Readme update (#240)

* updating quickstart instructions for readme

* adding mention of ode_model.md

README.md

@@ -31,13 +31,15 @@ Subject to change, current transmission dynamics follow this basic model
 
 ## Quick Start
 
-As a first pass at running model ODEs and inference of parameters, take a look at `example_end_to_end_run.py` to see the process of running our model. You will probably need to `pip install -r requirements.txt` to get started as well.
+As a first pass at running model ODEs and inference of parameters, take a look at `example_end_to_end_run.py` to see the process of running our model. You will probably need to `poetry install` to get started as well.
 
-Within `example_end_to_end_run.py` there is an optional `-infer` flag added from the terminal. This will kick off an example inference on synthetic data generated by the model itself and will produce different output.
+Within `example_end_to_end_run.py` there is an optional `--infer` flag added from the terminal. This will kick off an example inference on synthetic data generated by the model itself and will produce different output.
 
 To try out your own basic scenarios, check out the `config/` folder, where you can modify parameters within the four base `json` files as you see fit and see their impacts on the model back at `example_end_to_end_run.py`.
 
-If you are interested in understanding how the model is initialized, rather than looking through the model matricies yourself, the Scenarios team has created a Shiny application allowing for easy data visualization of the model's initial state! Simply run `visualizer_app.py` and navigate to http://localhost:8000/ and play with the data yourself.
+If you are interested in understanding how the model is initialized, rather than looking through the model matricies yourself, the Scenarios team has created a Shiny application allowing for easy data visualization of the model's initial state! Simply run `shiny_visualizers/visualizer_app.py` and navigate to http://localhost:8000/ and play with the data yourself.
+
+For a breakdown of the Ordinary Differential Equations at the heart of this model take a look at `ode_model.md`.
 
 ## Technical Details