Installation

It is highly recommended to use a distribution such as anaconda, which already contains many of the required packages.

Installing kinetics

To install the latest stable version of kinetics using pip, together with all the dependencies, run the following command:

pip install kinetics

Running in google colab

An easy way to get started quickly is to use a google colab. notebook.

In the first cell of the notebook, run !pip install kinetics to install the kinetics package.

Try this block of code in a google colab. notebook to get started quickly..

!pip install kinetics
import kinetics

# Define reactions
enzyme_1 = kinetics.Uni(kcat='enz1_kcat', kma='enz1_km', enz='enz_1', a='A',
                        substrates=['A'], products=['B'])

enzyme_1.parameters = {'enz1_kcat' : 100,
                       'enz1_km' : 8000}

# Set up the model
model = kinetics.Model(logging=False)
model.append(enzyme_1)
model.set_time(0, 120, 1000) # 120 mins, 1000 timepoints.

# Set starting concentrations
model.species = {"A" : 10000,
                 "enz_1" : 4,}
model.setup_model()

# Run the model
model.run_model()
model.plot_substrate('A')
model.plot_substrate('B', plot=True)

Prerequisite Software

You shouldn’t need to worry about this if using the anaconda python distribution, and pip install kinetics.

kinetics requires NumPy, SciPy, matplotlib, tqdm, pandas, SALib, seaborn, and deap,installed on your computer. Using pip, these libraries can be installed with the following command:

pip install numpy
pip install scipy
pip install matplotlib
pip install tqdm
pip install pandas
pip install salib
pip install deap
pip install seaborn

The packages are normally included with most Python bundles, such as Anaconda. In any case, they are installed automatically when using pip or setuptools to install kinetics.