Photosimulator 0.0.1

A photokinetic analysis package developed for the DeForest Group

Photosimulator

photokineticanalysis.py

PhotokineticAnalysis()
  

Functions:

PhotokineticAnalysis.check()
  

Checks that the inputs for the calculate_theoretical function are correct

PhotokineticAnalysis.calculate_theoretical()
  

This section allows for calculating theoretical photouncaging values using the following first order kinetic equation for photouncaging:

$Y = {Y_o} + (plateau-{Y_o})(1-exp(-K*x))$

${Y_o} = 0$

Plateau = 1

Input:

• Array of x values (Dosage)
• Photokinetic constant, k

Output:

• Table of x and corresponding y values (normalized to 1)
• Graph of theoretical data

PhotokineticAnalysis.calculate_experimental()
  

This section allows for calculating the photouncaging constant k using the first order kinetic equation:

$Y = {Y_o} + (plateau-{Y_o})(1-exp(-K*x))$

${Y_o} = 0$

Plateau = 1

Input:

• Excel file formatted such that the first column is labelled with the time unitstime and has all the time values and the corresponding y values labelled.

Output:

• Kinetic rate constand with standard deviation
• Table of x and corresponding y values (normalized to 1)
• Graph of theoretical data

photokineticanalysis.py

ChemotaxisSimulation()
  

Functions:

ChemotaxisSimulation.cell_movement()
  

This section allows for modeling cell migration in 2D. It is based off of a stochastic compartment model developed by Fadai et al. 2019.

Input:

• n:matrix size
• m:matrix size
• CC:location of initial cells
• V:compartment size
• rm: motility rate between 0-1, where 1 equates to faster cells
• rp: proliferation rate between 0-1, where 1 equates to max proliferation
• rd: death rate between 0-1, where 1 equates to max death rate
• tf: final dimensionless time
• C_start: if there is a chemotactic variable applied, when is it applied.
• C_end: if there is a chemotactic variable applied, when does it end.
• rhox: how the chemotactic variable is applied over space (i.e gradient,etc)

Output:

• n * m matrix with final cell positions

ChemotaxisSimulation.simulate()
  

This function plots cell position over time and saves a movie file.

Input:

• Title of movie file to be saved

Output:

• Movie file_name.gif