updated readme

Author: swo

README.md

@@ -1,23 +1,42 @@
-# Structure
-- analysis: Tools for analyzing divergences between rates at each depth, diversity of rates,
-  and the profiles for rates and concs.
+# Mystic
+
+An inferred biomass biogeochemical model of Mystic Lake. 
+
+- by: Scott W Olesen ([email protected])
+- development page: http://github.com/swo/mystic
+- main page: http://almlab.mit.edu/mystic.html
+
+## Dependencies
+
+- Matlab (developed with version 8)
+- Python (developed with version 2.7)
+
+## Installation
+    $ git clone http://github.com/swo/mystic.git
+
+## 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.
-- doc: Documentation of the model.
-- 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.
-- set\_matlab\_path.sh: Convenience tool for setting the matlab path when running scripts
-  from the terminal.
-
-# Usage
-
-You should be able to run the sensitivity analysis in parallel. For running on 20 nodes on coyote,
-
-```
-cat submit_0.sh | ssub -n 20
-```
+- 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.
+- set\_matlab\_path.sh: Convenience tool for setting the matlab path when running scripts from the terminal.
+
+## Usage
+
+### Interactive
+To run the model interactively,
+- Update `lake.cfg` with the desired parameters.
+- Under interactive, use `write_default_values_script.py` 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 `set_matlab_path.py` 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`.
+
+### Analysis
+To make a plot of the Jensen-Shannon divergences between the composition of rates at each depth, run the `analysis/divergenes/pipeline.sh`.
+
+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/pipeline.sh`.
+
+