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.