Creates an in silico system from a data-frame of genes in the system.
A data-frame of the genes existing in the system (see
An object of class
A Julia evaluator. If none provided select the current evaluator or create one if no evaluator exists.
An in silico system, that is a list of:
genes: the modified data-frame of genes;
edg: A data-frame of edges in the regulatory network of the system (1 row = 1 edge). It contains the following parameters:
from: gene ID of the edge origin (character).
to: gene ID of edge destination (character).
TargetReaction: Type of regulation (ID of the controlled reaction: "TC", "TL", "RD", "PD" or "PTM").
RegSign: Sign of the reaction ("1" for positive regulation, "-1" for negative regulation).
RegBy: Type of the regulator: "PC" for protein-coding regulation, "NC" for noncoding regulator,
"C" for regulatory complex.
mosystem: A list of the different regulatory networks (each corresponding to a different type of regulation) in the system and associated information. Elements are
PTMRN_edg: data-frames of edges for the different
regulatory networks, which in addition to the usual fields in the edg data frame, contain columns for kinetic parameters of the
complexes: a list of regulatory complexes composition. The names of the elements are the IDs of the complexes, and the
values are vectors of gene IDs constituting each regulatory complex.
complexeskinetics: a list of regulatory complexes kinetic parameters.
complexesTargetReaction: a list defining which expression step is targeted by each regulatory complex.
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