GitBook: [master] 10 pages and 2 assets modified

Author: dlebauer

.gitbook/assets/image (1).png

@@ -15,7 +15,7 @@
   * [Phenotractor Protocols](protocols/phenotractor-protocols.md)
   * [UAV Protocols](protocols/uav-protocols.md)
   * [Genomic Data](protocols/genomic-data.md)
-* [Data Use](user-manual/README.md)
+* [Data](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)
@@ -27,6 +27,7 @@
     * [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)
+    * [Maricopa UAV Data](user-manual/data-products/maricopa-uav-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)
@@ -58,4 +59,5 @@
   * [Communication and Collaboration](appendix/collaboration-tools.md)
   * [Glossary](appendix/glossary.md)
 * [References](references.md)
+* [TODO](todo.md)
 

.gitbook/assets/image.png

@@ -197,3 +197,16 @@ For the TERRA SNP the following were used:
 **Describe Experiment:** Enter an experiment name \(required\), your data processing version ie 1 for first time, Source if using TERRA Data, it’s TERRA \(required\), and Genome \(required and if you start typing it will find your loaded genome but be sure to verify version and id .\)  
 
 
+## KSU Genomics Pipeline / GBS/RIL Analysis
+
+### Data Access
+
+On Globus and Workbench
+
+
+
+* * |  |  |  |  |
+    | :--- | :--- | :--- | :--- |
+    |  |  |  |  \* |
+    |  |  |  |  \* |
+

SUMMARY.md

@@ -6,6 +6,8 @@ Authors: Rick Ward
 
 ## Abstract
 
+Multispectral data collected during seasons 1-5 at Maricopa using small unmanned aircraft systems, i.e. UAVs. Workflow includes image capture with cameras on UAV platforms, generation of georeferenced orthomosic reflectance and index \(e.g. NDVI\) geotiffs, extraction of plot level statistics within qgis with the aid of polygon shape files in which plot attributes are stored. Downstream users can access the radiometric and index data from the reflectance map geotiffs directly, or from the plot level data uploads.
+
 ## Materials
 
 ### Platforms
@@ -44,4 +46,5 @@ QGIS software was used to confirm geospatial alignment of NDVI geotiffs with sha
 * MicaSense: [https://www.micasense.com](https://www.micasense.com)
 * SenseFly [https://www.sensefly.com](https://www.sensefly.com)
 * QGIS [https://www.qgis.org](https://www.qgis.org)
+* Pix4D [https://www.Pix4D.com ](https://www.Pix4D.com%20)
 

protocols/genomic-data.md

@@ -1,4 +1,157 @@
 # References
 
-Geoffrey P. Morris, Davina H. Rhodes, Zachary Brenton, Punna Ramu, Vinayan Madhumal Thayil, Santosh Deshpande, C. Thomas Hash, Charlotte Acharya, Sharon E. Mitchell, Edward S. Buckler, Jianming Yu and Stephen Kresovich G3: GENES, GENOMES, GENETICS November 1, 2013 vol. 3 no. 11 2085-2094; [https://doi.org/10.1534/g3.113.008417](https://doi.org/10.1534/g3.113.008417)
+Morris, Geoffrey P., Davina H. Rhodes, Zachary Brenton, Punna Ramu, Vinayan Madhumal Thayil, Santosh Deshpande, C. Thomas Hash et al. "Dissecting genome-wide association signals for loss-of-function phenotypes in sorghum flavonoid pigmentation traits." G3: Genes, Genomes, Genetics 3, no. 11 \(2013\): 2085-2094. [https://doi.org/10.1534/g3.113.008417](https://doi.org/10.1534/g3.113.008417)
 
