Introduction

This repository contains the source code for an implementation of the spatially distributed mathematical model of the rat renal juxtamedullary afferent arteriole described in the following article:

R. Feldberg, M. Colding-Jørgensen, N.-H. Holstein-Rathlou. Analysis of interaction between TGF and the myogenic response in renal blood flow autoregulation. Am J Physiol Renal Physiol 269(4): F581--F593, 2013. PubMed ID: 7485545

This model has also been extended with a permeable glomerulus that calculates the hydrostatic pressure profile along the glomerular capillary bed and the single-nephron glomerular filtration rate.

Licence

This work is made available under the BSD 3-Clause license (see LICENSE).

Requirements

Version numbers listed below are known-good. Newer versions should also be fine; older versions may or may not work.

• A Fortran compiler (gfortran 4.4.7).

• The R statistical computing environment (version 2.15).

• The ggplot2 plotting library for R (version 0.9.3).

Structure

• model_base.f90: an implementation of the original afferent model.

• model_glom.f90: the extended model with an explicit glomerulus.

• sngfr.f90: generate lookup tables for the afferent arteriole response that can be used to determine SNGFR with no computational cost.

• tests.f90: test cases that reproduce figures from the original paper.

• cmdline.f90: parses command-line arguments.

• main.f90: model entry point.

Usage

1. Compile the model by running make from the root directory.

2. Run the model by executing ./bin/run_model. This will print out command-line documentation.

3. Run test cases that reproduce several figures from the original paper with ./bin/run_model test. The test cases will produce data files (*.ssv) in the working directory.

4. Plot the results of the test cases by executing ./bin/plot.R.

5. Generate a lookup table for model SNGFR by executing ./bin/run_model sngfr --glom. This can take a long time to complete.