ANIMO models

This page contains the ANIMO models used in published papers. Most of the figures of those papers were produced directly in ANIMO. The linked directories contain .cys (Cytoscape session) files with the ANIMO models and, where available, the experimental data used as reference for the models is provided as .csv (comma separated values) files.
  • Example model from ANIMO manual. [Models]
  • S. Schivo, J. Scholma, P.E. van der Vet, H.B.J. Karperien, J.N. Post, J.C. van de Pol and R. Langerak (2016). Modelling with ANIMO: between fuzzy logic and differential equations. BMC Systems Biology, 10. 56. ISSN 1752-0509. [Paper] [Models]
  • S. Schivo, J. Scholma, H.B.J. Karperien, J.N. Post, J.C. van de Pol and R. Langerak (2014). Setting parameters for biological models with ANIMO. In É. André, and G. Frehse, editors, Proceedings 1st International Workshop on Synthesis of Continuous Parameters (SynCoP 2014), Grenoble, France, Electronic Proceedings in Theoretical Computer Science. [Paper] [Models]
  • J. Scholma, S. Schivo, R. A. Urquidi Camacho, J.C. van de Pol, H.B.J. Karperien and J.N. Post (2014) Biological networks 101: computational modeling for molecular biologists. Gene, 533 (1). pp. 379-384. ISSN 0378-1119. [Paper] [Models]
  • S. Schivo, J. Scholma, B. Wanders, R. A. Urquidi Camacho, P.E. van der Vet, H.B.J. Karperien, R. Langerak, J.C. van de Pol and J.N. Post (2014) Modelling biological pathway dynamics with Timed Automata. IEEE Journal of Biomedical and Health Informatics, online pre-publication. ISSN 2168-2194. [Paper] [Models]
  • S. Schivo, J. Scholma, B. Wanders, R.A. Urquidi Camacho, P.E. van der Vet, H.B.J. Karperien, R. Langerak, J.C. van de Pol and J.N. Post (2012) Modelling biological pathway dynamics with Timed Automata. In: 2012 IEEE 12th International Conference on Bioinformatics and Bioengineering (BIBE 2012), 11-13 Nov 2012, Larnaca, Cyprus. pp. 447-453. IEEE Computer Society. ISBN 978-1-4673-4358-9. [Paper] [Models]