Symbolic flux analysis for genome-scale metabolic networks

BMC Systems Biology

Table 1 Performance of GJE versus SVD

Model	Publ.	Species	Reactions		Flux variables		CPU time (s)		ε SVD ×10^-12	Condition number
			Orig.	Open	Dep.	Indep.	SVD	GJE
Example		118	129	156	118	39	0.02	0.03	0.003	15
iPS189	[15]	433	350	482	413	69	0.3	0.4	0.07	31000
iND750	[16]	1177	1266	1561	1162	399	6.2	8.0	6.37	68000
AraGEM	[17]	1767	1625	2361	1720	641	19.7	34.2	12.65	3000
iAF1260	[18]	1972	2382	2773	1960	813	30.5	34.3	1.43	2800
Recon 1	[10]	3188	3742	4480	3169	1311	123.5	145.6	32.63	71000

Kernel computation times for numerical SVD and symbolic GJE for the example yeast network given in Figure 3 and five genome-scale metabolic networks. All techniques are described in Methods. The condition number was calculated for V_indep from Equation (9). The inversion of V_indep is required to directly compare SVD results with the solution found from GJE. The difference between the results is given by ε _SVD in Equation (11).

ISSN: 1752-0509