Continued Support of Essential SBML Software and Community Resources

对基本 SBML 软件和社区资源的持续支持

• 批准号: 8728878
• 负责人: MICHAEL HUCKA
• 金额: $ 49.96万
• 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 2016-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8728878
• 关键词: Biological Models; Biology; Code; Communities; Computer software; Databases; Development; Documentation; Evolution; Future Generations; Generations; Goals; Java; Language; Language Tests; Libraries; Modeling; Online Systems; Programming Languages; Research Infrastructure; Research Personnel; Resources; Shapes; Software Tools; Solutions; Support System; System; Systems Biology; Technology; Testing; Text; Translations; Update; Work; Writing; biological research; computer based Semantic Analysis; design; experience; meetings; microbial alkaline proteinase inhibitor; novel; open source; simulation; software systems; success; tool; web services; web site

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 inpuUoutput 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, 2012, over 250 software systems (both open-source and commercial) are known to support it worldwide. The experiences of the past three years make the present competing renewal application simultaneously easier and more difficult to write. It is easier because we know what needs to happen to support the current generation of SBML (Level 3); it is more difficult because the landscapes of both biological modeling and software technologies are changing rapidly, and while it is clear that SBML must evolve somehow, we cannot forecast or prescribe the details because the changes in SBML must be driven bottom-up by the modeling community. Our proposed solution to this dilema is to create resources that will enable the community to collectively define the shape of SBML to come, while continuing to provide support for important software resources for the SBML community. More specifically, we will (1) support and enhance SBML infrastructure, notably libSBML, JSBML, the Online SBML Validator, the SBML Test Suite, the Online SBML Test Suite and database, and the SBML Demonstrator; (2) encourage and guide the user community to develop still-unfinished SBML Level 3 packages; and (3) provide resources to help the community evolve SBML through (a) a redesigned SBML.org website with a new question- oriented discussion system, (b) a software code generator and prototyping (DEVISER, for "Design Explorer and Viewer for Iterative SBML Enhancement of Representations"), and (c) the development of RDF Schemas for SBML Level 3 and SBML Level 3 packages. We will use the products of Aim 3 to help engage the community in investigating how SBML should evolve, exploring different alternatives and questions in a way that minimizes impact on existing software tools.

系统生物学标记语言 (SBML) 是一种机器可读的模型表示 计算系统生物学中的软件工具语言。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， 消除翻译错误的机会并确保分析的共同起点 和模拟。之前对 GM070923 的工作帮助 SBML 作为事实上的标准得到了广泛支持 标准;截至 2012 年 10 月，超过 250 个软件系统（开源和商业） 众所周知，全世界都支持它。 过去三年的经验使得现在的续签申请竞争激烈 同时更容易写和更难写。这更容易，因为我们知道需要什么 恰好支持当前一代的 SBML（3 级）；这更困难，因为 生物建模和软件技术的格局正在迅速变化，同时 很明显，SBML 必须以某种方式发展，我们无法预测或规定细节，因为 SBML 的变化必须由建模社区自下而上驱动。我们提出的 解决这一困境的方法是创建资源，使社区能够共同定义 SBML 即将成型，同时继续为重要软件资源提供支持 为 SBML 社区。更具体地说，我们将 (1) 支持和增强 SBML 基础设施， 特别是 libSBML、JSBML、在线 SBML 验证器、SBML 测试套件、在线 SBML 测试套件和数据库，以及 SBML 演示器； (2)鼓励和引导用户 社区开发尚未完成的 SBML Level 3 包； (3) 提供资源来帮助 社区通过 (a) 重新设计 SBML.org 网站并提出一个新问题来发展 SBML： 面向讨论系统，(b) 软件代码生成器和原型设计（DEVISER，用于 “用于迭代 SBML 增强表示的设计浏览器和查看器”），以及 (c) 为 SBML Level 3 和 SBML Level 3 包开发 RDF 模式。 我们将使用 Aim 3 的产品来帮助社区参与调查 SBML 如何 应该不断发展，探索不同的替代方案和问题，以尽量减少对 现有的软件工具。