Continued Development and Support of Essential SBML Infrastructure Software

持续开发和支持基本 SBML 基础设施软件

• 批准号: 7988595
• 负责人: MICHAEL HUCKA
• 金额: $ 77.42万
• 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 2013-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7988595
• 关键词: Applications Grants; Award; Biology; Communities; Computer Simulation; Computer software; Databases; Development; Documentation; Ecology; Educational workshop; Elements; Evolution; Extensible Markup Language; Funding; Goals; International; Java; Journals; Language; Language Tests; Left; Libraries; Life Cycle Stages; Maintenance; Modeling; Online Systems; Output; Plug-in; Process; Programming Languages; Publishing; Research Infrastructure; Research Personnel; Resources; Rest; Role; Software Tools; Solutions; Support System; Systems Biology; Tail; Testing; Textbooks; Time; Translations; United States National Institutes of Health; Validation; Work; Writing; base; biological research; biological systems; community organizations; improved; meetings; microbial alkaline proteinase inhibitor; next generation; open source; programs; public health relevance; response; simulation; software development; software systems; tool; volunteer; web site; working group

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.

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。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。之前在GM070923上的工作帮助使SBML作为事实上的标准得到了广泛的支持；截至2009年10月，全世界已知有超过175个软件系统(包括开源和商业软件系统)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的功能。系统生物学建模界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回旋余地。然而，与此同时，还不可能将核心软件开发和维护的某些方面完全留给社区的其他成员作为自给自足的开源软件项目。因此，本申请是GM070923的续订建议，范围较窄，仅侧重于SBML软件。我们希望为SBML社区的利益再进行三年的额外软件开发和对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，我们将继续开发对libSBML的插件扩展以支持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Java版本的libSBML，以及SBML Level 3的正式模式。 公共卫生相关性：计算建模正日益成为生物学研究的一个重要方面，为了继续推进生物学建模，研究人员需要能够以大多数软件工具直接支持的开放格式创建、交换和发布模型。系统生物学中用于此目的的事实上的标准格式是系统生物学标记语言(SBML)。编写建模软件的软件开发人员和研究人员受益于拥有某些开放源代码的SBML软件资源，如API库(LibSBML)作为起点，而不必从头开始编写SBML支持。该项目的目标是开发、支持和增强大量已被证明对SBML使用社区至关重要的SBML软件资源。