terraref · dlebauer · Jan 22, 2018 · Sep 18, 2017 · Sep 18, 2017 · Sep 18, 2017
diff --git a/README.md b/README.md
@@ -2,11 +2,11 @@
 
 ## About this book
 
-This book describes the TERRA-REF data collection, computing, and analysis pipelines.
+This book describes the TERRA-REF data collection, computing, and analysis pipelines. The following links provide quick access to 
 
-* [What data is available?](/user/what-data-is-available.md)
-* [Where do I get the data?](/user/how-to-access-data.md)
-* [User tutorials](/tutorials.md)
+* [Available Data](/user/what-data-is-available.md)
+* [How to access data](/user/how-to-access-data.md)
+* [Hands on tutorials](/tutorials.md)
 
 ## About TERRA-REF
 
@@ -19,3 +19,4 @@ Our objectives are to ensure that the software and data in the reference data an
 ## Versions
 
 The first edition will be published in **November 2016**.
+
diff --git a/SUMMARY.md b/SUMMARY.md
@@ -32,13 +32,13 @@
     * [Phenotype data](products/trait-data.md)
     * [Point Cloud Data](products/point-cloud-data.md)
   * [How to Access Data](user/how-to-access-data.md)
-    * [Using Clowder (Sensor and Genoomics data)](user/using-clowder.md)
-    * [Using Globus (Sensor and Genomics data)](user/using-globus.md)
-    * [Using BETYdb (trait data, experimental metadata)](user/using-betydb.md)
-       * [Accessing BETYdb via ArcMap and other GIS software](accessing-betydb-with-arcmap.md) 
-    * [Using CoGe (Genomics)](user/using-coge.md)
-    * [Using CyVerse (Genomics)](user/using-cyverse.md)
-    * [Using Analysis Workbench (all data)](user/using-analysis-workbench.md)
+    * [Using Clowder \(Sensor and Genoomics data\)](user/using-clowder.md)
+    * [Using Globus \(Sensor and Genomics data\)](user/using-globus.md)
+    * [Using BETYdb \(trait data, experimental metadata\)](user/using-betydb.md)
+      * [Accessing BETYdb via ArcMap and other GIS software](accessing-betydb-with-arcmap.md)
+    * [Using CoGe \(Genomics\)](user/using-coge.md)
+    * [Using CyVerse \(Genomics\)](user/using-cyverse.md)
+    * [Using Analysis Workbench \(all data\)](user/using-analysis-workbench.md)
   * [Data Use Policy](user/data_release_policy.md)
   * [Manuscripts and Authorship Guidelines](manuscripts-and-authorship.md)
   * [Release / reprocessing schedule](user/release_schedule.md)
@@ -53,7 +53,7 @@
   * [Data Storage](data-storage.md)
   * [Data Transfer](data-transfer.md)
   * [Data Processing Pipeline](data-processing-pipeline.md)
-      * [Geospatial Time Series Structure](geostreams-structure.md)
+    * [Geospatial Time Series Structure](geostreams-structure.md)
   * [Data Backup](data-backup.md)
   * [Data Collection](data-collection.md)
   * [Data Product Creation](data-product-creation.md)

diff --git a/accessing-betydb-with-arcmap.md b/accessing-betydb-with-arcmap.md
@@ -1,12 +1,12 @@
-# Accessing BETYdb from GIS Software 
+# Accessing BETYdb from GIS Software
 
-Interested researchers can access BETYdb directly from GIS software such as ESRI ArcMap and QGIS. 
+Interested researchers can access BETYdb directly from GIS software such as ESRI ArcMap and QGIS.   
 In some cases direct access can simplify the use of spatial data in BETYdb data, but this convenience must be weighed against a more complex setup, limits of GIS software compatibility, and additional complexity of extracting data from a PostGIS SQL database.
 
 ## Overview
 
-Accessing the production BETYdb used by the TERRA REF program requires creating a secure shell tunnel (SSH) to a remote server. 
-After creating the tunnel, the database is accessed as if it were available on the local machine. 
+Accessing the production BETYdb used by the TERRA REF program requires creating a secure shell tunnel \(SSH\) to a remote server.   
+After creating the tunnel, the database is accessed as if it were available on the local machine.   
 A step-by-step process is given below.
 
 ## Configuration used for these instructions
@@ -18,13 +18,13 @@ A step-by-step process is given below.
 
 ## Setup
 
-### Request Access 
+### Request Access
 
-Request access [to the BETYdb server](https://identity.ncsa.illinois.edu/join/TU49BUUEDM) by following the link. 
-This will take you to the NCSA identity service. If you do not have an NCSA account, you will be asked to create one.
+Request access [to the BETYdb server](https://identity.ncsa.illinois.edu/join/TU49BUUEDM) by following the link.   
+This will take you to the NCSA identity service. If you do not have an NCSA account, you will be asked to create one.  
   This account and password will be used to login to the database server. Access will generally be granted within 24-hours.
 
