Abstract
KaSa is a static analyzer for Kappa models. Its goal is two-fold. Firstly, KaSa assists the modeler by warning about potential issues in the model. Secondly, KaSa may provide useful properties to check that what is implemented is what the modeler has in mind and to provide a quick overview of the model for the people who have not written it.
The cornerstone of KaSa is a fix-point engine which detects some patterns that may never occur whatever the evolution of the system may be. From this, many useful information may be collected: KaSa warns about rules that may never be applied, about potential irreversible transformations of proteins (that may not be reverted even thanks to an arbitrary number of computation steps) and about the potential formation of unbounded molecular compounds. Lastly, KaSa detects potential influences (activation/inhibition relation) between rules.
In this paper, we illustrate the main features of KaSa on a model of the extracellular activation of the transforming growth factor, TGF-b.
This material is based upon works partially sponsored by ANR (Chair of Excellence AbstractCell), the Defense Advanced Research Projects Agency (DARPA) and the U. S. Army Research Office under grant number W911NF-14-1-0367, and by the ITMO Plan Cancer 2014 (TGFSysBio project). The views, opinions, and/or findings contained in this article are those of the authors and should not be interpreted as representing the official views or policies, either expressed or implied, of ANR, DARPA, the U. S. Department of Defense, or ITMO.
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Contribution
Jérôme Feret (2010-present) and Kim Quyên Lý (2015–2017) are the main contributors of KaSa. KaSa is integrated within the Kappa modeling platform whose main architect is Pierre Boutillier. In particular, Pierre Boutillier has integrated KaSa in the user interface of Kappa which may be used either online, or locally. The model of the extracellular activation of the transforming growth factor, TGF-b, has been assembled by Jean Coquet (2012–2017), Nathalie Théret (2012-present), Pierre Vignet (2016-present), and Ferdinanda Camporesi (2016-present). Jérôme Feret has written the paper.
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Boutillier, P. et al. (2018). KaSa: A Static Analyzer for Kappa. In: Češka, M., Šafránek, D. (eds) Computational Methods in Systems Biology. CMSB 2018. Lecture Notes in Computer Science(), vol 11095. Springer, Cham. https://doi.org/10.1007/978-3-319-99429-1_17
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DOI: https://doi.org/10.1007/978-3-319-99429-1_17
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