This software is intended simulate sequencing experiments. There are two different implementations that intend to model the processes in the nucleus on different scales of detail.
Read the README of the Dense Nucleus Model which implements the position and movement of every protein around the defined DNA segment. It provides the largest level of detail. However, this also means that it contains many degrees of freedoms (e.g. hidden variables and hyper parameters) to adjust. Moreover, this is computationally heavy. It is not developed any further.
A lighter implementation is a Gillespie algorithm with the notion of space. Read the README here. It has less flexibility but is much quicker. This implementation is currently developed and further improved.
The software requires python (3.6 or higher) and pip to be installed. Run
python3 -m pip install -r requirements.txt
to install the necessary packages.