-### Confirm Access 
+### Confirm Access
 
 Use PuTTY or your preferred SSH client and your NCSA account. First open the terminal and then login to bety6.ncsa.illinois.edu using ssh from the command line:
 
@@ -34,28 +34,28 @@ ssh <login>@bety6.ncsa.illinois.edu
 
 After confirming access to bety6 logout by typing `exit`.
 
-### Create SSH Tunnel to BETYdb 
+### Create SSH Tunnel to BETYdb
 
-The following command will create an `SSH tunnel` from your computer to the BETYdb server: 
+The following command will create an `SSH tunnel` from your computer to the BETYdb server:
 
-_Note_ if have a postgres running on your desktop computer (using the default port 5432), you will need to stop it first.
+_Note_ if have a postgres running on your desktop computer \(using the default port 5432\), you will need to stop it first.
 
 ```sh
 ssh -L 5432:localhost:5432 <login>@bety6.ncsa.illinois.edu
 ```
 
-The above will bind the local port 5432 (first parameter) to port 5432 (second parameter), the default Postgres listening port, on the remote server. All traffic bound for port 5432 on your local machine will be automatically forwarded to the remote server. As a result, programs such as ArcGIS running on your computer will connect to the remote BETYdb as if it were on your computer.
+The above will bind the local port 5432 \(first parameter\) to port 5432 \(second parameter\), the default Postgres listening port, on the remote server. All traffic bound for port 5432 on your local machine will be automatically forwarded to the remote server. As a result, programs such as ArcGIS running on your computer will connect to the remote BETYdb as if it were on your computer.
 
-_Note_ **you will need to create the SSH connection with the tunnel every time you wish to
+_Note_ **you will need to create the SSH connection with the tunnel every time you wish to  
 access BETYdb from your local machine.**
 
-To keep the tunnel open, use 
+To keep the tunnel open, use
 
 ```sh
 ssh -Nf -L 5432:localhost:5432 <login>@bety6.ncsa.illinois.edu
 ```
 
-> _note for PuTTY  Users:_  you can configure Putty to remember these settings. In the navigation tree on the left-hand side, click Connection > SSH > Tunnels. Enter '5432' under Source port and 'localhost:5432' in the Destination field. Then click  session and save this configuration for future use.
+> _note for PuTTY  Users:_  you can configure Putty to remember these settings. In the navigation tree on the left-hand side, click Connection &gt; SSH &gt; Tunnels. Enter '5432' under Source port and 'localhost:5432' in the Destination field. Then click  session and save this configuration for future use.
 
 The next section of the guide will discuss accessing BETYdb using ArcMap, querying plots and joining these to the traits and experiments tables. The instructions for setting up a SSH tunnel will also work psql, pgAdmin3, QGIS, and other clients. Instructions for connecting via QGIS and ArcGIS Pro are provided below.
 
@@ -65,45 +65,45 @@ The next section of the guide will discuss accessing BETYdb using ArcMap, queryi
 
 BETYdb is configured with PostGIS geometry support. This allows ArcGIS Desktop clients to access geometry layers stored within BETYdb.
 
-> _Warning:_ ArcGIS releases prior to 10.3 required you to place the
-PostgreSQL libpq files in the ArcGIS client's bin directory. This is no
-longer required for the ArcGIS Desktop clients but some ESRI tools may
-still require the library be installed.*
+> _Warning:_ ArcGIS releases prior to 10.3 required you to place the  
+> PostgreSQL libpq files in the ArcGIS client's bin directory. This is no  
+> longer required for the ArcGIS Desktop clients but some ESRI tools may  
+> still require the library be installed.\*
 
