GitBook: [master] 20 pages and 5 assets modified

Author: dlebauer

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@@ -1,17 +1,13 @@
 # Introduction
 
-The [ARPA-E](https://arpa-e.energy.gov/)-funded [Transportation Energy Resources from Renewable Agriculture Phenotyping Reference Platform](http://terraref.org/) \(TERRA-REF\) program aims to transform plant breeding by using remote sensing to quantify plant traits such as plant architecture, carbon uptake, tissue chemistry, water use, and other features to predict the yield potential and stress resistance of 300+ diverse Sorghum lines.
 
-The data storage and computing system provides researchers with access to the reference phenotyping data and analytics resources using a high performance computing environment. The reference phenotyping data includes direct measurements and sensor observations, derived plant phenotypes, and genetic and genomic data.
-
-Our objectives are to ensure that the software and data in the reference data and computing pipeline are interoperable, reusable, extensible, and understandable. Providing clear definitions of common formats will make it easier to analyze and exchange data and results.
 
 ## About this book
 
 This book describes the TERRA-REF data collection, computing, and analysis pipelines. The following links provide quick access to:
 
-* [Available Data](what-data-is-available.md)
-* [How to access data](how-to-access-data.md)
+* [Available Data](user-manual/data-products/)
+* [How to access data](user-manual/how-to-access-data.md)
 * [Hands on tutorials](https://terraref.org/tutorials) \(external\)
 
 ## About TERRA-REF
@@ -31,6 +27,6 @@ This documentation is intended to enable a wide variety of user-groups to use an
 
 
 * **Plant Physiologists** interested in finding and contributing _**phenotyping protocols**_. Relevant sections include the[ scientific objectives](scientific-objectives-and-experimental-design.md) and [protocols](protocols/).
-* **Computer/Data Scientists** looking for **computer vision** and **machine learning** problems. See a complete list of [data products](/user-manual/data-products/README.md) and [how to access data](how-to-access-data.md).
+* **Computer/Data Scientists** looking for **computer vision** and **machine learning** problems. See a complete list of [data products](/user-manual/data-products/README.md) and [how to access data](user-manual/how-to-access-data.md).
 * **Engineers, Developers and Institutional IT** looking for an example of IT **infrastructure** required to turn big data into scientific understanding. See an overview of the [software](/software.md) used, the [developer manual](/developer-manual/README.md) and [technical documentation](/technical-documentation/README.md)
 

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@@ -15,7 +15,7 @@
   * [Phenotractor Protocols](protocols/phenotractor-protocols.md)
   * [UAV Protocols](protocols/uav-protocols.md)
   * [Genomic Data](protocols/genomic-data.md)
-* [User Manual](user-manual/README.md)
+* [Data Use](user-manual/README.md)
   * [Data Products](user-manual/data-products/README.md)
     * [Environmental conditions](user-manual/data-products/environmental-conditions.md)
     * [Fluorescence intensity imaging](user-manual/data-products/fluorescence-intensity-imaging.md)
@@ -27,14 +27,12 @@
     * [Meteorological data](user-manual/data-products/meteorological-data.md)
     * [Controlled Environment phenotype data](user-manual/data-products/plantcv-trait-data.md)
     * [Point Cloud Data](user-manual/data-products/point-cloud-data.md)
+  * [How to Access Data](user-manual/how-to-access-data.md)
   * [Data Use Policy](user-manual/data-use-policy.md)
   * [Manuscripts and Authorship Guidelines](user-manual/manuscripts-and-authorship-guidelines.md)
   * [Release / reprocessing schedule](user-manual/release-reprocessing-schedule.md)
-* [Software](software.md)
-* [Data](data.md)
-* [What Data is Available](what-data-is-available.md)
-* [How to Access Data](how-to-access-data.md)
 * [Technical Documentation](technical-documentation/README.md)
+  * [Software](technical-documentation/software.md)
   * [Data Standards](technical-documentation/data-standards/README.md)
     * [Existing Data Standards](technical-documentation/data-standards/existing-data-standards.md)
     * [Agronomic and Phenotype Data Standards](technical-documentation/data-standards/agronomic-and-phenotype-data-standards.md)

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@@ -1,10 +1,10 @@
 # Controlled Environment Phenotyping
 
-#### Donald Danforth Plant Science Center, Missouri
+## Donald Danforth Plant Science Center, Missouri
 
 The Automated controlled-environment phenotyping at the Donald Danforth Plant Science Center Bellwether Foundation Phenotyping Facility
 
-The [Bellwether Foundation Phenotyping Facility](https://www.danforthcenter.org/scientists-research/core-technologies/phenotyping) is a climate controlled 70 m2 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.
+The [Bellwether Foundation Phenotyping Facility](https://www.danforthcenter.org/scientists-research/core-technologies/phenotyping) is a climate controlled 70 m2 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. You can read more about the Danforth Plant Sciences Center Bellwether Foundation Phenotyping Facility on the [DDPSC website](https://www.danforthcenter.org/scientists-research/core-technologies/phenotyping).
 
 The Scanalyzer 3D platform at the [Bellwether Foundation Phenotyping Facility at the Donald Danforth Plant Science Center ](https://www.danforthcenter.org/scientists-research/core-technologies/phenotyping)consists of multiple digital imaging chambers connected to the Conviron growth house by a conveyor belt system, resulting in a continuous imaging loop. Plants are imaged from the top and/or multiple sides, followed by digital construction of images for analysis.
 
@@ -14,7 +14,7 @@ The Scanalyzer 3D platform at the [Bellwether Foundation Phenotyping Facility at
 
 The LemnaTec software suite is used to program and control the Scanalyzer platform, analyze the digital images and mine resulting data. Data and images are saved and stored on a secure server for further review or reanalysis.
 
