added section header; added pointer urls

Author: kimberlyh66

index.Rmd

@@ -8,6 +8,8 @@ output:
   bookdown::gitbook: default
 ---
 
+# Section 1: Traits {-}
+
 # Overview
 
 This book is intended to introduce users to TERRA REF data as quickly as possible. 
@@ -18,17 +20,26 @@ It introduces to the wide range of phenomics datasets generated by the TERRA Ref
 
 TODO: link to relevant parts of docs.terraref.org
 
+* Info on how to [request access to data](https://docs.terraref.org/user-manual/how-to-access-data/using-betydb-trait-data-experimental-metadata) 
+
 ## Ways of Acessing Data
 
 * Web Interfaces
+    + [Clowder](https://docs.terraref.org/user-manual/how-to-access-data/using-clowder-sensor-and-genoomics-data) (sensor and genomic data)
+    + [Globus](https://docs.terraref.org/user-manual/how-to-access-data/using-globus-sensor-and-genomics-data) (sensor and genomic data)
+    + [BETYdb](https://docs.terraref.org/user-manual/how-to-access-data/using-betydb-trait-data-experimental-metadata) (trait data and experimental metadata)
+    + [CoGe](https://docs.terraref.org/user-manual/how-to-access-data/using-coge-genomics) (genomic data)
 * Files
 * Programming APIs
+    + [BETYdb API](https://pecan.gitbook.io/betydb-data-access/api-for-url-based-queries)
 * API Clients
+    + [rOpenSci traits package](https://pecan.gitbook.io/betydb-data-access/ropensci-traits-package)
 
 ## Other Resources
 
-The TERRA REF website: terraref.org
-The TERRA REF Technical Documentation: docs.terraref.org
+The TERRA REF website: [terraref.org](http://terraref.org/)
+
+The TERRA REF Technical Documentation: [docs.terraref.org](docs.terraref.org)
 
 ## Contents
 
@@ -50,20 +61,20 @@ At a minimum, you should have:
 * An internet connection
 * Web Browser
 * A TERRA REF Beta User account
-  * If you have not done so, please sign up at terraref.org/beta
+    + If you have not done so, please sign up at [terraref.org/beta](terraref.org/beta)
 * Access to the data that you are using
-  * The tutorials will state which databases you will need access to
+    + The tutorials will state which databases you will need access to
 * Software:
-  * Software requirements vary with the tutorials, and may be complex
-  * 
+    + Software requirements vary with the tutorials, and may be complex
+
 
 ## Finding help
 
-* Slack
-* GitHub
-* Google
+- [Slack](terra-ref.slack.com)
+- [GitHub](https://github.com/terraref/tutorials)
+- [Google](https://www.google.com/)
 
-```{r}
+```{r, include = FALSE}
 knitr::opts_chunk$set(echo = FALSE, cache = TRUE)
 options(warn = -1)
 ```