+
+
+Reflectance Indices
+
+_Henrich, V., Krauss, G., Götze, C., Sandow, C._ \(2012\): **IDB - www.indexdatabase.de, Entwicklung einer Datenbank für Fernerkundungsindizes.** AK Fernerkundung, Bochum, 4.-5. 10. 2012. \([PDF](http://www.lap.uni-bonn.de/publikationen/posterordner/henrich_et_al_2012)\)
+
+_Henrich, V., Jung, A., Götze, C., Sandow, C., Thürkow, D., Gläßer, C._ \(2009\): **Development of an online indices database: Motivation, concept and implementation.** 6th EARSeL Imaging Spectroscopy SIG Workshop Innovative Tool for Scientific and Commercial Environment Applications Tel Aviv, Israel, March 16-18, 2009
+
+<table>
+  <thead>
+    <tr>
+      <th style="text-align:left">
+        <p>Apan, Armando; Held, Alex; Phinn, Stuart; Markley, John Formulation and
+          assessment of narrow-band vegetation indices from EO-1 hyperion imagery
+          for discriminating sugarcane disease 2003 2003 Spatial Sciences Institute
+          Conference: Spatial Knowledge Without Boundaries (SSC2003)</p>
+        <p>Bannari, A.; Morin, D.; Bonn, F.; Huete, A. R. A review of vegetation
+          indices 1995 Remote Sensing Reviews</p>
+        <p>Barnes, E.M.; Clarke, T.R.; Richards, S.E.; Colaizzi, P.D.; Haberland,
+          J.; Kostrzewski, M.; Waller, P.; Choi, C., Riley, E.; Thompson, T.; Lascano,
+          R.J.; Li, H.; Moran, M.S. Coincident detection of crop water stress, nitrogen
+          status and canopy density using ground based multispectral data 2000 Proc.
+          5th Int. Conf. Precis Agric</p>
+        <p>Barnes, J. D.; Balaguer, L.; Manrique, E.; Elvira, S.; Davison, A. W.
+          A Reappraisal of the Use of Dmso for the Extraction and Determination of
+          Chlorophylls-a and Chlorophylls-B in Lichens and Higher-Plants 1992 Environmental
+          and Experimental Botany</p>
+        <p>Blackburn, G. A. Spectral indices for estimating photosynthetic pigment
+          concentrations: A test using senescent tree leaves 1998 International Journal
+          of Remote Sensing</p>
+        <p>Carter, Gregory A. Ratios of leaf reflectances in narrow wavebands as
+          indicators of plant stress 1994 International Journal of Remote Sensing</p>
+        <p>Carter, Gregory A.; Cibula, William G.; Miller, Richard L. Narrow-band
+          Reflectance Imagery Compared with ThermalImagery for Early Detection of
+          Plant Stress 1996 Journal of Plant Physiology</p>
+        <p>Chappelle, E.W.; Kim, M.S.; McMurtrey, J.E. Ratio analysis of reflectance
+          spectra (RARS): an algorithm for the remote estimation of the concentrations
+          of chlorophyll a, chlorophyll b, and carotenoids in soybean leaves 1992
+          Remote Sensing of Environment</p>
+        <p>Chen, J.M. Evaluation of vegetation indices and a modified simple ratio
+          for boreal applications 1996 Canadian Journal of Remote Sensing</p>
+        <p>Daughtry, C. S. T.; Walthall, C. L.; Kim, M. S.; de Colstoun, E. Brown;
+          McMurtrey Iii, J. E. Estimating Corn Leaf Chlorophyll Concentration from
+          Leaf and Canopy Reflectance 2000 Remote Sensing of Environment</p>
+        <p>Daughtry, C.; Hunt, E. R.; Walthall, C. L.; Gish, T. J.; Liang, Shunlin;
+          Kramer, E.J. Assessing the Spatial Distribution of Plant Litter 2001 Proceedings
+          of the Tenth JPL Airborne Earth Science Workshop</p>
+        <p>Dobrowski, S. Z., Pushnik, J. C., Zarco-Tejada, P. J., &amp; Ustin, S.
+          L. (2005). Simple reflectance indices track heat and water stress-induced
+          changes in steady-state chlorophyll fluorescence at the canopy scale. Remote
+          Sensing of Environment, 97(3), 403-414.</p>
+        <p>Gamon, J. A.; Pe&#xF1;uelas, J.; Field, C. B. A narrow-waveband spectral
+          index that tracks diurnal changes in photosynthetic efficiency 1992 Remote
+          Sensing of Environment</p>
+        <p>Gamon, J. A.; Surfus, J. S. Assessing leaf pigment content and activity
+          with a reflectometer 1999 New Phytologist</p>
+        <p>Gitelson, A. A.; Kaufman, Y. J.; Stark, R.; Rundquist, D. Novel algorithms
+          for remote estimation of vegetation fraction 2002 Remote Sensing of Environment</p>
+        <p>Gitelson, A. A.; Merzlyak, M. N. Remote estimation of chlorophyll content
+          in higher plant leaves 1997 International Journal of Remote Sensing</p>
+        <p>Gitelson, Anatoly A.; Kaufman, Yoram J.; Merzlyak, Mark N. Use of a green
+          channel in remote sensing of global vegetation from EOS-MODIS 1996 Remote
+          Sensing of Environment</p>
+        <p>Gitelson, Anatoly A.; Keydan, Galina P.; Merzlyak, Mark N. Three-band
+          model for noninvasive estimation of chlorophyll, carotenoids, and anthocyanin
+          contents in higher plant leaves 2006 Geophys. Res. Lett.</p>
+        <p>Gitelson, Anatoly A.; Merzlyak, Mark N.; Zur, Y.; Stark, R.; Gritz, U.
+          Non-destructive and remote sensing techniques for estimation of vegetation
+          status 2001 Third European Conference on Precision Agriculture</p>
+        <p>Gitelson, Anatoly A.; Vi&#xF1;a, Andr&#xE9;s; Arkebauer, Timothy J.; Rundquist,
+          Donald C.; Keydan, Galina: Leavitt, Bryan Remote estimation of leaf area
+          index and green leaf biomass in maize canopies 2003 Geophys. Res. Lett.</p>
+        <p>Goel, Narendra S.; Qin, Wenhan Influences of canopy architecture on relationships
+          between various vegetation indices and LAI and Fpar: A computer simulation
+          1994 Remote Sensing Reviews</p>
+        <p>Guyot, G.; Baret, F.; Major, D. J. High spectral resolution: Determination
