The problems are grouped after the type of model space and data that are used. An overview is shown in the following tables with links to more detailed descriptions and problem files. Parameter estimation problems (a fixed structure is assumed) are given in the last table, and all such problems starts by "pe_".
All problems can be downloaded as a zip-file.
| Source system/model | Problem | #var | #exp | #pts | Noise | Best error |
|---|---|---|---|---|---|---|
| simpleLin | simpleLin1 | 3 | 3 | 13 | 0% | 8 |
| simpleLin2 | 8 | 13 | 10% | 140.2 | ||
| simpleFb | simpleFb1 | 3 | 4 | 7 | 0% | 7 |
| simpleFb2 | 4 | 7 | 5% | 42.14 | ||
| simpleFb3 | 1 | 7 | 0% | 7 | ||
| simpleFb4 | 1 | 7 | ~5%1 | 7.071 | ||
| osc | osc1 | 3 | 1 | 41 | 0% | 6.149 |
| osc2 | 1 | 41 | 3% | 87.34 | ||
| metabol | metabol1 | 5 | 12 | 7 | 0% | 30 |
| metabol2 | 12 | 21 | 10% | 751.6 | ||
| metabol3 | 12 | 21 | 20% | 861.1 | ||
| 3genes | 3genes1 | 8 | 16 | 21 | 0% | 39 |
| feedf | feedf1 | 6 | 16 | 51 | 0% | 1.760 |
| feedf2 | 6 | 16 | 51 | 5% | 1958 | |
| inhosc | inhosc1 | 4 | 4 | 51 | 0% | 9.863 |
| inhosc2 | 4 | 4 | 51 | 5% | 814.4 | |
| bifeedb | bifeedb1 | 5 | 16 | 51 | 0% | 8.444 |
| bifeedb2 | 5 | 16 | 51 | 5% | 2933 |
| Source system/model | Problem | #var | #exp | #pts | Noise | Best error |
|---|---|---|---|---|---|---|
| ss_cascade | ss_cascade1 | 3 | 8 | 41 | 0% | 14 |
| ss_cascade2 | 4 | 41 | 0% | 14 | ||
| ss_cascade3 | 8 | 41 | 5% | 476.7 | ||
| ss_branch | ss_branch1 | 4 | 3 | 21 | 0% | 17 |
| ss_branch2 | 6 | 51 | 0% | 17 | ||
| ss_branch3 | 5 | 20 | 0% | 17 | ||
| ss_branch4 | 4 | 20 | 0% | 17 | ||
| ss_branch5 | 4 | 20 | 2.5% | 142.1 | ||
| ss_branch6 | 5 | 31 | 0% | 18 | ||
| ss_5genes | ss_5genes1 | 5 | 10 | 11 | 0% | 23 |
| ss_5genes2 | 10 | 9 | 20% | 211.0 | ||
| ss_5genes3 | 10 | 3 | 0% | 23 | ||
| ss_5genes4 | 15 | 11 | 0% | 23 | ||
| ss_5genes5 | 10 | 11 | 0% | 23.00 | ||
| ss_5genes6 | 1 | 16 | 0% | 23 | ||
| ss_5genes7 | 10 | 20 | 0% | 23 | ||
| ss_5genes8 | 8 | 41 | 0% | 28 | ||
| ss_15genes | ss_15genes1 | 15 | 10 | 11 | 0% | 62 |
| ss_15genes2 | 20 | 11 | 10% | 1783 | ||
| ss_30genes | ss_30genes1 | 30 | 15 | 11 | 0% | 128 |
| ss_30genes2 | 20 | 11 | 10% | 3628 | ||
| ss_30genes3 | 8 | 41 | 0% | 128 | ||
| ss_feedf | ss_feedf1 | 6 | 16 | 51 | 0% | 0.1969 |
| ss_feedf2 | 6 | 16 | 51 | 5% | 1952 | |
| ss_inhosc | ss_inhosc1 | 4 | 4 | 51 | 0% | 0.1967 |
| ss_inhosc2 | 4 | 4 | 51 | 5% | 371.2 | |
| ss_bifeedb | ss_bifeedb1 | 5 | 16 | 51 | 0% | 1.097 |
| ss_bifeedb2 | 5 | 16 | 51 | 5% | 2491 |
| Source system/model | Problem | #var | #exp | #pts | Noise | Best error |
|---|---|---|---|---|---|---|
| gma_feedf | gma_feedf1 | 6 | 16 | 51 | 0% | 0.1777 |
| gma_feedf2 | 6 | 16 | 51 | 5% | 1917 | |
| gma_inhosc | gma_inhosc1 | 4 | 4 | 51 | 0% | 0.2059 |
| gma_inhosc2 | 4 | 4 | 51 | 5% | 371.4 | |
