Table 1 Key changes between the first published version of modelbase [12] and the current update
From: Constructing and analysing dynamic models with modelbase v1.2.3: a software update
Functionality | modelbase 0.2.5 | modelbase 1.2.3 |
|---|---|---|
Initialization | Model takes only parameters as an argument | Model takes as arguments all other model components as dictionaries |
Parameters | Hidden as a private attribute | Replaced with a vanilla dictionary |
Derived parameters | No function to calculate from other model parameters | Called on initialization and prior to any numerical operations |
Handling of time-dependent reactions | Time given in kwargs | Modifiers argument is introduced |
Simulation | Integration via timeCourse that takes an array of time points for Simulation | Integration via simulate that takes only the endpoint of the simulation, default starting point t = 0, otherwise starts where the last simulation ended |
Labelling features | Focused on carbon labelling problems | Reference of the word carbon was changed to label |
Method to calculate relative label distribution in steady-state | None available | Via LinearLabelModel |
Scan steady-state concentrations depending on parameter values | None available | Via parameter_scan |
SBML support | Export of model stoichiometries | Import of models that match the capabilities of modelbase and full export of models using ratelaw |
Metabolic Control Analysis support | None available | A full suite of methods to calculate and plot elasticities via mca module |
Predefined kinetic laws | None available | Via ratelaw module |
Plotting support | Time course plots | Phase-plane analysis |