Known Limitations

Starting values

Although the optimised time constants can be directly used as starting values for the next fit, this cannot be done with the spectra. The spectra are linearly fitted using QR decomposition, which quickly calculates the unique solution. It is therefore not necessary to set starting values for the spectra.

Time base

Make sure your smallest time point is 1 if you use Matlab v7.6. For unknown reasons that version fails to use the resample function. Shift the time axis such that this is the case. With this workaround everything should work normally. Only positive times are used in the analysis. If negative times need to be fitted (if signal in data starts before time zero), shift the collected time points with the required amount as data pre-processing step.

Importing models

If a model is imported via third-party software like Gepasi, make sure the metabolites are ordered properly. Meaning: Gepasi for instance generates a list of concentrations for each metabolite in the order of the creation of the metabolite. For example for a parallel model A->C and B->C, it creates first A and C, and then B. Matlab automatically sorts the species alphabetically. To avoid confusion, manually sort the metabolites in Gepasi (such that the final product is in the last column). The final order can be checked in the 'Plot' tab, where the order of the metabolites represented there is how it ultimately exports the SBML file.

Logo is replaced with figure axis

If the main GUI is selected while it has been asked to perform an action such as loading data, the logo might be replaced with a figure axis. Let the GUI finish the asked action, and this will not happen. Save your input file, restart the GUI, and load the saved input file to start with a clean GUI.

Setting user path

For the user's convenience, it is useful to let Matlab know where the main program and the folder containing all models permanently reside. If set correctly, Globe_Toolbox can be started from the command window without setting the current folder to Globe_Toolbox's main program folder. Therefore, Globe_Toolbox's folder has to be added to the search path by: File>Set Path>Add with Subfolders>. NB. There might be a problem with Windows (Vista) because of folder permissions, apparent from the message: 'Matlab cannot save changes to the path' or something similar. Save 'path.def' to your startup folder, and future sessions will know where to look. You can set your startup folder in Windows by appropriately changing the 'start in' box of Matlab's shortcut properties (which you then need to use to start a new Matlab session).

Stand-alone (compiled) version

In order to run this package without Matlab, the package needs to be compiled properly. Currently, this is not possible. The main reason is that the SimBiology toolbox is not supported by Matlab's 'deploytool'. When Matlab includes this toolbox, a compiled stand-alone version will be made available.