A specialized ODE integrator for the efficient computation of parameter sensitivities

BMC Systems Biology

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

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.

¹Abbreviations used: ERK = extracellular regulated kinase; EGF = epidermal growth factor; IL-6 = interleukin 6; FGF = fibroblast growth factor.

ISSN: 1752-0509