title: Modelling with ANIMO: between fuzzy logic and differential equations.
abstract: Computational support is essential in order to reason on the dynamics of biological systems. We have developed the software tool ANIMO (Analysis of Networks with Interactive MOdeling) to provide such computational support and allow insight into the complex networks of signaling events occurring in living cells. ANIMO makes use of timed automata as an underlying model, thereby enabling analysis techniques from computer science like model checking. Biology experts are able to use ANIMO via a user interface specifically tailored for biological applications. In this paper we compare the use of ANIMO with some established formalisms on two case studies.
  
  
  
  ANIMO is a powerful and user-friendly tool that can compete with existing continuous and discrete paradigms. We show this by presenting ANIMO models for two case studies: Drosophila melanogaster circadian clock, and signal transduction events downstream of TNF α and EGF in HT-29 human colon carcinoma cells. The models were originally developed with ODEs and fuzzy logic, respectively.
  
  
  
  Two biological case studies that have been modeled with respectively ODE and fuzzy logic models can be conveniently modeled using ANIMO. The ANIMO models require less parameters than ODEs and are more precise than fuzzy logic. For this reason we position the modelling paradigm of ANIMO between ODEs and fuzzy logic.
authors.affiliation: Formal Methods and Tools, Faculty of EEMCS, University of Twente, P.O. Box 217, Enschede, 7500AE, The Netherlands.
authors.forename: Stefano
authors.initials: S
authors.lastname: Schivo
authors.affiliation: Developmental BioEngineering, MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, P.O. Box 217, Enschede, 7500AE, The Netherlands.
authors.forename: Jetse
authors.initials: J
authors.lastname: Scholma
authors.affiliation: Human Media Interaction, Faculty of EEMCS, University of Twente, P.O. Box 217, Enschede, 7500AE, The Netherlands.
authors.forename: Paul E
authors.initials: PE
authors.lastname: van der Vet
authors.affiliation: Developmental BioEngineering, MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, P.O. Box 217, Enschede, 7500AE, The Netherlands.
authors.forename: Marcel
authors.initials: M
authors.lastname: Karperien
authors.affiliation: Developmental BioEngineering, MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, P.O. Box 217, Enschede, 7500AE, The Netherlands.
authors.forename: Janine N
authors.initials: JN
authors.lastname: Post
authors.affiliation: Formal Methods and Tools, Faculty of EEMCS, University of Twente, P.O. Box 217, Enschede, 7500AE, The Netherlands.
authors.forename: Jaco
authors.initials: J
authors.lastname: van de Pol
authors.affiliation: Formal Methods and Tools, Faculty of EEMCS, University of Twente, P.O. Box 217, Enschede, 7500AE, The Netherlands. r.langerak@utwente.nl.
authors.forename: Rom
authors.initials: R
authors.lastname: Langerak
mesh_terms: D000818:Animals; D057906:Circadian Clocks; D019295:Computational Biology / Q000379:methods*; D004331:Drosophila melanogaster / Q000166:cytology / Q000378:metabolism / Q000502:physiology; D004815:Epidermal Growth Factor / Q000378:metabolism; D017143:Fuzzy Logic; D019073:HT29 Cells; D006801:Humans; D015398:Signal Transduction; D012984:Software; D014409:Tumor Necrosis Factor-alpha / Q000378:metabolism
chemical_list: D014409:Tumor Necrosis Factor-alpha; D004815:Epidermal Growth Factor
keywords: Dynamic behaviour; Modelling; Signalling pathway; Timed automata