files for Smith & Shanley 2012 insulin signalling and oxidative stress project
fig1 fig2 fig3
figures 1-3 from the paper. fig2 and fig3 also contain data files (copasi output and experimental data) and R scripts used to make them.
==== equations sensit_analy supp_figs
as in the addional files of the paper
===
A lot of the development was done with SBML-shorthand (smbl-sh). See
http://www.staff.ncl.ac.uk/d.j.wilkinson/software/sbml-sh/
To use the smbl-sh (.mod) files and interconvert them with SBML (.xml) you will need the mod2smbl.py and sbml2mod.py scripts from the above URL.
==== catshorthand.py
put together smbl-sh .mod files as in eg (files in m8b2_module_files/) $ catshorthand m8b2_phosph.6.mod m8b2_jnk.6.mod > pj.mod 2> catsh.errlog
You can have the same species in both mod files; it is put only once in pj.mod, and the particle number/concentration from the first file (phosph.6 above) is used.
m8b2_module_files
shorthand (.mod) files for the 6 modules of the model (fig1 A-F), plus the python script that generates the foxo file.
m8b2_complete_model
the above 6 cat'ted together to make a complete model: m8b2_rapijf.6.mod m8b2_rapijf.6.xml with initial particle numbers (xml is the .mod converted to sbml) m8b2_after2mored.mod m8b2_after2mored.xml from the end of the 5 days equilibration with physiological insulin, plus 2 days more with low constant ins.