inferred biomass biogeochemical model of Mystic Lake
Switch branches/tags
Nothing to show
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Failed to load latest commit information.


An inferred biomass biogeochemical model of Mystic Lake.


  • Matlab (developed with version 8)
  • Python (developed with version 2.7)


$ git clone

File structure

  • analysis: Tools for analyzing divergences between rates at each depth, diversity of rates, and the profiles for rates and concs.
  • bin: Main matlab scripts
  • calibration: Tools for calibrating the model parameters using the measured rates and/or OTU data.
  • interactive: A script for running the model with easily-adjustable parameters and displaying the output.
  • sensitivity_analysis: Tools for analyzing the sensitivity of the rate profiles to the values for each of the input parameters.
  • lake.cfg: Configuration for different tools, with lists of the names for processes and some default values from which to generate scripts for the various tools.
  • Convenience tool for setting the matlab path when running scripts from the terminal.



To run the model interactively,

  • Update lake.cfg with the desired parameters.
  • Under interactive, use to create run_interactive_defaults.m, which supplies the values in lake.cfg to interactive.m.
  • In Matlab, run run_interactive.m. This requires the bin/ folder to be on Matlab's path. If running in the terminal, you can use the script to do this.
  • The output of the simulation is stored in concs_history and rates_history variables. You can write them to files using bin/write_data_to_files.m.


To make a plot of the Jensen-Shannon divergences between the composition of rates at each depth, run the analysis/divergenes/

To compare the simulated Shannon diversity of composition of rates with some observed diversity of rates, run analysis/diversity/get_diversity_depth.m.

To make timecourses and end-time plots for all the rates and chemical concentrations, run analysis/profiles/