| Pathway or subsystem | Pathway Builder models | Mathematical model | XPPaut file | Notes |
|---|---|---|---|---|
| Entire pathway | XML | |||
| ComK/Rok/AbrB subsystem | XML | Word | ODE | |
| ComK/Rok/AbrB subsystem rev 3 | XML | Word | ODE | |
| ComK/Rok/AbrB subsystem rev 5 | XML | Word | ODE | Model now has non-competetive binding for AbrB and Rok on comK |
| Pathway or subsystem | Description of experiment | xppaut set file | System constants | Data, graphs, etc. |
|---|---|---|---|---|
| ComK/Rok/AbrB subsystem | Simulation showing transient spike in ComK with decreasing AbrB concentration (concentration and time values are meaningless - qualitative results only) | SET | See SET file | GIF of system response to decreasing AbrB concentration |
| ComK/Rok/AbrB subsystem rev 5 | Simulation showing transient spike in ComK with decreasing AbrB concentration with more realistic parameters and time scale (althogh ComK concentration is off by a factor of 10) | SET | XLS | GIF of system response to decreasing AbrB concentration |
| ComK/Rok/AbrB subsystem rev 5 | Simulation showing transient spike in ComK with decreasing AbrB concentration with more realistic parameters and time scale (althogh ComK concentration is off by a factor of 10) - added ComK binding to Rok | SET | XLS | GIF of system response to decreasing AbrB concentration |
| ComK/Rok/AbrB subsystem rev 5 | Simulation showing near-steady state ComK concentrations after 15000 s post T0 as a function of AbrB concentration, which is held constant. | SET | XLS | GIF of ComK concentration as a function of constant AbrB concentration |
| ComK/Rok/AbrB subsystem rev 5 | 1 parameter system sensitivity experiments. | SET | XLS | Results |
| ComK/Rok/AbrB subsystem rev 5 | 2 parameter system sensitivity experiments. | SET | XLS | Results |
| ComK/Rok/AbrB subsystem rev 5 | Sensitivity equation results. | SET | XLS | Results |