Update the provided example notebooks

[Will-Raymond]

The current notebooks on the repository are out of date for the newer versions of rSNAPsim and need to be redone.

We need the following notebooks:

• Sequence manipulation
  Guides the user through manipulating a sequence and creating a POI object or mRNA object and all its features. Should show them the options such as codon optimization routines.

• Propensity calculation
  Show the user how to convert codons to stepping rates for a TASEP or ODE model. Shows various options for calculating these rates as well as how to overwrite or access specific rates.

• Model Solving
  Show the user how to solve the various models: ODE, TASEP, custom TASEP and their outputs

• Analyses
  Show the user what options there are to do with a solved model such as calculate correlations and ribosomal occupancy

• Model fitting
  Provide an example to the user of how to use the rSNAPsim to perform model fitting and selection using the optimization module.

• Experiment Design using rSNAPsim and rSNAPed
  Simulate multiple models to differentiate with different experiment types

• FSS model refit
  Provide and example of using rSNAPsim from start to beginning to fully fit a model and how the pipeline works