Center for Reproducible Systems for Biomedical Modeling

生物医学建模可重复系统中心

• 批准号: 10676065
• 负责人: Ion I. Moraru
• 金额: $ 128.94万
• 依托单位: UNIVERSITY OF WASHINGTON
• 依托单位国家: 美国
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-06-13 至 2024-02-29
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10676065
• 关键词: Acceleration; Behavior; Big Data Methods; Biological; Biological Process; Biomedical Engineering; Biomedical Research; Biophysics; Cell model; Cells; Community Services; Complex; Computer software; Data; Data Sources; Databases; Development; Educational workshop; Ensure; Equation; Goals; Individual; Journals; Medicine; Methods; Modeling; Online Systems; Ontology; Organizational Models; Publishing; Reader; Reporting; Reproducibility; Reproducibility of Results; Research; Research Personnel; Resources; Services; System; Systems Biology; Testing; Time; Training; Validation; Visualization; annotation system; biological systems; design; experimental study; heterogenous data; meetings; model building; model design; novel; precision medicine; predictive modeling; simulation; synthetic biology; tool; user-friendly; web-based tool

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.

总体而言：项目概要 可重复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，例如全细胞模型，可以指导精准医学和合成 生物学。建立综合模型的一种有前途的方法是将个体生物模型结合起来 流程。这需要可理解、可重复、可重用和可组合的个体模型 生物过程。 不幸的是，现有的模型很少是可复制、可重用或可组合的。例如，许多报道称 模型尚未发布，许多报告的模拟结果不可重复，并且很少有模型被 已注释。 最近，研究人员开发了几种标准表示形式，例如 SBML 和 SED-ML，以使得 模型可重复使用，并使模拟结果可重现。但还是很难理解， 重现并组合模型，因为我们缺乏记录所使用的数据源和假设的工具 为了建立模型，我们缺乏注释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，我们将使模型易于理解， 通过 (1) 开发这些缺失的模型构建、注释和可重复性、可重用性和可组合性 仿真工具以及 (2) 将这些工具和其他现有工具组合成用户友好的可重复建模 工作流程。最终，我们相信这个工作流程将帮助建模者创建可以指导的综合模型 医学和生物工程。 我们将努力构建广泛适用的独立于领域的工具。然而，为了帮助我们测试我们的工具，我们 最初将专注于细胞系统生物学模型的工具。为了确保中心的工具推进建模， 这些工具将与多个跨领域的激励性协作和服务项目一起开发。 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模型的可理解性、可重复性和可重用性，我们将 (1) 通过组织会议和发布观点来宣传可重复建模的重要性； (2)火车 研究人员通过组织研讨会和发布教程来进行可重复的建模； (3) 帮助 研究人员和期刊构建、注释、模拟、分析和验证模型。 该中心将是最早致力于使生物医学模型可重复的大规模努力之一，并且 鉴于人们日益关注生物医学研究的不可重复性，该中心将适时推出。我们 预计这个独特的中心将加速综合预测模型的开发 提高生物医学模型的可理解性、可重用性和可重复性。

项目成果

A modular and reusable model of epithelial transport in the proximal convoluted tubule.

近曲小管上皮运输的模块化且可重复使用的模型。

• 发表时间: 2022
• 影响因子: 3.7
• 作者: Noroozbabaee, Leyla;Blanco, Pablo J;Safaei, Soroush;Nickerson, David P
• 通讯作者: Nickerson, David P

Hierarchical semantic composition of biosimulation models using bond graphs.

使用键图的生物模拟模型的分层语义组成。

• 发表时间: 2021-05
• 影响因子: 4.3
• 作者: Shahidi, Niloofar;Pan, Michael;Safaei, Soroush;Tran, Kenneth;Crampin, Edmund J;Nickerson, David P
• 通讯作者: Nickerson, David P

Building the next generation of virtual cells to understand cellular biology.

构建下一代虚拟细胞以了解细胞生物学。

• 发表时间: 2023-09-19
• 影响因子: 3.4
• 作者: Johnson, Graham T;Agmon, Eran;Akamatsu, Matthew;Lundberg, Emma;Lyons, Blair;Ouyang, Wei;Quintero;Riel;Rafelski, Susanne;Horwitz, Rick
• 通讯作者: Horwitz, Rick

Recent advances in biomedical simulations: a manifesto for model engineering.

生物医学模拟的最新进展：模型工程宣言。

• 发表时间: 2019
• 作者: Hellerstein, Joseph L;Gu, Stanley;Choi, Kiri;Sauro, Herbert M
• 通讯作者: Sauro, Herbert M

Best Practices for Making Reproducible Biochemical Models.

制作可重复生化模型的最佳实践。

• 发表时间: 2020
• 影响因子: 9.3
• 作者: Porubsky, Veronica L;Goldberg, Arthur P;Rampadarath, Anand K;Nickerson, David P;Karr, Jonathan R;Sauro, Herbert M
• 通讯作者: Sauro, Herbert M