RunBioSimulations: an extensible web application that simulates a wide range of computational modeling frameworks, algorithms, and formats.
RunBioSimulations: an extensible web application that simulates a wide range of computational modeling frameworks, algorithms, and formats.
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DOI：
10.1093/nar/gkab411
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发表时间：
2021-07-02
影响因子：
14.9
通讯作者：
Karr JR
中科院分区：
文献类型：
--
作者：
Shaikh B;Marupilla G;Wilson M;Blinov ML;Moraru II;Karr JR
全面的预测计算模型对于科学、生物工程和医学具有巨大的潜力。实现更多预测模型的一种有前途的方法是组合多个子系统的子模型。为了捕获生物学的多个尺度，这些子模型可能需要多个建模框架和模拟算法。一些社区资源已经可用于使用其中许多框架和算法。然而，这些资源的多样性和数量使得为每个模型找到和使用合适的工具变得具有挑战性，特别是对于新手建模者和实验者来说。为了使这些资源更易于使用，我们开发了 RunBioSimulations (https://run.biosimulations.org)，这是一个用于执行各种模型的 Web 应用程序。 RunBioSimulations 利用社区资源，包括 BioSimulators，一个新的开放式模拟工具注册表。这些资源目前使 RunBioSimulations 能够执行 9 个框架和 44 种算法，并且它们使 RunBioSimulations 可扩展到其他框架和算法。 RunBioSimulations 还提供了共享模拟和交互式可视化结果的功能。我们预计 RunBioSimulations 将促进可重复性、刺激协作，并最终促进创建更具预测性的模型。 RunBioSimulations 是一个可扩展、标准驱动的 Web 应用程序，用于跨各种建模框架、模拟算法和模型格式执行模型，并可视化和共享其结果。
Comprehensive, predictive computational models have significant potential for science, bioengineering, and medicine. One promising way to achieve more predictive models is to combine submodels of multiple subsystems. To capture the multiple scales of biology, these submodels will likely require multiple modeling frameworks and simulation algorithms. Several community resources are already available for working with many of these frameworks and algorithms. However, the variety and sheer number of these resources make it challenging to find and use appropriate tools for each model, especially for novice modelers and experimentalists. To make these resources easier to use, we developed RunBioSimulations (https://run.biosimulations.org), a single web application for executing a broad range of models. RunBioSimulations leverages community resources, including BioSimulators, a new open registry of simulation tools. These resources currently enable RunBioSimulations to execute nine frameworks and 44 algorithms, and they make RunBioSimulations extensible to additional frameworks and algorithms. RunBioSimulations also provides features for sharing simulations and interactively visualizing their results. We anticipate that RunBioSimulations will foster reproducibility, stimulate collaboration, and ultimately facilitate the creation of more predictive models. RunBioSimulations is an extensible, standards-driven web application for executing models across a broad range of modeling frameworks, simulation algorithms, and model formats and visualizing and sharing their results.
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DOI：
10.1016/j.biosystems.2018.07.006
发表时间：
2018-09
期刊：
Bio Systems
影响因子：
--
作者：
Choi K;Medley JK;König M;Stocking K;Smith L;Gu S;Sauro HM
通讯作者：
Sauro HM
影响因子：
3
作者：
Bergmann FT;Adams R;Moodie S;Cooper J;Glont M;Golebiewski M;Hucka M;Laibe C;Miller AK;Nickerson DP;Olivier BG;Rodriguez N;Sauro HM;Scharm M;Soiland-Reyes S;Waltemath D;Yvon F;Le Novère N
通讯作者：
Le Novère N
影响因子：
4.3
作者：
Drawert B;Hellander A;Bales B;Banerjee D;Bellesia G;Daigle BJ Jr;Douglas G;Gu M;Gupta A;Hellander S;Horuk C;Nath D;Takkar A;Wu S;Lötstedt P;Krintz C;Petzold LR
通讯作者：
Petzold LR
影响因子：
1.9
作者：
Olivier, Brett G.;Bergmann, Frank T.
通讯作者：
Bergmann, Frank T.
影响因子：
9.9
作者：
Keating SM;Waltemath D;König M;Zhang F;Dräger A;Chaouiya C;Bergmann FT;Finney A;Gillespie CS;Helikar T;Hoops S;Malik-Sheriff RS;Moodie SL;Moraru II;Myers CJ;Naldi A;Olivier BG;Sahle S;Schaff JC;Smith LP;Swat MJ;Thieffry D;Watanabe L;Wilkinson DJ;Blinov ML;Begley K;Faeder JR;Gómez HF;Hamm TM;Inagaki Y;Liebermeister W;Lister AL;Lucio D;Mjolsness E;Proctor CJ;Raman K;Rodriguez N;Shaffer CA;Shapiro BE;Stelling J;Swainston N;Tanimura N;Wagner J;Meier-Schellersheim M;Sauro HM;Palsson B;Bolouri H;Kitano H;Funahashi A;Hermjakob H;Doyle JC;Hucka M;SBML Level 3 Community members
通讯作者：
SBML Level 3 Community members