Hierarchical semantic composition of biosimulation models using bond graphs.
Hierarchical semantic composition of biosimulation models using bond graphs.
复制标题
使用键图生物仿真模型的分层语义组成。
DOI：
10.1371/journal.pcbi.1008859
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发表时间：
2021-05
影响因子：
4.3
通讯作者：
Nickerson DP
中科院分区：
文献类型：
--
作者：
Shahidi N;Pan M;Safaei S;Tran K;Crampin EJ;Nickerson DP
模拟复杂的生物和生理系统并预测它们在不同条件下的行为仍然具有挑战性。将系统分解成更小、更易于管理的模块可以解决这一挑战，帮助模型开发和仿真。然而，生物学和生理学中现有的计算模型往往不是模块化的，因此很难组装成更大的模型。即使这是可能的，由于与物理定律或系统的生理行为不一致，所得到的模型也可能没有用处。在这里，我们提出了一种组合模型的通用方法，将基于能量的键合图方法与基于语义的注释相结合。这种方法改进了模型组合，并确保组合模型在物理上是可信的。作为一个例子，我们使用人体动脉循环模型演示了这种自动模型组成的方法。主要的好处是建模者可以花更多的时间来理解复杂的生物和生理系统的行为，而不用花更多的时间来争论模型的组成。生物和生理系统通常涉及多个潜在的过程、机制、结构和现象，这里称为子系统。每次从头开始对整个系统建模都需要付出巨大的努力。另一种方法是以模块化的方式对每个子系统建模，也就是说，包含用于连接到其他模块的有意义的接口。这些模块可以很容易地组合在一起，形成一个完整的系统模型。为了使组合模型保持一致，必须使用相同的建模方案来描述模块。实现这一目标的一种方法是使用符合物理守恒定律的基于能量的模型。在这里，我们提出了一种使用键合图实现这一目标的方法，它允许模块更快、更有效地组合在一起。首先，使用少量模板模块生成物理上合理的模块。然后在每个模块中添加一个有意义的接口来自动连接。通过将该方法应用于现有的循环系统模型并根据参考模型验证结果，说明了这种方法。
Simulating complex biological and physiological systems and predicting their behaviours under different conditions remains challenging. Breaking systems into smaller and more manageable modules can address this challenge, assisting both model development and simulation. Nevertheless, existing computational models in biology and physiology are often not modular and therefore difficult to assemble into larger models. Even when this is possible, the resulting model may not be useful due to inconsistencies either with the laws of physics or the physiological behaviour of the system. Here, we propose a general methodology for composing models, combining the energy-based bond graph approach with semantics-based annotations. This approach improves model composition and ensures that a composite model is physically plausible. As an example, we demonstrate this approach to automated model composition using a model of human arterial circulation. The major benefit is that modellers can spend more time on understanding the behaviour of complex biological and physiological systems and less time wrangling with model composition. Biological and physiological systems usually involve multiple underlying processes, mechanisms, structures, and phenomena, referred to here as sub-systems. Modelling the whole system every time from scratch requires a huge amount of effort. An alternative is to model each sub-system in a modular fashion, i.e., containing meaningful interfaces for connecting to other modules. Such modules are readily combined to produce a whole-system model. For the combined model to be consistent, modules must be described using the same modelling scheme. One way to achieve this is to use energy-based models that are consistent with the conservation laws of physics. Here, we present an approach that achieves this using bond graphs, which allows modules to be combined faster and more efficiently. First, physically plausible modules are generated using a small number of template modules. Then a meaningful interface is added to each module to automate connection. This approach is illustrated by applying this method to an existing model of the circulatory system and verifying the results against the reference model.
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影响因子：
4.5
作者：
Gennari JH;Neal ML;Galdzicki M;Cook DL
通讯作者：
Cook DL
DOI：
10.1177/0037549703040939
发表时间：
2003-12-01
影响因子：
1.6
作者：
Cuellar, AA;Lloyd, CM;Hunter, PJ
通讯作者：
Hunter, PJ
影响因子：
4.4
作者：
Diaz-Zuccarini, Vanessa;Pichardo-Almarza, Cesar
通讯作者：
Pichardo-Almarza, Cesar
DOI：
10.1098/rspa.2014.0459
发表时间：
2014-11-08
影响因子：
3.5
作者：
Gawthrop, Peter J.;Crampin, Edmund J.
通讯作者：
Crampin, Edmund J.
影响因子：
2.3
作者：
Cooling, M. T.;Hunter, P.;Crampin, E. J.
通讯作者：
Crampin, E. J.