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Fig. 1 | BMC Bioinformatics

Fig. 1

From: Periodic synchronization of isolated network elements facilitates simulating and inferring gene regulatory networks including stochastic molecular kinetics

Fig. 1

Implementation of GRNs in CaiNet. a Sketch of an exemplary GRN. GRNs in CaiNet may comprise elements of (extra)cellular input signals, elements of basic bi-molecular reactions combined to more complex biochemical reactions and gene elements combined to regulatory motives. b Sketch of the reaction rates entering the exemplary GRN. CaiNet provides analytical solutions to the evolution of molecule numbers in basic biochemical reactions and analytical effective two-state solutions of molecule numbers of different promoter structures of genes, which all are included into the unique modular simulation approach of CaiNet. The user can assign time profiles of input elements and reaction rates of bi-molecular reactions and genes. c Exemplary time trajectories for input elements. d Sketch of promoter structures implemented in CaiNet. e Sketch of the layout of elements including their kinetic parameters of the exemplary GRN in b set up in CaiNet via a GUI. f Sketch of the knockout tool applied to the exemplary GRN. The parameters of elements can be altered to simulate experimental conditions such as knockdown or knockout experiments

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BMC Bioinformatics

ISSN: 1471-2105

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