ncAABiokinetics

Kinetic model of non-canonical Amino Acid (ncAA) (Parameterized with data from experimental measurements of Azidohomoalanine, Aha) distribution and labeling as published by Saleh et al. (2023). Repository contains simulation scripts, and model files containing the system of ODEs evaluated.

Code authored by Tyler VanDyk, MSBME.

Data collected by Aya M. Saleh, PhD.

Contents

ODES.py - Python script containing an executable function doseRFBK for numerical integration of the system of ordinary differential equations (ODES) describing ncAA kinetics.

SystemFitting.py - Python script for fitting transport and incorporation parameters as described in the appropriate file from params to ground truth data recorded from experimental methods saved in gtdata

DosingRegimen.py - Python script for prediction of ncAA distribution and labeling according to a desired dosing regimen.

PRCC.zip - Files used by authors to generate partial rank correlation coefficient (PRCC) values for model parameters during model sensitivity analysis.

params - Directory containing '.csv' files with parameter names, best-fit values, fitting range, and standard error of fitting.

gtdata - Directory containing '.csv' file with experimentally recorded ground truth data for parameter fitting.