Figure 1
UML class diagram of modelbase software components. It consists of six classes, with LabelModel inheriting from Model and LabelSimulate inheriting from Simulate. ParameterSet and Analysis are special classes containing parameter sets and static methods for analysis respectively.
Table 1
Mathematical models originally published without the source-code, reconstructed in our lab using the modelbase package. The source code and examples are available from the GitHub repository of our lab https://github.com/QTB-HHU/.
| Process | Original publication | GitHub.com/QTB-HHU/ | Developer |
|---|---|---|---|
| Photosynthetic Electron Transport Chain | [15] | ./petc-modelbase | A.M. |
| Calvin-Benson-Bassham Cycle | [16] | ./cbb-modelbase | M.v.A. |
| Pentose Phosphate Pathway | [4, 17] | ./ppp-modelbase | T.N. |
Figure 2
Reproduction of the Figures from [15]. Simulated fluorescence trace obtained through Pulse Amplitude Modulation (PAM) under light induced (left) and anoxia induced (right) conditions. The dynamics of the fluorescence decrease corresponds to the activation of a specific photoprotective mechanism called state transitions, while the increase in the signal after the inducer (light or anoxia) is switched off relates to the relaxation of the mechanism.
Figure 3
Metabolite steady state concentrations dependent on the extra-stromal phosphate concentration simulated with the Poolman implementation of the Pettersson and Ryde-Pettersson model of the CBB cycle [16].
Figure 4
Formation of diverse Glc6P isotopomers in a haemolysate, obtained by solving the adapted model by Berthon et al. [17] reimplemented using modelbase.
Figure 5
Schematic representation of label incorporation by the CBB cycle intermediates.