Problem name Original problem reference Source system/Model #var #exp #pts Noise (%)
simpleLin1 Simple linear system 3 3 13 0
simpleLin2 8 13 10
simpleFb1 Simple feedback loop (McKinney et al., 2006) 3 4 7 0
simpleFb2 4 7 5
simpleFb3 1 7 0
simpleFb4 (McKinney et al., 2006) 1 7 ≈5a
osc1 An oscillator (Karnaukhov et al., 2007) 3 1 41 0
osc2 (Karnaukhov et al., 2007) 1 41 3
metabol1 (Gennemark and Wedelin, 2007) A metabolic pathway (Arkin and Ross, 1995) 5 12 7 0
metabol2 (Gennemark and Wedelin, 2007) 12 21 10
metabol3 (Gennemark and Wedelin, 2007) 12 21 20
3genes1 A 3-step gene network (Moles et al., 2003) 8 16 21 0
ss_cascade1 (Tsai and Wang, 2005) A cascaded pathway (Voit, 2000) 3 8 41 0
ss_cascade2 4 41 0
ss_cascade3 8 41 5
ss_branch1 (Voit and Almeida, 2004) A branched pathway (Voit, 2000) 4 3 21 0
ss_branch2 (Marino and Voit, 2006) 6 51 0
ss_branch3 (Tucker and Moulton, 2006) 5 20 0
ss_branch4 (Kutalik et al., 2007) 4 20 0
ss_branch5 (Kutalik et al., 2007) 4 20 2.5
ss_branch6 (Gonzalez et al., 2007) 5 31 0
ss_5genes1 (Kikuchi et al., 2003) A genetic network (Hlavacek and Savageau, 1996) 5 10 11 0
ss_5genes2 (Gennemark and Wedelin, 2007) 10 9 20
ss_5genes3 (Gennemark and Wedelin, 2007) 10 3 0
ss_5genes4 (Kimura et al., 2005) 15 11 0
ss_5genes5 (Daisuke and Horton, 2006) 10 11 0
ss_5genes6 (Cho et al., 2006) 1 16 0
ss_5genes7 (Tucker and Moulton, 2006) 10 20 0
ss_5genes8 (Tsai and Wang, 2005) 8 41 0
(Liu and Wang, 2008)
ss_15genes1 A genetic network (Maki et al., 2001) 15 10 11 0
ss_15genes2 20 11 10
ss_30genes1 A genetic network (Maki et al., 2001) 30 15 11 0
ss_30genes2 (Kimura et al., 2005) 20 11 10
ss_30genes3 (Liu and Wang, 2008) 8 41 0
cytokine1 (McKinney et al., 2006) Immunologic data (Rock et al., 2004) 4 1 7 10a
cytokine2 1 7 10a
ss_ethanolferm1 (Liu and Wang, 2008) Ethanol fermentation (Wang et al., 2001) 4 2 11–15 ≈30a
ss_ethanolferm2 3 11–19 ≈30a
ss_sosrepair1 (Cho et al., 2006) SOS repair system Escherichia coli (Ronen et al., 2002) 6 1 50 10a
ss_sosrepair2 1 50 10a
ss_cadBA1 (Gonzalez et al., 2007) cadBA network in E. coli (Kuper and Jung, 2005) 5 1 25 <20a
ss_cadBA2 1 25 <20a
ss_clock1 (Daisuke and Horton, 2006) Mice cell cycle (Barrett et al., 2005) 7 1 12 ≈10a
ss_clock2 1 12 ≈10a