Abstract
BackgroundComputational 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.ResultsANIMO 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.ConclusionsTwo 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12918-016-0286-z) contains supplementary material, which is available to authorized users.
Highlights
Computational support is essential in order to reason on the dynamics of biological systems
Modelling oscillation in Drosophila Melanogaster circadian clock To demonstrate that results obtained with ANIMO are comparable to results from widely used modelling approaches, we present an ANIMO model of the circadian clock in Drosophila Melanogaster
In this paper we discussed the placement of ANIMO among other modelling paradigms and tools, highlighting ANIMO’s strong points
Summary
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. It provides an interesting paradigm to enhance network diagrams with an underlying formal description of network components and their interactions For this purpose a wealth of different modeling paradigms has been proposed (see [2] for an overview). When dealing with complex biological networks, executable biology models are useful to understand the non-linear dynamics and the entailed emergent properties of the networks. In those cases, an ANIMO model can be used as a support to obtain insight based on abstract representations of the interactions occurring inside living cells. Other applications of ANIMO models include performing in silico experiments and the storage and transfer of knowledge on biological networks
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