How to create a model with SbioDesktop

Basic rules

A model consists of states or species that are connected with rate constants. These rate constants determine the speed with which the concentration or population in one state flows in to the other connected state. Some basic rules need to be obeyed when constructing a model so that the final basis spectra plotted correspond to the correct state.

- Rule 1

  Give each state a name, but the first letter should be a unique capital letter in increasing alphabetical order (i.e. A, B, etc.). This is important because the state that has the last letter in alphabetical order has zero spectral amplitude. Obviously, this limits the number of states to 26.

- Rule 2

  The state with the last letter symbolises the finally formed state, and can be seen as a 'population sink' state. Use this state as your last species. In the global analysis results, the amplitude of this state (representing a spectrum for instance) is not shown as it has zero amplitude. For example, consider a two-state model with rate constant k1 (the inverse of life time) connecting states A and B. B is the last letter in the alphabet, so represents the 'sink'. A has start population 1, and flows into B which has start population 0. After some time, B has population or concentration 1, while A has 0. However, B is the last letter, so it possesses a flat line as spectrum. The results of a global analysis therefore only will show the spectrum of A. So even if A has a long-lived or infinite lifetime on the used time base, B still has zero amplitude. If the final spectrum in your data has still amplitude (which is different from the start spectrum), you can model this by introducing state C, and giving state B a very long life time.

  The final state can be also be used for example to represent a 'ground state' (in difference spectroscopy this means that the original spectroscopic state has been reformed, so it will have zero amplitude since it is normalised to this state). The final state and ground state can therefore be modelled by the same state.

- Rule 3

  The rate constants have the format k1, k2,.. k10, k11, etc. up to 99 . It is important that the second (for 1-9) or second and third (for 10 to 99) characters are numbers. Typical starting values are 1, 0.10, 0.001, etc. in decreasing order.

Sbiodesktop quick manual

Launch the desktop by executing sbiodesktop in your command window. Create your own model by starting a new project 'File/New Project'; Add a reaction in 'Reactions', f.i. 'A -> B' (with spaces). Use 'Mass-action' as 'Kinetic law'. Go to 'Kinetic law' tab, and make a new 'Forward rate parameter', f.i. 'k1'. Go to 'Rate species' tab, and set 'InitialAmount', f.i. 1 (this is the initial concentration, i.e. a boundary value in the differential equations to be numerically solved). Run a simulation by pressing 'Simulate/start' or Ctrl+T to check if your model works. ALWAYS do a simulation run to check if your model is working and doing what your requirements are. You can also check out how one of the supplied models is built and use those as examples. Go to the command window, and execute for instance

modelobj=sbmlimport('seq2.xml')

followed by

simbiology(modelobj)

The sbiodesktop opens, and you can explore the settings for the 2 component sequential model. 2 Component means that two time constants k1 and k2 are defined which characterise the transitions from species A → B and from B → C.

The sbiodesktop allows you to view and modify your model graphically. The loaded model looks like this:

Before a model is to be used in global analysis, run it first and check if the concentration profiles for each state behave as expected. The results on a 500 s (log) time base are shown below.

Here the time base has been extend to 500 seconds. This and many more calculation options can be set in the ‘Configuration Settings’ window under ‘Model Variable Settings’ in your model. Export your model in .SBML format by right clicking the 'Model session' to make it useable for the global analysis package.

In a similar way more complicated models can be constructed that contain equilibriums, and combinations of parallel and sequential models. Remember to ALWAYS do a simulation run before attempting to use your model in a global analysis to ensure the model performs as expected.

See Also

- SbioDesktop