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Table 1 Models

From: BioPreDyn-bench: a suite of benchmark problems for dynamic modelling in systems biology

Model ID B1 B2 B3 B4 B5 B6
Model Ref [25] [23] [24] [26] [27] [29]
Cell S. cerevisiae E. coli E. coli CHO Generic Drosophila
       melanogaster
Description Metabolic: Metabolic: Metabolic: CCM Metabolic Signal Developmental
level genome scale CCM & transcription   transduction GRN (spatial)
Parameters 1759 116 178 117 86 37
Dynamic states 276 18 47 34 26 108 –212
Observed states 44 9 47 13 6 108 –212
Experiments 1 1 1 1 10 1
Data points 5280 110 7567 169 96 1804
Data type simulated measured simulated simulated simulated measured
Noise level σ=5% real no noise variable σ=5% real
  1. Main features of the benchmark models. The standard deviation, σ, is given in those cases where artificial noise with constant variance was added to the data.