Continued Support and Development of SBML and Essential SBML Infrastructure

持续支持和开发 SBML 和基本 SBML 基础设施

• 批准号: 7468496
• 负责人: MICHAEL HUCKA
• 金额: $ 56.36万
• 依托单位: CALIFORNIA INSTITUTE OF TECHNOLOGY
• 依托单位国家: 美国
• 财政年份: 2004
• 资助国家: 美国
• 起止时间: 2004-02-01 至 2010-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7468496
• 关键词: Architecture; Area; Beds; Biochemical Reaction; Biological; Biology; Communities; Compatible; Complex; Computer software; Data; Data Files; Databases; Depth; Development; Documentation; Education and Outreach; Educational workshop; Environment; Event; Evolution; Failure; Funding Agency; Grant; Language; Language Development; Language Tests; Libraries; Modeling; National Institute of General Medical Sciences; Nature; Online Systems; Output; Pathway interactions; Plug-in; Publishing; Reading; Research Infrastructure; Research Personnel; Series; Software Tools; Source; Standards of Weights and Measures; Stream; Support System; System; Systems Biology; Testing; Today; Translations; Work; Writing; base; experience; member; open source; programs; research and development; simulation; software systems; synthetic biology; tool

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.

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。它提供了一种以工具独立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可能性，并确保了分析和模拟的共同起点。这是该领域迄今为止最成功的工作，目前有超过100个软件系统支持SBML，并且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，是在生物学中广泛使用定量建模的关键一步，因为它允许研究人员更轻松、更准确地发表和建立彼此的工作。该提案是对三年拨款（NIGMS GM070923）的竞争性延续申请，该拨款自2004年以来为SBML开发提供了主要资金来源。我们建议开展一系列工作，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)继续发展和演变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，并将SBML应用于合成生物学中的建模问题）；(2)开发SBML与最近两项互补项目BioPAX和SBGN之间的接口；(3)继续开发和支持libSBML，这是最流行的开源应用程序编程接口（API）库，用于读取、编写和操作SBML文件和数据流；(4)在集成软件环境中开发SBML Level 3的参考实现；(5)开发一个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。