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种有用的，并且在越来越多的情况下，是预测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的工作，生物医学计算标准，进一步改善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标准，如SBML（模型定义），SBGN（图形网络表示）和MIASE/SED-ML（仿真描述）。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与他人的努力，并在此过程中帮助改善社区中的软件供应。在这个新的提案中，我们强调了三个方面的努力：1）继续改善我们的基础设施，特别是教程和文档; 2）提出和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难以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的手段来描述模拟应该如何实际进行。我们正尝试开始这方面的工作，并建议在征询社会人士的意见后，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直接将疾病和生物医学过程的完整模型描述嵌入电子出版作品中，例如电子书和电子期刊文章。在实践中，我们设想一个研究人员在一个标准的查看器中查看文档，并通过简单地用鼠标选择图形来请求建模和复制特定图形所需的所有信息。这将允许研究人员以最小的努力再现模拟。作为这项工作的测试，我们将开发一套分叉工具，我们认为这将是最苛刻的测试模拟描述标准。

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.