Reference environment for the manuscript ['Predictive modelling of gene expression from transcriptional regulatory elements'](http://dx.doi.org/10.1093/bib/bbu034)

### Overview

This is the reference environment for the manuscript ['Predictive modelling of gene expression from transcriptional regulatory elements'](http://dx.doi.org/10.1093/bib/bbu034) (Budden, D. M., Hurley, D. G. & Crampin, E. J. Predictive modelling of gene expression from transcriptional regulatory elements. Brief. Bioinform. bbu034 (2014). doi:10.1093/bib/bbu034.  It executes code to reproduce specific results described in the manuscript.   You can find more information about this research at the [project page here](http://uomsystemsbiology.github.io/publications/budden2014predictive/).  

To find other versions of this reference environment, see Other Links below.  To learn more about reference environments, [see the detailed description here](http://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](http://dx.doi.org/10.1093/bib/bbu034)

[Project page link](http://uomsystemsbiology.github.io/publications/budden2014predictive/)

[Docker container](https://hub.docker.com/r/uomsystemsbiology/budden2014predictive/)

[Vagrant-managed virtual machine](https://github.com/uomsystemsbiology/budden2014predictive_reference_environment)