-1. Click on the ArcCatalog icon (on right edge of ArcMap window) to open the ArcCatalog Tree
+1. Click on the ArcCatalog icon \(on right edge of ArcMap window\) to open the ArcCatalog Tree
 2. In the tree, click on 'Database Connections' and then "Add Database Connnections". A Database Connection dialog window will open.
 3. Within the dialog box:
-```
-Database Platform: PostgreSQL
-Instance: localhost
-Authentication Type: Database authentication
-User name: viewer
-Password: DelchevskoOro 
-Database: select bety (if everything else is correct)
-```
+   ```
+   Database Platform: PostgreSQL
+   Instance: localhost
+   Authentication Type: Database authentication
+   User name: viewer
+   Password: DelchevskoOro 
+   Database: select bety (if everything else is correct)
+   ```
 4. Click OK
-4. The connection will be saved as "Connection to localhost.sde", right
-click and rename to it to "TERRA REF BETYdb trait database" to allow easy reuse.
-5. Click on the Add Layer icon (black cross over yellow diamand) button to open the Add Data dialog window.
-6. Under 'Look in' on the second line choose 'Database Connections'. 
-7. Select the "TERRA REF BETYdb trait database" that created above
-8. Select the bety.public.sites table and click 'Add'. 
-   - This 'sites' table is the only table in the database with a geospatial 'geometry' data type.
-   - Any of the other tables can also be added, as described below.
-6. The New Query Layer dialog will be displayed asking for the Unique Identifier Field for the layer. For the bety.public.sites table, the unique identifier is the "sitename" field. 
-7. Click Finish.
-
-> _Warning_: ArcMap does not support the big integer format used by BETYdb
-as primary keys and those fields will not be visible or available for
-selection. In most cases you should be able to use other fields as
-unique identifiers.*
+5. The connection will be saved as "Connection to localhost.sde", right
+   click and rename to it to "TERRA REF BETYdb trait database" to allow easy reuse.
+6. Click on the Add Layer icon \(black cross over yellow diamand\) button to open the Add Data dialog window.
+7. Under 'Look in' on the second line choose 'Database Connections'. 
+8. Select the "TERRA REF BETYdb trait database" that created above
+9. Select the bety.public.sites table and click 'Add'. 
+   * This 'sites' table is the only table in the database with a geospatial 'geometry' data type.
+   * Any of the other tables can also be added, as described below.
+10. The New Query Layer dialog will be displayed asking for the Unique Identifier Field for the layer. For the bety.public.sites table, the unique identifier is the "sitename" field. 
+11. Click Finish.
+
+> _Warning_: ArcMap does not support the big integer format used by BETYdb  
+> as primary keys and those fields will not be visible or available for  
+> selection. In most cases you should be able to use other fields as  
+> unique identifiers.\*
 
 ### Modifying the Query Layer
 
-BETYdb contains one geometry table called betydb.public.sites containing
-the boundaries for each plot. Because the plot boundaries can change each season, and even within season, different 
-plot definitions may be used (e.g. to subset plots or exclude boundary rows), there is significant overlap that can cause confusion
-when displayed. 
+BETYdb contains one geometry table called betydb.public.sites containing  
+the boundaries for each plot. Because the plot boundaries can change each season, and even within season, different   
+plot definitions may be used \(e.g. to subset plots or exclude boundary rows\), there is significant overlap that can cause confusion  
+when displayed.   
 In general, you will want to use the query layer to limit plots to a single season and a single definition.
 
 1. Right click the bety.public.sites layer and choose properties. 
@@ -115,39 +115,39 @@ For more advanced selection of sites by experiment or season, you can join the `
 
 ### Joining Additional BETYdb Tables
 
-Additional tables can be added and joined to the sites table. Tables can
-be added just like any other layer. In this case, we'll add
-bety.public.traits_and_yields_view and join it to the bety.public.sites
+Additional tables can be added and joined to the sites table. Tables can  
+be added just like any other layer. In this case, we'll add  
+bety.public.traits\_and\_yields\_view and join it to the bety.public.sites  
 layer.
 
 1. To create a join with other tables, start by adding the desired table. 
-2. Follow instructions above to add the bety.public.traits_and_yields_view 
+2. Follow instructions above to add the bety.public.traits\_and\_yields\_view 
 3. On this table the unique identifier is a group of columns, so select sitename, cultivar, scientificname, trait, date, entity, and method as the unique identifiers. 
-2. Right click on the bety.public.sites layer.
-3. Under 'Joins and Relates' select 'Join'.
-3. Choose sitename (from bety.public.sites) in part 1
-4. Choose bety.public.traits_and_yields_view in part 2
-5. Choose sitename in part 3
-6. Click OK
+4. Right click on the bety.public.sites layer.
+5. Under 'Joins and Relates' select 'Join'.
+6. Choose sitename \(from bety.public.sites\) in part 1
+7. Choose bety.public.traits\_and\_yields\_view in part 2
+8. Choose sitename in part 3
+9. Click OK
 
 ### Creating a Thematic View
 
-The final section describes how to create a thematic view of the
-bety.public.sites layer based on the mean attribute where the trait is
-NDVI from the bety.public.traits_and_yields_view. Remove any previous
-joins from bety.public.sites (right click bety.public.sites --> joins and relates --> remove join) prior to performing this procedure because we will be selecting the NDVI data by creating a query layer 
-from bety.public.traits_and_yields_view prior to the join.
+The final section describes how to create a thematic view of the  
+bety.public.sites layer based on the mean attribute where the trait is  
+NDVI from the bety.public.traits\_and\_yields\_view. Remove any previous  
+joins from bety.public.sites \(right click bety.public.sites --&gt; joins and relates --&gt; remove join\) prior to performing this procedure because we will be selecting the NDVI data by creating a query layer   
+from bety.public.traits\_and\_yields\_view prior to the join.
 
