Biological networks 101: Computational modeling for molecular biologists

Scholma, Jetse; Schivo, Stefano; Camacho, Ricardo A. Urquidi; Pol, Jaco van de; Karperien, Marcel; Post, Janine N.

doi:10.1016/j.gene.2013.10.010

Cited by 25 publications

(35 citation statements)

References 16 publications

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“…ANIMO (Analysis of Networks with Interactive MOdeling) [28,27,26,31] is a software tool that supports the modeling of biological signaling pathways by adding a dynamic component to traditional static representations of signaling networks. ANIMO allows to compare the behavior of a model with wet-lab data, and to explore such behavior in a user-friendly way.…”

Section: Application: Animo a Tool For Analyzing Kinase Pathwaysmentioning

confidence: 99%

“…The ANIMO tool has been validated on several realistic biological case studies for which experimental data was available in the literature, and it has been demonstrated how to create models that faithfully fit experimental data [28,27,26,31]. Moreover, ANIMO is being used in on-going research on chondrocyte signaling in relation to osteoarthritis, where the final objective is to enhance cartilage tissue engineering strategies [29,30,37].…”

Section: Application: Animo a Tool For Analyzing Kinase Pathwaysmentioning

confidence: 99%

“…In Section 5 we discuss the correctness and make our implementation efficient. In Section 6 we describe how our approach has been implemented into the tool ANIMO that has already been used in biological research [28,27,26,31], and Section 7 contains conclusions and directions for further research.…”

Section: Introductionmentioning

confidence: 99%

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Discretization of Continuous Dynamical Systems Using UPPAAL

Schivo

Langerak

2017

ModelEd, TestEd, TrustEd

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We want to enable the analysis of continuous dynamical systems (where the evolution of a vector of continuous state variables is described by differential equations) by model checking. We do this by showing how such a dynamical system can be translated into a discrete model of communicating timed automata that can be analyzed by the UPPAAL tool. The basis of the translation is the well-known Euler approach for solving differential equations where we use fixed discrete value steps instead of fixed time steps. Each state variable is represented by a timed automaton in which the delay for taking the next value is calculated on the fly using the differential equations. The state variable automata proceed independently but may notify each other when a value step has been completed; this leads to a recalculation of delays. The approach has been implemented in the tool ANIMO for analyzing biological kinase networks in cells. This tool has been used in actual biological research on osteoarthritis dealing with systems where the dimension of the state vector (the number of nodes in the network) is in the order of one hundred.

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Section: Application: Animo a Tool For Analyzing Kinase Pathwaysmentioning

confidence: 99%

Section: Application: Animo a Tool For Analyzing Kinase Pathwaysmentioning

confidence: 99%

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Discretization of Continuous Dynamical Systems Using UPPAAL

Schivo

Langerak

2017

ModelEd, TestEd, TrustEd

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“…However, a lack of familiarity with the formalisms underlying many available tools hampers their direct application by biology experts. ANIMO (Analysis of Networks with Interactive MOdeling, [2,19,22,18]) is a software tool based on the formalism of Timed Automata [1] that supports the modeling of biological signaling pathways by adding a dynamic component to traditional static representations of signaling networks. ANIMO allows to compare the behavior of a model with wet-lab data, and to explore such behavior in a user-friendly way.…”

Section: Introductionmentioning

confidence: 99%

Improving the Timed Automata Approach to Biological Pathway Dynamics

Langerak

Pol

Post

et al. 2017

Lecture Notes in Computer Science

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Abstract. Biological systems such as regulatory or gene networks can be seen as a particular type of distributed systems, and for this reason they can be modeled within the Timed Automata paradigm, which was developed in the computer science context. However, tools designed to model distributed systems often require a computer science background, making their use less attractive for biologists. ANIMO (Analysis of Networks with Interactive MOdeling) was built with the aim to provide biologists with access to the powerful modeling formalism of Timed Automata in a user friendly way. Continuous dynamics is handled by discrete approximations. In this paper we introduce an improved modeling approach that allows us to considerably increase ANIMO's performances, opening the way for the analysis of bigger models. Moreover, this improvement makes the introduction of model checking in ANIMO a realistic feature, allowing for reduced computation times. The user interface of ANIMO allows to rapidly build non-trivial models and check them against properties formulated in a human-readable language, making modeling a powerful support for biological research.

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“…ANIMO was developed in collaboration with biologists, and is used in biological studies 5,6 . While ANIMO is made to be user-friendly and make the biologist feel "at home", the initial impression may not be entirely positive due to the requirements for its installation.…”

Section: Introductionmentioning

confidence: 99%

webANIMO: Improving the accessibility of ANIMO

et al. 2016

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ANIMO is a Cytoscape 3 app to model biological signalling pathways. Useful analyses can be performed and displayed to the user in an effective way. However, all this power comes at a cost: the additional software requirements for ANIMO have been hindering its widespread adoption. Our goal has been to provide beginner to intermediate ANIMO users with a simpler and more effective platform to perform their research: webANIMO. The minimalistic interface provides everything the regular ANIMO user needs for the most common tasks. Adding the fact that it is a web interface removes any software requirements from the equation. This article describes how webANIMO works: its client/server architecture, how Cytoscape and ANIMO compatibility was maintained, the visualization techniques implemented and other general design decisions.

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Biological networks 101: Computational modeling for molecular biologists

Cited by 25 publications

References 16 publications

Discretization of Continuous Dynamical Systems Using UPPAAL

Discretization of Continuous Dynamical Systems Using UPPAAL

Improving the Timed Automata Approach to Biological Pathway Dynamics

webANIMO: Improving the accessibility of ANIMO

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