Welcome to Pleione v1.5 documentation!

Pleione is a python3 package that implement methods that are common to traditional modeling frameworks, and apply them to analyze Rule-Based Models.

Here you’ll find the necessary documentation to install and use the methods in Pleione. At the moment, Pleione parameterizes Rule-Based Models written either in BioNetGen (BioNetGen) or kappa language (Kappa). Models are simulated with BNG2 (BioNetGen2, PMID 27402907), NFsim (NFsim, PMID 26556387), KaSim (KaSim, PMID 29950016), or PISKaS (PISKaS, PMID 29175206). Please contact us or write an issue to include your favorite stochastic simulator to Pleione (https://github.com/glucksfall/pleione/issues).

Pleione implements a Genetic Algorithm with elitism, on the contrary to BioNetFit (BioNetFit, PMID 26556387) that implements a parents selection within a distribution probability that is inverse to the rank. Nonetheless, Pleione’s methods to parameterize Rule-Based Models include both, a uniform or inverse to the rank probability to select models from within an elite or all models.

The plan to add methods into Pleiades (pleiades) includes a sensitivity analysis and a parameterization employing a Particle Swarm Optimization protocol. You could write us if you wish to add methods into pleione or aid in the development of them.

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