New Naming Convention

production_rates sheet

• Both SystematicName and StandardName columns must be deleted and replaced with a single id column.
• production_rate must be singular in the column name, but plural in the sheet name, i.e production_rates.

degradation_rates sheet

• Both SystematicName and StandardName columns must be deleted and replaced with a single id column.
• degradation_rate must be singular in the column name, but plural in the sheet name, i.e degradation_rates.

optimization_parameters

The following modifications must be implemented:

• Everything from alpha to MaxFunEval must be left alone, as these variable names are built-in to fmincon. Everything else must be changed to snake case.
• time must be changed into expression_timepoints and simtimes must be changed to simulation_timepoints.
• Both systematic names and standard names must be deleted and replaced with an id column.
• degradation_rates and production_rates must be singular in the column name, but plural in the sheet name.
• threshold_b must be a column in threshold_b sheet.
• Rows must be changed to rows targets and columns must be changed to cols regulators.
• Sigmoid should be changed to Model. For it to work correctly, Model must be "Sigmoid" or "MM".