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https://dx.doi.org/10.48550/ar...
Article . 2014
License: arXiv Non-Exclusive Distribution
Data sources: Datacite
DBLP
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Setting Parameters for Biological Models With ANIMO

Authors: Stefano Schivo; Jetse Scholma; Marcel Karperien; Janine N. Post; Jaco van de Pol; Rom Langerak;

Setting Parameters for Biological Models With ANIMO

Abstract

ANIMO (Analysis of Networks with Interactive MOdeling) is a software for modeling biological networks, such as e.g. signaling, metabolic or gene networks. An ANIMO model is essentially the sum of a network topology and a number of interaction parameters. The topology describes the interactions between biological entities in form of a graph, while the parameters determine the speed of occurrence of such interactions. When a mismatch is observed between the behavior of an ANIMO model and experimental data, we want to update the model so that it explains the new data. In general, the topology of a model can be expanded with new (known or hypothetical) nodes, and enables it to match experimental data. However, the unrestrained addition of new parts to a model causes two problems: models can become too complex too fast, to the point of being intractable, and too many parts marked as "hypothetical" or "not known" make a model unrealistic. Even if changing the topology is normally the easier task, these problems push us to try a better parameter fit as a first step, and resort to modifying the model topology only as a last resource. In this paper we show the support added in ANIMO to ease the task of expanding the knowledge on biological networks, concentrating in particular on the parameter settings.

Country
Netherlands
Related Organizations
Keywords

FOS: Computer and information sciences, cs.CE, METIS-304060, parameter synthesis, Molecular Networks (q-bio.MN), q-bio.MN, Experimental data, Computational modeling, QA75.5-76.95, EWI-24659, FMT-TOOLS, Computational Engineering, Finance, and Science (cs.CE), biological networks, Electronic computers. Computer science, FOS: Biological sciences, QA1-939, Quantitative Biology - Molecular Networks, Computer Science - Computational Engineering, Finance, and Science, IR-91060, signal transduction, Mathematics

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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
10
Average
Average
Top 10%
Green
gold