Reference environment for the manuscript ['Modelling the conditional regulatory activity of methylated and bivalent promoters'](http://dx.doi.org/10.1186/s13072-015-0013-9)

Overview

This is the reference environment for the manuscript ['Modelling the conditional regulatory activity of methylated and bivalent promoters'](https://dx.doi.org/10.1186/s13072-015-0013-9) (1Budden, D. M., Hurley, D. G. & Crampin, E. J. Epigenetics Chromatin 8, 21 (2015)).  It executes code to reproduce specific results described in the manuscript.   You can find more information about this research at the [project page here](https://uomsystemsbiology.github.io/budden2015treeome/).  

To find other versions of this reference environment, see Other Links below.  To learn more about reference environments, [see the detailed description here](https://uomsystemsbiology.github.io/reference-environments/).

Instructions for use

This version of the reference environment is a live image as a bootable read-only ISO.  To use it:

- Install a virtualization tool like [VirtualBox](https://www.virtualbox.org/), then
- Create a new virtual machine in the virtualization tool with a virtual CD/DVD-ROM drive
- Mount the ISO in the drive
- Boot the machine.  

This will start a virtual machine with scripts to run which reproduce results described in the manuscript.  

Other links

[Manuscript link](https://dx.doi.org/10.1186/s13072-015-0013-9)

[Project page link](https://uomsystemsbiology.github.io/budden2015treeome/)

[Docker container](https://hub.docker.com/r/uomsystemsbiology/budden2015treeome/)

[Vagrant-managed virtual machine](https://github.com/uomsystemsbiology/budden2015treeome_reference_environment)