Center for Reproducible Systems for Biomedical Modeling

总体情况：项目总结 可复制生物医学建模中心的长期目标是实现全面的预测 生物系统模型，如全细胞模型，可以指导精确医学和合成 生物学。建立综合模型的一种有希望的方法是将个体生物学模型结合起来 流程。这需要可理解的、可复制的、可重用的和可组合的个体模型 生物过程。 不幸的是，很少有现有的模型是可复制、可重用或可组合的。例如，许多人报告说 模型没有发布，许多报告的模拟结果不可重现，很少有模型可以重现 带注释的。 最近，研究人员开发了几种标准表示，如SBML和SED-ML，以使 模型可重复使用，并使模拟结果可重现。然而，它仍然很难理解， 复制和组合模型，因为我们缺乏记录数据来源和使用的假设的工具 在建立模型时，我们缺乏注解变量和方程含义的工具，也缺乏通用的 模拟器。 为了实现全面模型的长期目标，我们将使模型变得易于理解， 可复制、可重用和可组合，通过(1)开发这些缺失的模型构建、注释和 模拟工具和(2)将这些工具和其他现有工具组合成用户友好的可重现的建模 工作流程。最终，我们相信此工作流将帮助建模师创建全面的模型，以指导 医学和生物工程。 我们将努力构建广泛适用的与领域无关的工具。然而，为了帮助我们测试工具，我们 最初将专注于细胞的系统生物学模型的工具。为了确保该中心的工具先进的建模， 这些工具将与几个激励性的协作和服务项目一起开发，这些项目跨越 广泛的建模方法以及生物学和应用领域。 为了进一步提高生物医学建模的可理解性、重复性和可重用性，我们将(1) 通过组织会议和发表观点来宣传可复制建模的重要性；(2)培训 研究人员通过组织研讨会和发布教程，以可重复的方式进行建模；以及(3)帮助 研究人员和期刊构建、注释、模拟、分析和验证模型。 该中心将是使生物医学模型可重现的首批大规模努力之一， 鉴于人们越来越关注生物医学研究的不可再生性，该中心将得到及时的支持。我们 预计这个独特的中心将通过以下方式加快全面预测模型的开发 提高生物医学建模的可理解性、可重用性和重复性。

OVERALL: PROJECT SUMMARY The long-term goal of the Center for Reproducible Biomedical Modeling is to achieve comprehensive predictive models of biological systems, such as whole-cell models, that can guide precision medicine and synthetic biology. One promising way to build comprehensive models is to combine models of individual biological processes. This requires understandable, reproducible, reusable, and composable models of individual biological processes. Unfortunately, few existing models are reproducible, reusable, or composable. For example, many reported models are not published, many reported simulation results are not reproducible, and few models are annotated. Recently, researchers have developed several standard representations such as SBML and SED-ML to make models reusable and make simulation results reproducible. However, it is still difficult to understand, reproduce, and combine models because we lack tools for recording the data sources and assumptions used to build models, we lack tools for annotating the meanings of variables and equations, and we lack a universal simulator. Toward our long-term goal of achieving comprehensive models, we will make models understandable, reproducible, reusable, and composable by (1) developing these missing model building, annotation, and simulation tools and (2) combining these and other existing tools into a user-friendly reproducible modeling workflow. Ultimately, we believe this workflow will help modelers create comprehensive models that can guide medicine and bioengineering. We will strive to build broadly-applicable domain-independent tools. However, to help us to test our tools, we will initially focus on tools for systems biology models of cells. To ensure the center's tools advance modeling, the tools will be developed in conjunction with several motivating collaborative and service projects that span a wide range of modeling methods and biological and application domains. To further advance the understandability, reproducibility, and reusability of biomedical modeling, we will (1) promote the importance of reproducible modeling by organizing meetings and publishing perspectives; (2) train researchers to conduct modeling reproducibly by organizing workshops and publishing tutorials; and (3) help researchers and journals build, annotate, simulate, analyze, and verify models. The center would be one of the first large-scale efforts to make biomedical modeling reproducible, and the center would be timely given the increasing concern about the irreproducibility of biomedical research. We anticipate that this unique center will accelerate the development of comprehensive predictive models by enhancing the understandability, reusability, and reproducibility of biomedical modeling.