Wenskovitch John E, Harris Leonard A, Tapia Jose-Juan, Faeder James R, Marai G Elisabeta
Electronic Visualization Lab, Department of Computer Science, University of Illinois at Chicago, 60607 Chicago, USA.
BMC Bioinformatics. 2014 Sep 25;15(1):316. doi: 10.1186/1471-2105-15-316.
Mechanistic models that describe the dynamical behaviors of biochemical systems are common in computational systems biology, especially in the realm of cellular signaling. The development of families of such models, either by a single research group or by different groups working within the same area, presents significant challenges that range from identifying structural similarities and differences between models to understanding how these differences affect system dynamics.
We present the development and features of an interactive model exploration system, MOSBIE, which provides utilities for identifying similarities and differences between models within a family. Models are clustered using a custom similarity metric, and a visual interface is provided that allows a researcher to interactively compare the structures of pairs of models as well as view simulation results.
We illustrate the usefulness of MOSBIE via two case studies in the cell signaling domain. We also present feedback provided by domain experts and discuss the benefits, as well as the limitations, of the approach.
描述生化系统动态行为的机制模型在计算系统生物学中很常见，尤其是在细胞信号传导领域。开发此类模型家族，无论是由单个研究团队还是同一领域内的不同团队进行，都面临着重大挑战，从识别模型之间的结构异同到理解这些差异如何影响系统动态。
我们展示了一个交互式模型探索系统MOSBIE的开发和特点，该系统提供了识别家族内模型异同的实用工具。使用定制的相似性度量对模型进行聚类，并提供一个可视化界面，使研究人员能够交互式地比较成对模型的结构以及查看模拟结果。
我们通过细胞信号传导领域的两个案例研究说明了MOSBIE的有用性。我们还展示了领域专家提供的反馈，并讨论了该方法的优点和局限性。
