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：项目摘要 可再生生物医学建模中心的长期目标是实现全面的预测性 生物系统的模型，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个有希望的方法是将个体生物学模型联合收割机 流程.这就需要可理解的、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的，可重用的，或组合。例如，许多人报告说， 模型没有公布，许多报告的模拟结果是不可重现的，很少有模型是 注释。 最近，研究人员开发了几种标准表示法，例如SBML和SED-ML，以使 模型可重复使用，使仿真结果可再现。然而，这仍然很难理解， 复制和联合收割机模型，因为我们缺乏记录数据源和使用的假设的工具 为了建立模型，我们缺乏注释变量和方程含义的工具，我们缺乏一个通用的 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 仿真工具和（2）将这些和其他现有工具组合成用户友好的可再现建模 工作流最终，我们相信这个工作流程将帮助建模人员创建全面的模型， 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。为了确保该中心的工具能够推进建模， 这些工具将与几个激励合作和服务项目一起开发，这些项目跨越 广泛的建模方法和生物和应用领域。 为了进一步提高生物医学建模的可理解性、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出版教程可重复地进行建模;（3）帮助 研究人员和期刊构建、注释、模拟、分析和验证模型。 该中心将是第一个大规模的努力，使生物医学模型可重复， 考虑到人们对生物医学研究的不可复制性日益关注，该中心将是及时的。我们 预计这一独特的中心将通过以下方式加速全面预测模型的开发： 增强生物医学建模的可理解性、可重用性和再现性。

项目成果

Hierarchical semantic composition of biosimulation models using bond graphs.

使用键图生物仿真模型的分层语义组成。

• DOI: 10.1371/journal.pcbi.1008859
• 发表时间: 2021-05
• 期刊: PLoS computational biology
• 影响因子: 4.3
• 作者: Shahidi N;Pan M;Safaei S;Tran K;Crampin EJ;Nickerson DP
• 通讯作者: Nickerson DP

SysMod: the ISCB community for data-driven computational modelling and multi-scale analysis of biological systems.

• DOI: 10.1093/bioinformatics/btab229
• 发表时间: 2021-11-05
• 期刊: Bioinformatics (Oxford, England)
• 作者: Dräger A;Helikar T;Barberis M;Birtwistle M;Calzone L;Chaouiya C;Hasenauer J;Karr JR;Niarakis A;Rodríguez Martínez M;Saez-Rodriguez J;Thakar J
• 通讯作者: Thakar J

VSCode-Antimony: a source editor for building, analyzing, and translating antimony models.

• DOI: 10.1093/bioinformatics/btad753
• 发表时间: 2023-12-01
• 期刊: Bioinformatics (Oxford, England)

A semantics, energy-based approach to automate biomodel composition.

• DOI: 10.1371/journal.pone.0269497
• 发表时间: 2022
• 期刊: PloS one
• 影响因子: 3.7

libsbmljs-Enabling web-based SBML tools.

• DOI: 10.1016/j.biosystems.2020.104150
• 发表时间: 2020-07
• 期刊: Bio Systems
• 作者: Medley JK;Hellerstein J;Sauro HM
• 通讯作者: Sauro HM