Model as published on 2013-10-09. (fork of rgm's kidney_core)



This repository contains the source code for the whole-kidney model that was introduced in the following article:

Moss R & Thomas SR. Hormonal regulation of salt and water excretion: a mathematical model of whole-kidney function and pressure-natriuresis. Am J Physiol Renal Physiol, 2013. DOI: 10.1152/ajprenal.00089.2013

Installation instructions are provided in the file INSTALL.

Running the model

Thanks to the Systems Biology Laboratory at the University of Melbourne, the model is available as a pre-configured virtual environment.

This is the easiest way to obtain a working version of the model, as it automatically performs all of the installation steps.


This work is dual-licensed. You have the choice of which licence applies, either the CeCILL or CeCILL-C licence (

  • CeCILL v2.0 is similar to, and compatible with, the GNU GPL (clause 5.3.4). The terms for this licence are in the file 'Licence_CeCILL_V2-en.txt'.

  • CeCILL-C v1.0 is similar to, and compatible with, the GNU LGPL, which allows closed-source products to use this work under certain conditions. The terms for this licence are in the file 'Licence_CeCILL-C_V1-en.txt'.

This work was created in 2012 by Robert Moss and S. Randall Thomas, in the CNRS UMR 8081 (IR4M) research unit.


This repository contains the following files and directories:

  • api/: documentation generated from the source-code by running make doc.

  • bin/: contains the model binary (simulate) and other utilities.

  • figures/ : scripts that produce the figures from the model paper.

  • lib/: contains the model simulation C library (libkidney.a).

  • models/: contains various whole-kidney models in serialised JSON form.

  • notes/: additional documentation and diagrams.

  • share/: support files used to generate source-code documentation.

  • share/c_example/: an example of using the model from a C program.

  • share/data/: published data against which to compare the model dynamics.

  • src/: the source-code for the model simulation.