Name
Abstract | ||
|---|---|---|
Living cells are constantly subjected to a plethora of environmental stimuli that require integration into an appropriate cellular response. This integration takes place through signal transduction events that form tightly interconnected networks. The understanding of these networks requires capturing their dynamics through computational support and models. ANIMO (analysis of Networks with Interactive Modeling) is a tool that enables the construction and exploration of executable models of biological networks, helping to derive hypotheses and to plan wet-lab experiments. The tool is based on the formalism of Timed Automata, which can be analyzed via the UPPAAL model checker. Thanks to Timed Automata, we can provide a formal semantics for the domain-specific language used to represent signaling networks. This enforces precision and uniformity in the definition of signaling pathways, contributing to the integration of isolated signaling events into complex network models. We propose an approach to discretization of reaction kinetics that allows us to efficiently use UPPAAL as the computational engine to explore the dynamic behavior of the network of interest. A user-friendly interface hides the use of Timed Automata from the user, while keeping the expressive power intact. Abstraction to single-parameter kinetics speeds up construction of models that remain faithful enough to provide meaningful insight. The resulting dynamic behavior of the network components is displayed graphically, allowing for an intuitive and interactive modeling experience. |
Year | DOI | Venue |
|---|---|---|
2014 | 10.1109/JBHI.2013.2292880 | BIBE |
Keywords | DocType | Volume |
crosstalk-driven networks,animo,biological pathway dynamic modelling,wet-lab experiments,signaling pathway,finite automata,cellular biophysics,human computer interaction,domain-specific language,timed automata,neurophysiology,signal transduction events,signalling pathway,analysis of networks with interactive modelling,tightly interconnected networks,cellular response,biological pathway dynamic,uppaal model checker,animo method,user friendly interface,complex networks,analysis of networks with interactive modeling,formal semantics,molecular biophysics,reaction kinetics,formal languages,signalling molecule,dynamic behavior,biological cells,computational engine,dynamic cell behaviour,environmental stimuli,timed automata formalism,signalling event model,signalling network,reaction kinetic discretization,complex biological interaction network analysis,signalling network representation,modeling,bioinformatics,signalling molecules,biological network,modelling,dynamic behaviour,living cells,complex biological interaction,biological pathway dynamics,biological cell,formal verification,drugs,analysing complex interaction network,growth factors,data models,automata,computational modeling,kinetic theory | Journal | 18 |
Issue | ISSN | ISBN |
3 | 2168-2208 | 978-1-4673-4357-2 |
Citations | PageRank | References |
7 | 0.45 | 6 |
Authors | ||
9 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| Stefano Schivo | 1 | 7 | 1.80 |
| Jetse Scholma | 2 | 15 | 1.31 |
| Brend Wanders | 3 | 11 | 1.58 |
| Ricardo A. Urquidi Camacho | 4 | 7 | 0.45 |
| paul e van der vet | 5 | 132 | 33.20 |
| Marcel Karperien | 6 | 15 | 1.31 |
| Rom Langerak | 7 | 308 | 39.16 |
| Jaco Van De Pol | 8 | 1022 | 78.19 |
| Janine N. Post | 9 | 16 | 1.93 |