Getting Started

Installation

BasiCO is is finally available in pypi:

pip install copasi-basico

however you can pip install it using:

pip install git+https://github.com/copasi/basico.git

Currently there is one additional package available that provides support for PEtab and petab-select, that can be installed using

pip install copasi-basico[petab]

or

pip install git+https://github.com/copasi/basico.git#egg=basico[petab]

Use the package

To start using the package, you simply import it:

>>> from basico import *

Loading a Model

You can load either COPASI, or SBML files directly using the load_model() command:

>>> load_model('brusselator.cps')

You can also load a model by providing a URL:

>>> load_model('https://fairdomhub.org/models/287/download?version-1')

We also provide a number of example models, that you can directly load with the installation. See get_examples() and load_example().

Models from the BioModels Database and JWS can also be directly loaded ( jws_online, biomodels, load_biomodel())

>>> load_biomodel(206)

Interrogating the Model

To find out what is in a model, you could use the corresponding functions:

• get_species()

• get_reactions()

• get_parameters()

• get_compartments()

Analogous you can also set all of these, by providing the name of the element to modify:

• set_species()

• set_reaction()

• set_parameters()

• set_compartment()

New elements are added with:

• add_species()

• add_reaction()

• add_parameter()

• add_compartment()

And removed with:

• remove_species()

• remove_reaction()

• remove_parameter()

• remove_compartment()

Analyzing the Model

Currently the following analysis tasks have been included:

• task_timecourse

• task_steadystate

• task_parameterestimation

Saving a Model

Saving a model, is done by calling save_model():

>>> save_model('model_3.cps')

will save the file model_3.cps in the current folder. To export the model to SBML use:

>>> save_model('model_3.xml', type-'sbml')