Quantitative Molecular Models for Biological Processes: Modeling of Signal Transduction Networks with ANIMO

Sakshi Khurana, Janet Huisman, Stefano Schivo, Janine N Post*

*Corresponding author for this work

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

Abstract

Computational modeling of biological networks is increasing in popularity due to the increased demand for understanding biological processes. This understanding requires integration of a variety of experimental data that allows understanding of complex mechanisms regulating cell and tissue function. However, the mathematical complexity of many modeling tools have thusfar prevented broad adaptation and effective use by molecular biologists. In this chapter, we show by example how one can start building a model in ANIMO and how to adapt the model to experimental data. We show how this model can be used for simulating network activities, testing hypotheses, and how to improve the model using wet-lab data.

Original languageEnglish
Title of host publicationOsteoporosis and Osteoarthritis
EditorsAndre J. van Wijnen, Marina S. Ganshina
Place of PublicationNew York, NY
PublisherHumana Press
Chapter10
Pages141-161
Number of pages21
Edition2
ISBN (Electronic)9781071609897
ISBN (Print)9781071609880
DOIs
Publication statusPublished - 27 Sep 2020

Publication series

SeriesMethods in molecular biology
Volume2221
ISSN1064-3745

Keywords

  • Modeling tool
  • Computational model
  • Signal transduction network
  • Signaling pathways
  • Signaling cross talk
  • WNT
  • NFkB
  • TGF beta

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    Khurana, S., Huisman, J., Schivo, S., & Post, J. N. (2020). Quantitative Molecular Models for Biological Processes: Modeling of Signal Transduction Networks with ANIMO. In A. J. van Wijnen, & M. S. Ganshina (Eds.), Osteoporosis and Osteoarthritis (2 ed., pp. 141-161). Humana Press. Methods in molecular biology, Vol.. 2221 https://doi.org/10.1007/978-1-0716-0989-7_10