Review SED-ML files that purport to reproduce multiple published figures

[jonrkarr]

Often different figures involve different simulations. However, COPASI can only handle 1 simulation at a time. As a result, these SED-ML may have plot that don't reproduce published simulation results as advertised; they involve the right variables for figures, but involve different initial conditions and parameter values.

Example:

• BIOMD0000000949/Chitnis2008.sedml#plot_5_task1
• BIOMD0000000949/Chitnis2008.sedml#plot_6_task1

These have the same the correct variables for Figure 3, but Figure 3 involves a different initial conditions and parameter values than Figure 2 (plot_1_task1, plot_2_task1, plot_3_task1, plot_4_task1).

[jonrkarr]

Todo

• [ ] Use Python to identify all SED-ML files that have multiple tasks and multiple plots
• [ ] Extract the paths of these SED-ML files and the ids and names of these plots, say to a CSV file
• [ ] Quickly identify plots whose ids and/or names suggest they may be duplicates
• [ ] Open up the affected SED-ML files in COPASI
• [ ] Identify any unintended plots by comparing the plots COPASI generates to the curation notes
• [ ] Edit the affect SED-ML files (version in the manual-fixes subdirectory) to remove unintended plots from the SED-ML
• [ ] Save these SED-ML files
• [ ] Commit changes to this repository