The top level directory contains:

cosmos2015-proceedings.pdf:
the Proceedings for the 2015 CoSMoS workshop, held in York, UK. The proceedings include a paper about the CellBranch simulation by Greaves et al. which details the kind of results that can be obtained using the simulation.

v1.0b_simulation/
the source code for the CellBranch simulation, as well as an executable jar in the directory above the source.

Python_data_generation/
Python scripts to generate artificial cistrome data and experimental cistrome data (from ChIP-Seq data)

cluster_scripts/
to run batch jobs on the local SGE enabled cluster

R_data_analysis/
to process the resulting the batches of simulation outputs and produce output graphs