-1. Right click bety.public_traits_and_yields_view table and select properties
+1. Right click bety.public\_traits\_and\_yields\_view table and select properties
 2. Click on the Definition Query tab
 3. Add the line "trait = 'NDVI'" to the Definition Query box
 4. Click OK
 5. Follow the steps defined in Joining Additional BETYdb Tables
 6. Right click on the bety.sites layer and choose properties
 7. Choose the Symbology tab
-8. Under the Show section, choose Quantities --> Graduated Colors
+8. Under the Show section, choose Quantities --&gt; Graduated Colors
 9. Under the Fields Value selection choose mean
-10.  Click OK
+10. Click OK
 
 ## Connecting to Other GIS Software
 
@@ -160,11 +160,11 @@ This assumes you have followed instructions for ArcMAP to create a database conn
 * Open ArcCatalog
   * Under database connections, you will find the connection made above, called 'TERRA REF BETYdb.sde'
   * right click this and select 'properties'
-  * copy the file path (it should look like `C:\Users\<USER NAME>\AppData\Roaming\ESRI\Desktop10.4\ArcCatalog\TERRA REF BETYdb.sde`
+  * copy the file path \(it should look like `C:\Users\<USER NAME>\AppData\Roaming\ESRI\Desktop10.4\ArcCatalog\TERRA REF BETYdb.sde`
 * Open ArcGIS Pro
-   * Under the Insert tab, select connections --> 'add database'
-   * paste the path to 'TERRA REF BETYdb.sde' in the directory navigation bar
-   * select 'TERRA REF BETYdb.sde'
+  * Under the Insert tab, select connections --&gt; 'add database'
+  * paste the path to 'TERRA REF BETYdb.sde' in the directory navigation bar
+  * select 'TERRA REF BETYdb.sde'
 
 ### QGIS
 
@@ -192,3 +192,4 @@ After you have connected via ssh to the PostGIS server, the `pgsql2shp` function
 pgsql2shp -f terra_plots.shp -h localhost -u bety -P bety bety \ 
          "SELECT sitename, geometry FROM sites"
 ```
+
diff --git a/data-sources.md b/data-sources.md
@@ -1,25 +1,27 @@
-#Data Sources
+# Field Sites and Platforms
 
-## Field phenotyping
-####Maricopa Agricultural Center (MAC), Arizona
+## Field phenotyping research sites
 
-Over 300 sorghum accessions and recombinant inbred lines were planted at the University of Arizona Maricopa Agricultural Center and USDA Arid Land Research Station in Maricopa, Arizona. Field Scanner
+### Maricopa Agricultural Center (MAC), Arizona
+
+The Maricopa field site is located at the the University of Arizona Maricopa Agricultural Center and USDA Arid Land Research Station in Maricopa, Arizona. At this site, we have deployed the following phenotyping platforms.
 
 - The [**Lemnatec Scanalyzer Field System**](http://www.lemnatec.com/products/hardware-solutions/scanalyzer-field/) is the largest field crop analytics robot in the world. This high-throughput phenotyping field-scanning robot has a 30-ton steel gantry that autonomously moves along two 200-meter steel rails while continuously imaging the crops growing below it with a diverse array of [cameras and sensors](http://terraref.org/articles/lemnatec-scanalyzer-field-sensors/).
 - The **PhenoTractor** is fitted with a sensor frame that supports a real time kinematic (RTK) satellite navigation antenna, a sonar transducer,  an infrared temperature (IRT) scanner, and three [GreenSeeker crop sensing systems](http://www.trimble.com/agriculture/greenseeker.aspx).
 - **UAV** (release V1)
-- **Manually Collected Field Data** - Data will be collected manually to verify the sensor-collected data.
+- **Manually Collected Field Data** - Data will are collected manually using standard field methods. These measurements are used to calibrate and validate phenotypes derived from sensor-collected data.
 
 
 ### Kansas State University
 
+
 - Tractor - coming 2017
 
 - UAV - coming 2017
 
 ------------------
 ## Controlled-environment phenotyping
-####Donald Danforth Plant Science Center, Missouri
+#### Donald Danforth Plant Science Center, Missouri
 
 The [Bellwether Foundation Phenotyping Facility](https://www.danforthcenter.org/scientists-research/core-technologies/phenotyping) is a climate controlled 70 m<sup>2</sup> growth house with a conveyor belt system for moving plants to and from fluorescence, color, and near infrared imaging cabinets. This automated, high-throughput platform allows repeated non-destructive time-series image capture and multi-parametric analysis of 1,140 plants in a single experiment.
 

diff --git a/field-sites-and-platforms.md b/field-sites-and-platforms.md