-You can read more about the Danforth Plant Sciences Center Bellwether Foundation Phenotyping Facility on the [DDPSC website](https://www.danforthcenter.org/scientists-research/core-technologies/phenotyping).
+
 
 ## Experiments LT1A \(TM015\) and LT1B \(TM016\)
 

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@@ -1,6 +1,6 @@
 # Genomics
 
-Genomic data includes whole-genome resequencing data from the [HudsonAlpha Institute for Biotechnology](https://hudsonalpha.org/), Alabama for 384 samples for accessions from the sorghum Bioenergy Association Panel \(BAP\) and genotyping-by-sequencing \(GBS\) data from Kansas State University for 768 samples from a population of sorghum recombinant inbred lines \(RIL\).
+[Whole genome resequencing](experimental-design-genomics.md) is being carried out on ~400 sorghum accessions to understand the landscape of genetic variation in the selected germplasm and enable high-resolution mapping of bioenergy traits with genome wide association studies \(GWAS\). Additionally, ~200 sorghum recombinant inbred lines \(RILs\) will be characterized with ~400,000 genetic markers using genotyping-by-sequencing \([Morris et al., 2013](http://www.g3journal.org/content/early/2013/09/13/g3.113.008417)\) for trait dissection in the RIL population and testcross hybrids of the RIL population.
 
 ## Whole-genome resequencing
 

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@@ -1,27 +1,14 @@
----
-description: >-
-  The Maricopa field site is located at the the University of Arizona Maricopa
-  Agricultural Center and USDA Arid Land Research Station in Maricopa, Arizona.
----
-
 # The Maricopa Agricultural Center \(MAC\)
 
-## Published Experiments
-
-### Season 4
-
-### Season 6
+The Maricopa field site is located at the the [University of Arizona Maricopa Agricultural Center](http://cals-mac.arizona.edu/) and [USDA Arid Land Research Station in Maricopa](https://www.ars.usda.gov/pacific-west-area/maricopa-arizona/us-arid-land-agricultural-research-center/), Arizona.
 
-## Unpublished Experiments
-
-## Season 1 sorghum \(April - July 2016, unpublished\)
+## Season 1 sorghum \(April - July 2016\)
 
 [Three hundred thirty one lines were planted in Season 1](https://docs.google.com/spreadsheets/d/1QQaWc0UaQQKfEtnSO1G2za8tKU2huC0_VYMBqm5CKAo/edit#gid=796817704).
 
 #### Planting maps
 
 * [Under the scanner system](https://docs.google.com/spreadsheets/d/1QQaWc0UaQQKfEtnSO1G2za8tKU2huC0_VYMBqm5CKAo/edit#gid=1066629008)
-* [West the scanner system](https://docs.google.com/spreadsheets/d/1QQaWc0UaQQKfEtnSO1G2za8tKU2huC0_VYMBqm5CKAo/edit#gid=193038411)
 
 #### Planting Design
 
@@ -37,22 +24,7 @@ description: >-
 | RILs | 3 | 130 RILs plus 10 repeats of a single line/rep | Incomplete Block \(row-column alpha lattice design\) |
 | Uniformity | 17 | 2 lines \(forage, PS\) | None - Same line planted in single range |
 
-**West of scanner system**
-
-| **Experiment** | **Reps** | **Treatments** | **Experimental design** |
-| :--- | :--- | :--- | :--- |
-| BAP | 1 | 30 lines \(12 PS, 12 sweet, 6 grain\) | None - single rep planted for observation |
-| RILs | 3 | 60 RILs | Incomplete Block \(row-column alpha lattice design\) |
-
-### Automated Phenotpying
-
-The [Lemnatec Scanalyzer Field Gantry 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/).
-
-Twelve sensors are attached to the gantry system. Detailed information for each sensor including name, variable measured, and field of view are [available here](https://docs.google.com/spreadsheets/d/1Nfabx_n1rNlO6NW3olD8MAibJ3KHnOMmMwOYYw4wwGc/pubhtml?gid=1886254108&single=true&widget=true&headers=false). The planned sensor missions and their objectives for 2016 are [available here](https://docs.google.com/spreadsheets/d/1Nfabx_n1rNlO6NW3olD8MAibJ3KHnOMmMwOYYw4wwGc/pubhtml?gid=2092320800&single=true&widget=true&headers=false).
-
-### Manually Collected Field Data
-
-emergence vigor emergence final stand counts plant heights node and tiller counts on marked plants phenology growth stage data leaf desiccation ratings radiation interception managements Incomplete harvest yield data
+### 
 
 ## Season 2 sorghum \(August - November 2016, unpublished\)
 
@@ -74,9 +46,21 @@ same as season 1
 
 plant heights managements emergence vigor emergence final stand counts node and tiller counts on marked plants leaf length and width on marked plants, one date
 
-## Durum wheat \(unpublished\)
+## Season 3 Durum wheat 
 
 #### [Experimental design](https://docs.google.com/spreadsheets/d/15hLUFquat4T-8-ejBKTHRYGgGO1LL3w6UwMQ6jxHA8E/edit#gid=1274912251)
 
 #### [Automatically and manually collected field data plan](https://docs.google.com/spreadsheets/d/15hLUFquat4T-8-ejBKTHRYGgGO1LL3w6UwMQ6jxHA8E/edit#gid=623178992)
 
+## Season 4
+
+## Season 5
+
+## Season 6
+
+## Season 7
+
+## Season 8
+
+## Season 9
+