Krishnan Shaji, van Avesaat Mark, Troost Freddy J, Hendriks Henk Fj, de Graaf Albert A
Microbiology and Systems Biology, TNO, Utrechtseweg 48, P,O, Box 360, 3700 AJ Zeist, The Netherlands.
Theor Biol Med Model. 2014 Jun 10;11:28. doi: 10.1186/1742-4682-11-28.
In-silico models that attempt to capture and describe the physiological behavior of biological organisms, including humans, are intrinsically complex and time consuming to build and simulate in a computing environment. The level of detail of description incorporated in the model depends on the knowledge of the system's behavior at that level. This knowledge is gathered from the literature and/or improved by knowledge obtained from new experiments. Thus model development is an iterative developmental procedure. The objective of this paper is to describe a new plug and play scheme that offers increased flexibility and ease-of-use for modeling and simulating physiological behavior of biological organisms.
This scheme requires the modeler (user) first to supply the structure of the interacting components and experimental data in a tabular format. The behavior of the components described in a mathematical form, also provided by the modeler, is externally linked during simulation. The advantage of the plug and play scheme for modeling is that it requires less programming effort and can be quickly adapted to newer modeling requirements while also paving the way for dynamic model building.
As an illustration, the paper models the dynamics of gastric emptying behavior experienced by humans. The flexibility to adapt the model to predict the gastric emptying behavior under varying types of nutrient infusion in the intestine (ileum) is demonstrated. The predictions were verified with a human intervention study. The error in predicting the half emptying time was found to be less than 6%.
A new plug-and-play scheme for biological systems modeling was developed that allows changes to the modeled structure and behavior with reduced programming effort, by abstracting the biological system into a network of smaller sub-systems with independent behavior. In the new scheme, the modeling and simulation becomes an automatic machine readable and executable task.
试图捕捉和描述包括人类在内的生物机体生理行为的计算机模拟模型，在计算环境中构建和模拟本质上是复杂且耗时的。模型中纳入的描述细节程度取决于该层面系统行为的知识。这些知识从文献中收集和/或通过新实验获得的知识加以完善。因此，模型开发是一个迭代的过程。本文的目的是描述一种新的即插即用方案，该方案为生物机体生理行为的建模和模拟提供了更高的灵活性和易用性。
该方案要求建模者（用户）首先以表格形式提供相互作用组件的结构和实验数据。建模者提供的以数学形式描述的组件行为在模拟过程中进行外部链接。即插即用方案用于建模的优势在于它所需的编程工作量较少，并且能够快速适应更新的建模要求，同时也为动态模型构建铺平了道路。
作为示例，本文对人类经历的胃排空行为动态进行了建模。展示了该模型在预测肠道（回肠）不同类型营养输注情况下胃排空行为方面的灵活性。这些预测通过一项人体干预研究得到验证。发现预测半排空时间的误差小于6%。
开发了一种用于生物系统建模的新即插即用方案，通过将生物系统抽象为具有独立行为的较小子系统网络，以减少编程工作量的方式允许对建模结构和行为进行更改。在新方案中，建模和模拟成为一项自动的机器可读且可执行的任务。
