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Table 2 Systems biology test models and their key characteristics, namely number of states (n x ), number of parameters (n p ), number of non-zeros of the Jacobians nnz(J f ), integration time interval (t), and biological system described by the model

From: A specialized ODE integrator for the efficient computation of parameter sensitivities

Model n x n p nnz(J f ) nnz(J Jf ) t Comments
Hornberg et al.[37] 8 19 22 32 [0,100] Steady state, ERK1 phosphorylation and kinase/phosphatase control.
Kholodenko et al.[38] 23 51 137 372 [0,100] Steady state, short term signaling by the EGF receptor.
Singh et al.[39] 66 109 323 846 [0,35 000] Steady state, IL-6 signal transduction in hepatocytes.
Borisov et al.[40] 90 136 468 2156 [0,1 000] Steady state, insulin-EGF network interactions in mitogenic signaling.
Ung et al.[41] 200 314 956 4038 [0,4 000] Steady state, regulation of EGFR endocytosis and EGFR-ERK signaling by crosstalk.
Elowitz & Leibler [42] 6 8 12 18 [0,1 000] Oscillatory, synthetic network of transcriptional regulators.
Leloup & Goldbeter [43] 10 48 30 52 [0,300] Oscillatory, circadian oscillations of PER and TIM proteins in Drosophila.
Wolf et al.[44] 13 40 47 99 [0,300] Oscillatory, autonomous metabolic oscillations in continuous culture of S. cerevisiae.
Goldbeter & Pourquié [45] 20 73 47 76 [0,300] Oscillatory, segmentation clock by crosstalk of Notch, Wnt, and FGF pathways.
Xie & Kulasiri [46] 24 49 57 107 [0,100] Oscillatory, circadian rhythms in Drosophila with interlocked feedback loops.
  1. 1Abbreviations used: ERK = extracellular regulated kinase; EGF = epidermal growth factor; IL-6 = interleukin 6; FGF = fibroblast growth factor.