cmml-inflam

A collection of stochastic process models used in the modelling the evolution of CMML.

All features of our software are described in detail in our full API documentation.

More details on CMML modeling and inflammation can be found in these papers:

References

Installation procedure

---

One way to install the module is to download the repositiory to your machine of choice and type the following commands in the terminal.

git clone https://github.com/I-Bouros/cmml-inflam.git
cd ../path/to/the/file

A different method to install this is using pip:

pip install -e .

Usage

import cmmlinflam

# create and run a Gillespie routine for a STEM cell population for given time frame
algo = cmmlinflam.StemGillespie()
algo.simulate_fixed_times(parameters, start_time, end_time)

# create and run a Gillespie routine for a STEM cell population until criterion is met
algo = cmmlinflam.StemGillespie()
algo.simulate_criterion(parameters, criterion)

# create and run a Gillespie routine for a STEM cell population until fixation
algo = cmmlinflam.StemGillespie()
algo.simulate_fixation(parameters)

Contributing

Pull requests are welcome. For major changes, please open an issue first to discuss what you would like to change.

Please make sure to update tests as appropriate.

License

MIT