Intructions on reproducing figures from Guidry et al 2017, "Ca2+ transient duration explains the difference between isotonic and isometric cardiac end-systolic force-length relations".

1)      Download openCMISS from http://opencmiss.org/

2)      Download the models and code from 	https://models.physiomeproject.org/workspace/4ca

3)      Determine which model/ protocol pair(s) you need to run in order to generate all necessary data for the figure you wish to reproduce. 	To do this refer to the Physiome Journal paper titled "Computational model of cardiac excitation-contraction for simulating isometric and isotonic end-systolic force-length relations".

	*The python protocols for the simulations are set to output the data required to reproduce the figures from Guidry et al 2017.  In other words, the Matlab code expects specific filenames. Adjusting the preset sarcomere length or afterload values will affect the production of figures in Matlab.*    

4)      Run the models according to the command structure below.  Keep the default parameter values in order to replicate figures.

>> python.opencmiss.old Python Protocol Main Model  

5)      The output files will be saved in the same folder as the models according to the following naming protocol:

WL = work-loop contraction
isometric = isometric contraction
F = fixed Ca2+
D = dynamic Ca2+

Work-loop contraction csv files will contain “afterload” followed by a number in the name.  This is the value of the afterload the contraction was run at (e.g.  WL_D_afterload0.2576.csv)

Isometric  contraction csv files will contain “SL” followed by a number in the name.  This is the value of the sarcomere length the contraction was run at (e.g. Isometric_D_SL2.231.csv)

If the csv file contains data from a work-loop contraction run with fixed Ca2+, the file will contain “afterload” followed by a number in the name as well as “CaiSL” followed by a number. The CaiSL number signifies the sarcomere length of the isometric contraction from which the fixed Ca2+ was emulated (e.g.  WL_F_afterload0.1911_CaiSL2.024.csv).

6)      After all necessary data are generated, run the section in Guidry2017_Figures.m that corresponds with the figure you wish to reproduce (look at the heading of each section).