Prion Aggregate (Propagon) Replication Rates & Asymmetric Transmission

Code for estimation of replication rate and asymmetric distribution using experimental aggregate count publication: PLOS Computational Biology Article

Prion aggregates, cell division dynamics, and transmission of aggregates.

Included:

• propagon_data_raw: Folder containing experimental aggregate count datasets for six prion variants.
  
• propagon_data_filtered_iqr: Folder containing aggregate counts data filtered for outliers.
  
• propagon_data_down_sampled: Folder containing aggregate counts data downsampled in time.
  
• Example_Simulate_Data.m: The script shows how to generate simulated data using the functions in the /code/ folder.
  
• Example_Parameter_Estimation.m: The script shows how to apply the adaptive Metropolis algorithm to simulated and experimental data.
  

Mathematical Modeling and Replication Rate Estimation

1. Prion aggregate count experiments.
   
2. Structured model, aggregate distribution, and cell division.
   
3. Prion aggregate counts for six prion variants.
   
4. Adaptive Metropolis estimates of prion aggregate replication rates.
   
5. Adaptive Metropolis estimates of prion aggretate transmission bias.
   

Note: The appearance of increasing variance over time is a visual artifact from viewing iterations on a logarithmic scale.