7. Controlling INCA option/settings

INCA enables control over many parameters when running analysis, such as the number of restarts during flux estimation or turning on/off INCAs natural abundance adjustment. In the GUI these are adjusted in the “Options” menu. Each parameter is described in depth in the INCA manual (See section 4.1 Menu functions in the INCA manual).

The INCAWrapper also allow users to modify the options. This can be done through the define_options() function. This function takes any number of keyword arguments, where the keyword has to match a valid INCA option variable. The exact names of the option variables and their default values can be found in the INCA documentation, which is located in your INCA distribution. You can find this in <your-inca-folder>/doc/inca/class/@option/option.html on your local computer if you have INCA installed. A few examples of commonly used options are:

  • fit_starts the number of restarts of the flux estimation algorithm, default 1.

  • sim_na adjust for natural abundance in labelled atoms, default true.

  • sim_more adjust for natural abundance in unlabelled atoms, default true

  • sim_ss simulate only steady state isotopomer distributions (i.e. NOT INST-MFA), default true.

The INCAWrapper leaves all options that are not modified at their default value.

In most of the tutorials in this documentation we will modify one or more option(s), please refer to the other tutorials for how to use the define_options() function in a realistic setting. However, here we will do a very quick demonstration.

First, we load the incawrapper package.

[1]:

import incawrapper

Now, we create a new INCAScript, change all the options described above and add the changes to the options block in the INCAScript.

[2]:

script = incawrapper.INCAScript() # Create a new script
script.add_to_block(
    "options",
    incawrapper.define_options(fits_starts=100, sim_na=False, sim_more=False, sim_ss=False)
)
print(script)

clear functions

% REACTION BLOCK


% TRACERS BLOCK


% FLUXES BLOCK


% MS_FRAGMENTS BLOCK


% POOL_SIZES BLOCK


% EXPERIMENTAL_DATA BLOCK


% MODEL BLOCK


% MODEL MODIFICATIONS BLOCK


% OPTIONS BLOCK
m.options = option('fits_starts', 100, 'sim_na', false, 'sim_more', false, 'sim_ss', false)

mod2stoich(m); % make sure the fluxes are feasible

% RUNNER BLOCK

The above INCAScript cannot run because it does not hold any model, but we can see how the options are modified in the script.