Continued Support and Development of SBML and Essential SBML Infrastructure

描述(由申请人提供)：系统生物学标记语言(SBML)是用于计算系统生物学中的软件工具的机器可读模型表示语言。它提供了一种以独立于工具的方式表示生化反应网络的定量模型的方法。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机会，并确保了分析和模拟的共同起点。这是迄今为止在这一领域最成功的努力，目前有100多个软件系统支持SBML，每月都会发布更多与SBML兼容的工具。在软件工具之间交换模型的通用、开放格式的广泛接受是在生物学中更广泛地使用定量建模的关键一步，因为它允许研究人员更容易和更准确地发表和建立彼此的工作。这项提案是对三年期赠款(NIGMS GM070923)的竞争性延续申请，自2004年以来，该赠款一直是SBML开发的主要资金来源。我们建议进行一系列努力，旨在支持和增强SBML和关键的SBML软件基础设施，开发SBML测试框架，并支持SBML社区。我们的具体目标是：(1)继续开发和发展SBML语言(包括完成剩余的SBML 3级工作，组织SBML研讨会和其他教育活动，并应用SBML对合成生物学中的问题进行建模)；(2)开发SBML与最近的两项免费工作BioPAX和SBGN之间的接口；(3)继续开发和支持libSBML，这是用于读、写和操作SBML文件和数据流的最流行的开源应用编程接口(API)库；(4)在集成软件环境中开发SBML 3级的参考实现；以及(5)开发全面的测试套件和相关设施，用于测试不同软件工具中SBML实现的完整性和质量。

DESCRIPTION (provided by applicant): The Systems Biology Markup Language (SBML) is a machine-readable model representation language for software tools in computational systems biology. It provides a means of representing quantitative models of biochemical reaction networks in a tool-independent fashion. 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. It is the most successful effort in this area to date, with over 100 software systems supporting SBML today and more SBML-compatible tools being announced monthly. The broad acceptance of a common, open format for exchanging models between software tools is a crucial step towards wider use of quantitative modeling in biology, because it allows researchers to publish and build upon each other's work with greater ease and accuracy. This proposal is a competing continuation application to the three-year grant (NIGMS GM070923) that has provided the major source of funding for SBML development since 2004. We propose to undertake a series of efforts aimed at supporting and enhancing SBML and critical SBML software infrastructure, developing an SBML testing framework, and supporting the SBML community. Our specific aims are: (1) continue development and evolution of the SBML language (including the completion of remaining SBML Level 3 work, organizing SBML workshops and other educational events, and applying SBML to modeling problems in synthetic biology); (2) develop interfaces between SBML and two recent complimentary efforts, BioPAX and SBGN; (3) continue developing and supporting libSBML, the most popular open-source application programming interface (API) library for reading, writing and manipulating SBML files and data streams; (4) develop a reference implementation of SBML Level 3 in an integrated software environment; and (5) develop a comprehensive test suite and associated facilities for testing the completeness and quality of SBML implementations in different software tools.