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Modelling with ANIMO: between fuzzy logic and differential equations

Overview of attention for article published in BMC Systems Biology, July 2016
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Title
Modelling with ANIMO: between fuzzy logic and differential equations
Published in
BMC Systems Biology, July 2016
DOI 10.1186/s12918-016-0286-z
Pubmed ID
Authors

Stefano Schivo, Jetse Scholma, Paul E. van der Vet, Marcel Karperien, Janine N. Post, Jaco van de Pol, Rom Langerak

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.

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Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 37 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 37 100%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 8 22%
Student > Master 7 19%
Student > Bachelor 5 14%
Researcher 4 11%
Other 3 8%
Other 7 19%
Unknown 3 8%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 10 27%
Engineering 6 16%
Agricultural and Biological Sciences 5 14%
Computer Science 5 14%
Medicine and Dentistry 3 8%
Other 2 5%
Unknown 6 16%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 1. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 28 April 2017.
All research outputs
#18,345,259
of 23,577,654 outputs
Outputs from BMC Systems Biology
#775
of 1,139 outputs
Outputs of similar age
#270,370
of 368,034 outputs
Outputs of similar age from BMC Systems Biology
#18
of 31 outputs
Altmetric has tracked 23,577,654 research outputs across all sources so far. This one is in the 19th percentile – i.e., 19% of other outputs scored the same or lower than it.
So far Altmetric has tracked 1,139 research outputs from this source. They receive a mean Attention Score of 3.6. This one is in the 26th percentile – i.e., 26% of its peers scored the same or lower than it.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 368,034 tracked outputs that were published within six weeks on either side of this one in any source. This one is in the 22nd percentile – i.e., 22% of its contemporaries scored the same or lower than it.
We're also able to compare this research output to 31 others from the same source and published within six weeks on either side of this one. This one is in the 35th percentile – i.e., 35% of its contemporaries scored the same or lower than it.