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Quick fix of usage.rst
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llegregam committed Oct 24, 2023
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Expand Up @@ -43,10 +43,31 @@ The :file:`yaml` configuration file contains all parameters required to calculat
thus key to ensure **reproducibility** of the flux calculation process. A configuration file is generated automatically by
PhysioFit during flux calculation; it can also be created or edited manually.

Here is an example of a configuration file:

.. image:: _static/usage/config_example.JPG
:scale: 80%
Here is an example of a configuration file: ::

iterations: 100
mc: true
model:
bounds:
Ace_M0: (1e-06, 50)
Ace_q: (-50, 50)
Glc_M0: (1e-06, 50)
Glc_q: (-50, 50)
X_0: (0.001, 10)
growth_rate: (0.001, 3)
model_name: Steady-state batch model
parameters_to_estimate:
Ace_M0: 1
Ace_q: 1
Glc_M0: 1
Glc_q: 1
X_0: 1
growth_rate: 1
path_to_data: ..\data\test-data_single_exp.tsv
sds:
Ace: 0.2
Glc: 0.2
X: 0.2

For a description of all calculation parameters, check the section below.

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