Continued Development and Maintenance of the Systems Biology Workbench

描述(由申请人提供)：细胞过程的定量分析和模拟正在成为一个有用的工具，在越来越多的情况下，成为预测性生物医学研究不可或缺的工具。在这项提案中，我们的目标是继续我们在生物医学计算标准方面的工作，并进一步改进我们的模拟软件基础设施。我们的工作涉及与美国和欧洲的许多同事密切合作，特别是在标准制定方面。在过去的几年里，我们一直致力于开发SBML(模型定义)、SBGN(图形网络表示)和MIASE/SED-ML(模拟描述)等标准。此外，我们还提供了软件比较工具，使其他开发人员能够衡量他们相对于其他开发人员所做的努力，并在此过程中帮助改进社区中的软件供应。在这个新的提案中，我们强调了三个方面的工作：1)继续改进我们的基础设施，特别是教程和文档；2)提出并开发一个模拟描述标准；2)开发一个分叉分析套件。计算模型最令人沮丧的方面之一是很难复制其他研究人员发表的模拟。我们目前有系统生物学标记语言(SBML)作为事实上的标准模型描述格式，但我们没有任何标准手段来描述模拟应该如何实际进行。我们现正尝试展开这方面的工作，并建议与社会人士磋商，探讨和发展这方面的标准。与此相关，我们还打算开发必要的基础设施和工具包，使作者和期刊出版商能够在电子书和电子期刊文章等电子出版作品中直接嵌入对疾病和生物医学过程的完整模型描述。在实践中，我们设想研究人员在标准查看器中查看文档，并通过简单地用鼠标选择图表来请求建模和复制特定图表所需的所有信息。这将允许研究人员以最小的努力重现模拟。作为对这一努力的测试，我们将开发一套分支工具，我们认为这将是对模拟描述标准要求最高的测试。

DESCRIPTION (provided by applicant): Quantitative analysis and simulation of cellular processes is becoming a useful and in an increasing number of cases, an indispensible tool for predictive biomedical research. In this proposal we aim to continue our work on biomedical computational standards together with further improvements to our simulation software infrastructure. Our work involves close collaboration with numerous colleagues in the United States and Europe particularly in relation to standards development. Over the last few years we have been heavily involved in efforts aimed at developing standards such as SBML (Model definition), SBGN (Graphical network representation) and MIASE/SED-ML (Simulation description). In addition we have provided software comparison tools to enable other developers to gauge their efforts against others and in the process helped improve software provision in the community. In this new proposal we highlight three areas of effort: 1) Continue to improve our infrastructure, particularly tutorials and documentation; 2) To propose and develop a simulation description standard; 2) Develop a bifurcation analysis suite. One of the most frustrating aspects of computational models is the difficulty in replicating simulations published by other researchers. We currently have the systems biology markup language (SBML) as the de facto standard model description format but we do not have any standard means to describe how a simulation should actually be carried out. There are tentative efforts to begin such a process and we propose to explore and develop such as standard in consultation with the community. Related to this we also intend to develop the necessary infrastructure and toolkits to enable authors and journal publishers to directly embed complete model descriptions of disease and biomedical processes in electronic published work, for example e-books and electronic journal articles. In practice we envisage a researcher viewing the document in a standard viewer and requesting all information required to model and replicate a particular graph by simply selecting the graph with the mouse. This would allow a researcher to reproduce a simulation with minimal effort. As a test of this effort we will develop a suite of bifurcation tools which we feel will be the most demanding test for a simulation description standard.