Energy-based Analysis of Biomolecular Pathways: supporting software

Virtual Reference Environment (VRE) for the project:
Energy-based Analysis of Biomolecular Pathways
The corresponding publication is at https://arxiv.org/a/gawthrop_p_1.html

The file vre.iso is a bootable iso image.
This can be used to boot a virtual machine such as virtualbox.
Double-click the icon 'run_experiments.sh' and select
'Execute in Terminal' to reproduce the results of the paper.
The results appear in Examples/vre_out.pdf

The file vre_out.pdf is the expected VRE output.

mtt and xmtt are made available by typing:
source ~/Examples/mtt/bin/mttrc ~/Examples/mtt
Type 'mtt --versions' to check.
Type 'mtt' for more information
Type 'mtt manual' for too much information
Type 'xmtt&' for a GUI to mtt

The file vre_examples.tgz contains the sources.

General bond graph information is at
http://www.gawthrop.net/BondGraphs/

Virtual Reference Environments are described by:
Daniel G. Hurley, David M. Budden, and Edmund J.
Crampin. Virtual reference environments: a simple way
to make research reproducible. Briefings in
Bioinformatics, 2014. doi:10.1093/bib/bbu043.