Continued Support of Essential SBML Software and Community Resources

系统生物学标记语言(SBML)是一种机器可读的模型表示 计算系统生物学中软件工具的语言。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， 排除翻译错误的机会并确保分析的共同起点 和模拟。之前在GM070923上的工作帮助使SBML在事实上得到广泛支持 标准；截至2012年10月，超过250个软件系统(包括开放源码和商业软件) 在世界范围内都支持它。 过去三年的经验使目前的续签申请具有竞争性 同时，写作也更容易，也更难。这更容易，因为我们知道需要什么 碰巧支持当前一代SBML(第3级)；这更加困难，因为 生物建模和软件技术的格局都在迅速变化，虽然 很明显，SBML必须以某种方式演变，我们不能预测或规定细节，因为 SBML中的更改必须由建模社区自下而上地驱动。我们的建议 解决这一困境的办法是创建资源，使社区能够集体定义 SBML的形态即将到来，同时继续为重要的软件资源提供支持 对于SBML社区来说。更具体地说，我们将(1)支持和加强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 社区开发仍未完成的SBML Level 3包；以及(3)提供资源帮助 社区通过以下方式发展SBML：(A)重新设计SBML.org网站，提出新问题-- 面向讨论的系统，(B)软件代码生成器和原型(设计者，用于 “用于迭代SBML表示增强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的产品帮助社区调查SBML如何 应该不断发展，探索不同的替代方案和问题，将影响降至最低 现有的软件工具。

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.