+          of specral shifts between the red and the near infrared 1988 International
+          Archives of Photogrammetry and Remote Sensing</p>
+        <p>Haboudane, Driss; Miller, John R.; Pattey, Elizabeth; Zarco-Tejada, Pablo
+          J.; Strachan, Ian B. Hyperspectral vegetation indices and novel algorithms
+          for predicting green LAI of crop canopies: Modeling and validation in the
+          context of precision agriculture 2004 Remote Sensing of Environment</p>
+        <p>Haboudane, Driss; Miller, John R.; Tremblay, Nicolas; Zarco-Tejada, Pablo
+          J.; Dextraze, Louise Integrated narrow-band vegetation indices for prediction
+          of crop chlorophyll content for application to precision agriculture 2002
+          Remote Sensing of Environment</p>
+        <p>Hardinsky, M. A.; Lemas, V. The influence of soil salinity, growth form,
+          and leaf moisture on the spectral reflectance of Spartina alternifolia
+          canopies 1983 Photogrammetric Engineering and Remote Sensing</p>
+        <p>Hern&#xE1;ndez-Clemente, R., Navarro-Cerrillo, R. M., Su&#xE1;rez, L.,
+          Morales, F., &amp; Zarco-Tejada, P. J. (2011). Assessing structural effects
+          on PRI for stress detection in conifer forests. Remote Sensing of Environment,
+          115(9), 2360-2375.</p>
+        <p>Herrmann, I.; Karnieli, A.; Bonfil, D. J.; Cohen, Y.; Alchanatis, V. SWIR-based
+          spectral indices for assessing nitrogen content in potato fields 2010 International
+          Journal of Remote Sensing</p>
+        <p>Huete, A. R. A soil-adjusted vegetation index (SAVI) 1988 Remote Sensing
+          of Environment</p>
+        <p>Huete, A. R.; Liu, H. Q.; Batchily, K.; van Leeuwen, W. A comparison of
+          vegetation indices over a global set of TM images for EOS-MODIS 1997 Remote
+          Sensing of Environment</p>
+        <p>Hunt Jr, E. Raymond; Rock, Barrett N. Detection of changes in leaf water
+          content using Near- and Middle-Infrared reflectances 1989 Remote Sensing
+          of Environment</p>
+        <p>Kaufman, Y. J.;Tanre, D. Atmospherically resistant vegetation index (ARVI)
+          for EOS-MODIS 1992 Geoscience and Remote Sensing, IEEE Transactions on</p>
+        <p>Lichtenthaler, Hartmut K. Vegetation Stress: an Introduction to the Stress
+          Concept in Plants 1996 Journal of Plant Physiology</p>
+        <p>Merzlyak, Mark N.; Gitelson, Anatoly A.; Chivkunova, Olga B.; Rakitin,
+          Victor Y. U. Non-destructive optical detection of pigment changes during
+          leaf senescence and fruit ripening 1999 Physiologia Plantarum</p>
+        <p>Penuelas J., Baret F., Filella I. Semi-empirical indices to assess carotenoids/chlorophyll
+          a ratio from leaf spectral reflectance 1995 Photosynthetica</p>
+        <p>Penuelas, J.; Filella, I.; Biel, C.; Serrano, L.; Save, R. The reflectance
+          at the 950&#x96;970 nm region as an indicator of plant water status 1993
+          International Journal of Remote Sensing</p>
+        <p>Pe&#xF1;uelas, J.; Gamon, J. A.; Fredeen, A. L.; Merino, J.; Field, C.
+          B. Reflectance indices associated with physiological changes in nitrogen-
+          and water-limited sunflower leaves 1994 Remote Sensing of Environment</p>
+        <p>Penuelas, Josep; Filella, Iolanda; Gamon, John A. Assessment of photosynthetic
+          radiation-use efficiency with spectral reflectance 1995 New Phytologist</p>
+        <p>Pinty, B.; Verstraete, M. M. GEMI: a non-linear index to monitor global
+          vegetation from satellites 1992 Plant Ecology</p>
+        <p>Rondeaux, Genevi&#xE8;ve; Steven, Michael; Baret, Fr&#xE9;d&#xE9;ric Optimization
+          of soil-adjusted vegetation indices 1996 Remote Sensing of Environment</p>
+        <p>Roujean, Jean-Louis; Breon, Fran&#xE7;ois-Marie Estimating PAR absorbed
+          by vegetation from bidirectional reflectance measurements 1995 Remote Sensing
+          of Environment</p>
+        <p>Rouse, J.W., Jr.; Haas,R.H.; Schell, J.A.; Deering, D.W. Monitoring the
+          vernal advancement and retrogradation (green wave effect) of natural vegetation
+          1973 Prog. Rep. RSC 1978-1</p>
+        <p>Sims, Daniel A.; Gamon, John A. Relationships between leaf pigment content
+          and spectral reflectance across a wide range of species, leaf structures
+          and developmental stages 2002 Remote Sensing of Environment</p>
+        <p>Tucker, C. J.; Elgin Jr, J. H.; McMurtrey Iii, J. E.; Fan, C. J. Monitoring
+          corn and soybean crop development with hand-held radiometer spectral data
+          1979 Remote Sensing of Environment</p>
+        <p>Vogelmann, J.E.; Rock, B.N.; Moss, D.M. Red Edge Spectral Measurements
+          from Sugar Maple Leaves 1993 International Journal of Remote Sensing</p>
+        <p>Zarco-Tejada, P. J.; Miller, J. R.; Noland, T. L.; Mohammed, G. H.; Sampson,
+          P. H. Scaling-up and model inversion methods with narrow-band optical indices
+          for chlorophyll content estimation in closed forest canopies with hyperspectral
+          data 2001 IEEE Transactions on Geoscience and Remote Sensing</p>
+        <p>Zarco-Tejada, Pablo J., Alberto Berj&#xF3;n, Ra&#xFA;l L&#xF3;pez-Lozano,
+          John R. Miller, P. Mart&#xED;n, Victoria Cachorro, M. R. Gonz&#xE1;lez,
+          and A. De Frutos. &quot;Assessing vineyard condition with hyperspectral
+          indices: Leaf and canopy reflectance simulation in a row-structured discontinuous
+          canopy.&quot; Remote Sensing of Environment 99, no. 3 (2005): 271-287.</p>
+      </th>
+    </tr>
+  </thead>
+  <tbody></tbody>
+</table>

