/nephron

Computational models for epithelial transport along the nephron.

Primary LanguagePython

About

This is latest version of sex-specific mathematical models for epithelial transport along the nephron implemented in Python 3. Related research papers are listed below. Please cite appropriately. To improve computation time, parallel computation of different types of nephron is implemented for the multiple nephron model.

Instructions

To run the parallel simulation code use command: python3 parallel_simulate.py --sex [option] --species [option] --type [option] --diabetes [option] --inhibition [option] --pregnant [option]

The options here are:

sex: Male, Female (required);

species: human, rat, mouse (required);

type: superficial, multiple (required);

diabetes: Severe, Moderate, Non (optional, default: Non);

pregnant: mid, late (optional, default: non, only for female rat);

inhibition: ACE, SGLT2, NHE3-50, NHE3-80, NKCC2-70, NKCC2-100, NCC-70, NCC-100, ENaC-70, ENaC-100, SNB-70, SNB-100 (optional, default: None).

unx: N, Y (optional, default: N)

Notes:

  • Human only have ACE and SGLT2 inhibition cases. The others are for rats.
  • pregnancy: only has been characterized for normal pregnant rat superficial nephron at this time (i.e., not done for humans and for diabetes, also multiple nephron)

Understanding output

All the output files' names are in following structure: 'sex_species_segment_concentration/flow_of_solute_in_compartment.txt'.

Here is an example: female_rat_ccd_con_of_Cl_in_Bath.txt. It contains interstitial concentration of Chloride along cortical collecting duct in female rat.

Another example: male_hum_pt_flow_of_Na_in_Lumen.txt. It contains luminal flow of Sodium along proximal convolute tubule in male human.

These results are scaled per nephron.

The unit of concentration from outputs is mmol/L (mM).

The unit of volume is nl/min.

The unit of flow is pmol/min.

/plot/ contains some example scripts for plotting output

Related Work

Please cite appropriate paper(s) when using this model.

Published papers:

Previous versions

Previous versions of this model code are available here.