| gma_bifeedb | gma_bifeedb1 | 5 | 16 | 51 | 0% | 0.2546 |
| gma_bifeedb2 | 5 | 16 | 51 | 5% | 2480 |
| Source system/model | Problem | #var | #exp | #pts | Noise | Best error |
|---|---|---|---|---|---|---|
| cytokine | cytokine1 | 4 | 1 | 7 | 10%1 | 25.92 |
| cytokine2 | 1 | 7 | 10%1 | 42.17 | ||
| ss_ethanolferm | ss_ethanolferm1 | 4 | 3 | 11-19 | ~30%1 | 127.4 |
| ss_ethanolferm2 | 2 | 11-15 | ~30%1 | 1308 | ||
| ss_sosrepair | ss_sosrepair1 | 6 | 1 | 50 | 10%1 | 2642 |
| ss_sosrepair2 | 1 | 50 | 10%1 | 2823 | ||
| ss_cadBA | ss_cadBA1 | 4 | 1 | 25 | <20%1 | 750.6 |
| ss_cadBA2 | 1 | 25 | <20%1 | 709.1 | ||
| ss_clock | ss_clock1 | 7 | 1 | 12 | ~10%1 | 928.4 |
| ss_clock2 | 1 | 12 | ~10%1 | 814.5 |
| Source system/model | Problem | #var | #exp | #pts | Noise | Best error |
|---|---|---|---|---|---|---|
| 3genes | pe_3genes1 | 8 | 16 | 21 | 0% | 0.0 |
| pe_3genes2f | 16 | 21 | 3% | 1286 | ||
| pe_3genes2 | 16 | 21 | 3% | 1214 | ||
| pe_3genes3f | 16 | 21 | 5% | 3128 | ||
| pe_3genes3 | 16 | 21 | 5% | 2309 | ||
| 4genes | pe_4genes1 | 11 | 16 | 21 | 0% | 0.0 |
| 5genes | pe_5genes1 | 14 | 16 | 21 | 0% | 0.0 |
| 6genes | pe_6genes1 | 17 | 16 | 21 | 0% | 0.0 |
| pinene | pe_pinene | 5 | 1 | 9 | 5%1 | 9.936 |
| ss_cascade | pe_ss_cascade1 | 3 | 8 | 41 | 0% | 0.0 |
| ss_branch | pe_ss_branch4 | 4 | 4 | 20 | 0% | 0.0 |
| ss_30genes | pe_ss_30genes2f | 30 | 20 | 11 | 10% | 3240 |
| pe_ss_30genes2 | 20 | 11 | 10% | 3004 | ||
| pe_feedf | pe_feedf1 | 6 | 16 | 51 | 0% | 1.653 |
| pe_feedf2 | 6 | 16 | 51 | 5% | 1856 | |
| pe_inhosc | pe_inhosc1 | 4 | 4 | 51 | 0% | 9.815 |
| pe_inhosc2 | 4 | 4 | 51 | 5% | 799.6 | |
| pe_bifeedb | pe_bifeedb1 | 5 | 16 | 51 | 0% | 8.449 |
| pe_bifeedb2 | 5 | 16 | 51 | 5% | 2814 | |
| pe_ss_feedf | pe_ss_feedf1 | 6 | 16 | 51 | 0% | 0.1004 |
| pe_ss_feedf2 | 6 | 16 | 51 | 5% | 1825 | |
| pe_ss_inhosc | pe_ss_inhosc1 | 4 | 4 | 51 | 0% | 0.1259 |
| pe_ss_inhosc2 | 4 | 4 | 51 | 5% | 338.7 | |
| pe_ss_bifeedb | pe_ss_bifeedb1 | 5 | 16 | 51 | 0% | 1.767 |
| pe_ss_bifeedb2 | 5 | 16 | 51 | 5% | 2363 | |
| pe_gma_feedf | pe_gma_feedf1 | 6 | 16 | 51 | 0% | 0.01967 |
| pe_gma_feedf2 | 6 | 16 | 51 | 5% | 1772 | |
| pe_gma_inhosc | pe_gma_inhosc1 | 4 | 4 | 51 | 0% | 0.1229 |
| pe_gma_inhosc2 | 4 | 4 | 51 | 5% | 341.3 | |
| pe_gma_bifeedb | pe_gma_bifeedb1 | 5 | 16 | 51 | 0% | 1.506 |
| pe_gma_bifeedb2 | 5 | 16 | 51 | 5% | 2386 |
#var = number of dependent variables, #exp = number of experimental conditions with different initial conditions and/or input functions, #pts = number of data-points per time-series. Noise is added from a Gaussian distribution with standard deviation given as a certain percentage (denoted Noise) of each experimental value. Problem names starting with ss_ correspond to S-systems.
1) Estimate from or assumption about data.