protocols/uav-protocols.md

@@ -0,0 +1,12 @@
+# TODO
+
+UAV Protocols: Vasit and Rick
+
+UAV Data inventory: Vasit and Rick
+
+Review and update genomics, including make sure data are available, why and where CoGe: Nadia, Scott, Noah, Geoff
+
+Field Scanner Operations, Calibration: Jeffrey
+
+
+

references.md

@@ -1,4 +1,4 @@
-# Data Use
+# Data
 
 ## Overview
 

todo.md

@@ -2,11 +2,11 @@
 
 You can access genomics data in one of the following locations:
 
-* Download via [Globus](https://github.com/terraref/documentation/tree/56f669dc870b3c3921bfc029914545574e70f8df/products/user/using-globus.md).
-* The [CyVerse Data Store](https://github.com/terraref/documentation/tree/56f669dc870b3c3921bfc029914545574e70f8df/products/user/using-cyverse.md) for download or use within the CyVerse computing environment.
-* The [CoGe](https://github.com/terraref/documentation/tree/56f669dc870b3c3921bfc029914545574e70f8df/products/user/using-coge.md) computing environment.
+* Download via [Globus](../how-to-access-data.md#globus-browse-and-transfer-files).
+* The [CyVerse Data Store](../how-to-access-data.md#cyverse) for download or use within the CyVerse computing environment.
+* The [CoGe](../how-to-access-data.md#coge) computing environment.
 
-See [Data use policy](https://github.com/terraref/documentation/tree/56f669dc870b3c3921bfc029914545574e70f8df/products/user/data_release_policy.md) before continuing.
+Please review our [data use policy](../data-use-policy.md).
 
 The data is structured on both the TERRA-REF strorage \(accessible via Globus and Workbench\) and CyVerse Data Store infrastructures as follows:
 
@@ -47,3 +47,16 @@ Raw data are in gzip FASTQ format. 768 samples are available. For a list of line
 
 Combined genotype calls are available in VCF format.
 
+## KSU Genomics Pipeline / GBS/RIL analysis
+
+### Raw Data
+
+* genomics/raw\_data/ril/gbs
+  *  H5JYFBCXY\_1\_fastq.txt
+  *  H5JYFBCXY\_2\_fastq.txt
+  * Key\_ril\_terra
+
+### Derived Data
+
+* genomics/derived\_data/ril/gbs/kansas\_state/version1/imp\_TERRA\_RIL\_SNP.vcf
+