBML, the SBML Test Suite, the SBML Demonstrator, SBMLeditor, and the online SBML validator; in addition, we will continue to develop plug-in extensions to libSBML to support SBML Level 3 language packages and develop an online database of SBML Test Suite results; and finally, we will undertake development of new software resources, specifically a Java version of libSBML, and formal schemas for SBML Level 3. 1 PUBLIC HEALTH RELEVANCE: Computation modeling is increasingly becoming a crucial aspect of biological research, and for modeling in biology to continue moving forward, researchers need to be able to create, exchange and publish models in an open format that is directly supported by most software tools. The de facto standard format for this purpose in systems biology is the Systems Biology Markup Language (SBML). Software developers and researchers who write software for modeling benefit by having certain open-source SBML software resources such as an API library (libSBML) available as starting points instead of having to program SBML support from scratch. The goals of this project are to develop, support and enhance a number of SBML software resources that have proven to be essential for the SBML-using community.