Continued Support and Development of SBML

描述(申请人提供)：分子生物学家越来越认识到，在目前正在收集的大量复杂实验数据的背景下，亚细胞机制的计算建模对于理解人类生物学和推进医学研究至关重要。如果要共享、评估和合作开发模型，生物界需要达成一致的信息标准。系统生物学标记语言(SBML)正在成为一种事实上的标准交换格式，用于表示生化反应系统的形式、定性和定量模型。这项提议的长期目标是支持和进一步开发SBML和相关的软件基础设施，以造福于计算生物学社区。具体目标如下： 1.与软件开发人员和用户社区合作，(A)继续发展SBML，并将该语言扩展到具有开发人员所要求的功能的SBML级别3，以及(B)使SBML语言开发过程正规化，并将其控制权移交给社区。 2.维护和扩展用于使用SBML的现有软件库，其设施用于(A)读取和编写SBML Level 3，(B)读取包括CelIML在内的其他格式的模型定义，以及(C)将模型定义转换为其他格式，例如CelIML、MatLab、数学、超文本标记语言等。 3.编写文件，包括使用SBML的“最佳做法”指南，并履行培训职能，帮助教育软件开发人员和建模人员使用SBML和可用于使用SBML的软件工具。

DESCRIPTION (provided by applicant): Molecular biologists are increasingly realizing that computational modeling of sub-cellular mechanisms is crucial for making sense of human biology and advancing medical research in the context of the vast quantities of complex experimental data that are now being collected. The biology community needs agreed-upon information standards if models are to be shared, evaluated and developed co-operatively. The Systems Biology Markup Language (SBML) is becoming a de facto standard exchange format for representing formal qualitative and quantitative models of systems of biochemical reactions. The long-term objectives of this proposal are to support and further develop SBML and related software infrastructure for the benefit of the computational biology community. The specific aims are the following: 1. Work with the community of software developers and users to (a) continue evolving SBML and extending the language into SBML Level 3 with features developers have been requesting, and (b) formalize the SBML language development process and transfer its control to the community. 2. Maintain and extend existing software libraries for working with SBML with facilities for (a) reading and writing SBML Level 3, (b) reading model definitions in other formats including CelIML, and (c) transforming model definitions into other formats such as CelIML, MATLAB, Mathematica, HTML, and others. 3. Produce documentation, including a "best practices" guide to working with SBML, and performing training functions to help educate software developers and modelers in the use of SBML and the software tools available for working with the language.