README

Code to regenerate the figures for the preprint The dynamic fitness landscape of ageing haematopoiesis through clonal competition.

Instructions to reproduce each figure can be found in the following jupyter notebooks:

• sde.ipynb
• abc/posteriors.ipynb
• dynamics.ipynb

Requirements

This code needs Python greater or equal to 3.9.7 and the following requirements:

1. a Python jupyter kernel with hscpy installed
2. the processed data of Mitchell et al. that can be downloaded from here
3. The output of the simulations that can be either downloaded from here or regenerated with the Rust binary.

1. The Python kernel

A Python environment available as a jupyter kernel (preferably named as hsc-draft) with hscpy version v0.4.11 installed.

One way to do it:

• create a directory for the environment mkdir ~/venvs/
• create an empty environment python -m venv ~/venvs/hsc-draft
• activate the environment source ~/venvs/hsc-draft/bin/activate
• install the hscpy package pip install git+https://github.com/fraterenz/[email protected]
• install ipykernel package pip install ipykernel
• make the environment available as a jupypter kernel python -m ipykernel install --user --name hsc-draft
• run the notebooks to regenerate the images

2. The donor data

• Get the processed data of Mitchell et al. from here or with wget "https://www.dropbox.com/scl/fi/vsuebfgfcegdoqtuvcsan/mitchell-data.tar.gz?rlkey=favnmgl4ccd246bfnikazg513&st=jrpq5ldf&dl=0" --output-document="mitchell-data.tar.gz"
• create a directory mkdir ./mitchell
• untar the data with with gzip: tar xvf mitchell-data.tar.gz --directory=./mitchell

3. The output of the simulations

The output of the simulations can either downloaded from here or generated with the Rust binary hsc with version v4.3.7. To download the data without regenerating them:

• Get them from here or with wget "https://www.dropbox.com/scl/fi/pjtvnbtk5euxwylsz8pob/data.tar.gz?rlkey=l96bsmfis00473epg78yae43m&st=yo8bxi55&dl=0" --output-document="data.tar.gz"
• untar the data with with gzip: tar xvf data.tar.gz

The other option is to regenerate the data with the binary hsc, that can be either downloaded or compiled from the source code (requires Rust to be installed). To compile from source, get the code from here and compile it with cargo cargo b --release.