analysis of lysine and arginine vacuolar transport by dynamic labeling

Instructions This dataset contains source data and scripts used to generate figure panels and tables describing analysis of lysine and arginine vacuolar transport in budding yeast using dynamic labeling assays. important note In order to precisely recreate the results, we recommend installing the scripts on a computer running Mac OS and python 3.13, which is what we used for the analysis. Download the Jupyter notebook (detailed_model.ipynb), R script (manuscript_plots.R) and the Data folder (data.zip). Extract the Zip file in the same location as the Jupyter notebook and the R script. First, run the jupyter notebook (one can conveniently use VS code). Beforehand, ensure that the required modules were installed: from path import Path import numpy as np # common mathematical functions import pandas as pd # enables working with dataframes import matplotlib.pyplot as plt # a standard plotting package for python import seaborn as sns # extra tools for plotting (such as violin plots) from tqdm import tqdm import itertools import os from symbolic_compartmental_model import SymbolicCompartmentalModel #package to parametrize compartmental models Next run the R script (use R studio). Also, ensure that the required packages were installed: library(stringr)library(reshape2)library(data.table)library(plyr)library(dplyr)library(gplots)library(gridExtra)library(RColorBrewer)library(ggplot2)library(openxlsx)library(tidyr)library(shuffle)library(stringr) Pre-computed outputs of the scripts can be found in the results folder (results.zip).