Computational Modeling of Complex Protein Activity Networks

Stefano Schivo, Jeroen Leijten, Marcel Karperien, Janine N. Post*

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingChapterAcademicpeer-review


Because of the numerous entities interacting, the complexity of the networks that regulate cell fate makes it impossible to analyze and understand them using the human brain alone. Computational modeling is a powerful method to unravel complex systems. We recently described the development of a user-friendly computational tool, Analysis of Networks with Interactive MOdeling (ANIMO). ANIMO is a powerful tool to formalize knowledge on molecular interactions. This formalization entails giving a precise mathematical (formal) description of molecular states and of interactions between molecules. Such a model can be simulated, thereby in silico mimicking the processes that take place in the cell. In sharp contrast to classical graphical representations of molecular interaction networks, formal models allow in silico experiments and functional analysis of the dynamic behavior of the network. In addition, ANIMO was developed specifically for use by biologists who have little or no prior modeling experience. In this chapter, we guide the reader through the ANIMO workflow using osteoarthritis (OA) as a case study. WNT, IL-1β, and BMP signaling and cross talk are used as a concrete and illustrative model.
Original languageEnglish
Title of host publicationProtein Phosphorylation
EditorsClaude Prignet
Place of PublicationUnited Kingdom
Number of pages24
ISBN (Print)978-953-51-3625-5
Publication statusPublished - 29 Nov 2017
Externally publishedYes


  • WNT, IL1β, BMP, cartilage, computational model, ANIMO, cell signaling, network modeling


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