Update EmrE main analysis README

kda_paper/fig_13-15__8_state_emre_model/main_analysis/README.md

@@ -4,7 +4,8 @@ Code to analyze the EmrE [free-exchange transport model](https://doi.org/10.1085
 
 **Warning:** KDA is in flux and not API stable. The latest known working KDA commit hash: `b63d5f2`
 
-## Usage
+
+## Generating Figures
 
 The modules here provide the ability to generate many different figures based on the 8-state model of EmrE. To generate _all_ figures, run the following:
 
@@ -16,7 +17,9 @@ $ python plot_emre_8_state.py
 $ python generate_figures.py
 ```
 
-All generated figures can be found in either `plots/figures` or `plots/flux_graphs`. The raw data for each figure (7A, 7B, etc.) can be found in `data`. Here is a list of the key figures from the paper:
+All generated figures can be found in either `plots/figures` or `plots/flux_graphs`. The raw data for each figure (7A, 7B, etc.) can be found in `data`. 
+
+Here is a list of the key figures from the paper:
 
 - `emre_8_state_model.png`: kinetic diagram for the 8-state model of EmrE
 - `all_cycles.*`: All valid cycles for the 8-state model of EmrE (Figure 13)
@@ -25,4 +28,4 @@ All generated figures can be found in either `plots/figures` or `plots/flux_grap
 - `fig_7A_flux_diagram_RAA_1E-08.*`, `fig_7A_flux_diagram_RAA_1E+00.*`, `fig_7A_flux_diagram_RAA_1E+08.*`: kinetic diagrams with transition-flux-weighted edges for alternating access rate biasing (Figures 14b-14d). The legends for each are included separately (i.e. `fig_7A_flux_diagram_RAA_1E+00_legend.*`).
 - `fig_7B_flux_diagram_kAA_1E+02_Roff_1E-10.*`, `fig_7B_flux_diagram_kAA_1E+02_Roff_1E+00.*`, `fig_7B_flux_diagram_kAA_1E+02_Roff_1E+02.*`: kinetic diagrams with transition-flux-weighted edges for substrate off-rate biasing (Figures 15b-15d). The legends for each are included separately.
 
-NOTE: `generate_figures.py` uses previously generated data (`main_analysis/data/all_figure_data.csv`) and sympy expressions (located in `main_analysis/fig_functions`) to speed up code execution. `all_figure_data.csv` can be re-generated using `generate_fig_data.py`. To generate new sympy expressions at run time, simply delete all files in the `main_analysis/fig_functions` directory and re-run `generate_figures.py`. 
+**NOTE:** `generate_figures.py` uses previously generated data (`main_analysis/data/all_figure_data.csv`) and sympy expressions (located in `main_analysis/fig_functions`) to speed up code execution. `all_figure_data.csv` can be re-generated using `generate_fig_data.py`. To generate new sympy expressions at run time, simply delete all files in the `main_analysis/fig_functions` directory and re-run `generate_figures.py`.