Computational Modeling of Complex Protein Activity Networks

Research output: Chapter in Book/Report/Conference proceedingChapter

Abstract

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.
LanguageEnglish
Title of host publicationProtein Phosphorylation
EditorsClaude Prignet
PublisherIntechOpen
Pages155-178
Number of pages24
ISBN (Electronic)978-953-51-3626-2
ISBN (Print)978-953-51-3625-5
DOIs
StatePublished - 29 Nov 2017

Fingerprint

Computational Modeling
Computer Simulation
Molecular interactions
Proteins
Protein
Workflow
Osteoarthritis
Functional analysis
Modeling
Large scale systems
Brain
Concretes
Interaction
Molecules
Graphical Representation
Cell
Crosstalk
Functional Analysis
Formal Model
Formalization

Keywords

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

Cite this

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title = "Computational Modeling of Complex Protein Activity Networks",
abstract = "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.",
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Computational Modeling of Complex Protein Activity Networks. / Schivo, Stefano ; Leijten, Jeroen; Karperien, Marcel; Post, Janine N.

Protein Phosphorylation. ed. / Claude Prignet. IntechOpen, 2017. p. 155-178.

Research output: Chapter in Book/Report/Conference proceedingChapter

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N2 - 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.

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Schivo S, Leijten J, Karperien M, Post JN. Computational Modeling of Complex Protein Activity Networks. In Prignet C, editor, Protein Phosphorylation. IntechOpen. 2017. p. 155-178. Available from, DOI: 10.5772/intechopen.69804