add an overview of the repo

Author: alistairewj

README.md

@@ -1,14 +1,28 @@
-# MIMIC Code Repository [![Build Status](https://travis-ci.org/MIT-LCP/mimic-code.svg?branch=master)](https://travis-ci.org/MIT-LCP/mimic-code) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.821872.svg)](https://doi.org/10.5281/zenodo.821872)[![Join the chat at https://gitter.im/MIT-LCP/mimic-code](https://badges.gitter.im/MIT-LCP/mimic-code.svg)](https://gitter.im/MIT-LCP/mimic-code?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
+# MIMIC Code Repository [![Build Status](https://travis-ci.org/MIT-LCP/mimic-code.svg?branch=master)](https://travis-ci.org/MIT-LCP/mimic-code) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.821872.svg)](https://doi.org/10.5281/zenodo.821872) [![Join the chat at https://gitter.im/MIT-LCP/mimic-code](https://badges.gitter.im/MIT-LCP/mimic-code.svg)](https://gitter.im/MIT-LCP/mimic-code?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
 
 This is a repository of code shared by the research community. The repository is intended to be a central hub for sharing, refining, and reusing code used for analysis of the [MIMIC critical care database](https://mimic.physionet.org). To find out more about MIMIC, please see: https://mimic.physionet.org
 
 You can read more about the code repository in the following open access paper: [The MIMIC Code Repository: enabling reproducibility in critical care research](https://doi.org/10.1093/jamia/ocx084).
 
+## Brief introduction
+
+The repository is organized as follows:
+
+* [benchmark](/benchmark) - Various speed tests for indices
+* [buildmimic](/buildmimic) - Scripts to build MIMIC-III in a relational database management system (RDMS), in particular [postgres](/buildmimic/postgres) is our RDMS of choice
+* [concepts](/concepts) - Useful views/summaries of the data in MIMIC-III, e.g. demographics, organ failure scores, severity of illness scores, durations of treatment, easier to analyze views, etc. The paper above describes these in detail.
+* [notebooks](/notebooks) - A collection of R markdown and Jupyter notebooks which give examples of how to extract and analyze data
+* [notebooks/aline](/notebooks/aline) - An entire study reproduced in the MIMIC-III database - from cohort generation to hypothesis testing
+* [tests](/tests) - You should always have tests!
+* [tutorials](/tutorials) - Similar to the notebooks folder, but focuses on explaining concepts to new users
+
+## Acknowledgement
+
 If you use code or concepts available in this repository, we would be grateful if you would cite the above paper as follows:
 
 > Johnson, Alistair EW, David J. Stone, Leo A. Celi, and Tom J. Pollard. "The MIMIC Code Repository: enabling reproducibility in critical care research." Journal of the American Medical Informatics Association (2017): ocx084.
 
-You can also directly cite the repository using the above DOI from Zenodo.
+If including a hyperlink to the code, we recommend you use the DOI from Zenodo rather than a GitHub URL: https://doi.org/10.5281/zenodo.821872
 
 ## How to contribute