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Translating BNGL models into Kappa our experience

Kim Quyen Ly 1
1 ANTIQUE - Analyse Statique par Interprétation Abstraite
DI-ENS - Département d'informatique de l'École normale supérieure, Inria de Paris
Abstract : So as to test the Kappa development tools on more examples, we translated the models provided with the BNGL distribution, into Kappa. In this talk, we report about our experience. The translation was quite straight-forward except for few interesting issues that we detail here. Firstly the use of static analysis has exposed some glitches in the modelling of some pathways in the models of the BNGL distribution. We explain how static analysis has helped us to detect, locate, and correct these flaws. Secondly, expanding BNGL rules using equivalent sites into rules with uniquely identified sites is not so easy when one wants to preserve faithfully the kinetics of interactions. We recall the semantics of BNGL for equivalent sites, and explain how to perform such translation.
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https://hal.inria.fr/hal-01613604
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Submitted on : Wednesday, October 11, 2017 - 7:42:45 AM
Last modification on : Tuesday, May 4, 2021 - 2:06:02 PM
Long-term archiving on: : Friday, January 12, 2018 - 12:46:53 PM

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Kim Quyen Ly. Translating BNGL models into Kappa our experience. 2017, pp.4. ⟨hal-01613604⟩

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