Updates the README.

README.md

@@ -1,23 +1,35 @@
 # BUDE Alanine Scan
 
+This repository contains the code for the BAlaS web application. The application
+consists of three services: the front-end server, a service that runs the BudeAlaScan
+jobs and a database for the job queue and holding the results. Each of these services
+run inside of a Docker container.
+
+## References
+
+[Wood CW et al (2020) BAlaS: fast, interactive and accessible computational alanine-scanning using BudeAlaScan, Bioinformatics, btaa026.](https://doi.org/10.1093/bioinformatics/btaa026)
+
+[Ibarra AA et al (2019) Predicting and Experimentally Validating Hot-Spot Residues at Protein–Protein Interfaces, ACS Chem. Biol., 14, 2252-2263.](https://doi.org/10.1021/acschembio.9b00560)
+
 ## Building and Running
 
-A few steps are required to run the application:
-
-1. Add the ISAMBARD dependencies to the `dependencies_for_isambard/` folder.
-   SCWRL is the most vital of these.
-2. Add an `nginx.conf` file to `web/instance/`. Instance contains all the
-   potentially sensitive files (secret keys etc) in the application, which
-   **SHOULD NOT BE ADDED TO VERSION CONTROL!**
-3. `cd` to `web/elm-src/` and type `elm make Main.elm
-   --output=../static/elm/bals.js --debug`. Remove the debug flag if the app is
-   being used in production. _This step requires the Elm toolchain to be
-   installed._
-4. Run `docker-compose up --build`.
-
-Once these steps have been taken the application should be available on
-`0.0.0.0:3803`. If modifications are made to the Elm application recompile the
-Elm code and fully refresh your browser (`ctrl+shift+r` generally). If you make
-changes to the back-end code restart the Docker containers.
+To build and run the application (in development mode), you need to have
+[Docker](https://www.docker.com/) installed on your computer. Once Docker is installed,
+there are a few steps required to run the application:
+
+1. Clone the repository to your computer (or fork it and clone if you plan to make
+   alterations!)
+1. Download the Linux version of Scwrl 4 and add it to the `dependencies\_for\_isambard/`
+   folder.
+1. Download and install the Elm compiler: `npm install -g elm`
+1. `cd web/elm-src`
+1. `elm make Main.elm --debug --output=../static/elm/bals.js`
+1. Run `docker-compose up --build`.
+
+Once these steps have been taken the application should be available on `0.0.0.0:3803`.
+This docker-compose.yml creates a shared volume between your computer and the Docker
+container, which means that you can modify the web app, recompile the Elm code and fully
+refresh your browser (`ctrl+shift+r` generally) and the changes will be live. If you
+make changes to the back-end code restart the Docker containers.
 
 Good luck, have fun and feel free to report any issues on the GitHub page.