Table 2 Computations of elementary modes in a realistic metabolic network (central metabolism of Escherichia coli). Computations were performed on a typical PC with AMD Athlon XP 3000 + CPU and 1 GB RAM. Abbreviations: Form = formiate, Ac = acetate, Glc = glucose, Succ = succinate, Asp = aspartate, Glyc = glycerol, Eth = ethanol, Lac = lactate, CO2 = carbon dioxide.
From: Computation of elementary modes: a unifying framework and the new binary approach
| Â | S1 | S2 | S3 | |||
|---|---|---|---|---|---|---|
substrates | Glc | Glc, Succ, Glyc, Ac | Glc, Succ, Glyc, Ac, Asp | |||
products | Ac, Form, Eth, Lac, CO2 | Ac, Form, Eth, Lac, CO2 | Ac, Form, Eth, Lac, CO2, Succ | |||
#reactions (q) # metabolites (m) | 106 (28 reversible) 89 | 110 (28 reversible) 89 | 112 (28 reversible) 89 | |||
compressed network: # reactions # metabolites | 42 (17 reversible) 25 | 47 (17 reversible) 26 | 51 (17 reversible) 28 | |||
final number of elementary modes | 27,100 | 507,632 | 2,450,787 | |||
| Â | binary NSA | NSA | binary NSA | NSA | binary NSA | NSA |
computation time | 0.16 min (9.63 sec) | 0.54 min (32.20 sec) | 51.20 min | 116.77 min | 1546 min (25.78 h) | not finished |
back transformation | 0.13 min (7.97 sec) | Â | 2.57 min | Â | 13 min | Â |
total computation time | 0.29 min (17.60 sec) | 0.54 min (32.20 sec) | 53.77 min | 116.77 min | 1559 min (25.98 h) | Â |