book.bib

@inproceedings{burnette2018,
  author = {Burnette, Maxwell and Rohde, Gareth S. and Fahlgren, Noah and Sagan, Vasit and Sidike, Paheding and Kooper, Rob and Terstriep, Jeffrey A. and Mockler, Todd and Andrade-Sanchez, Pedro and Ward, Rick and Maloney, J. D. and Willis, Craig and Newcomb, Maria and Shakoor, Nadia and LeBauer, David},
  booktitle = {ACM International Conference Proceeding Series},
  doi = {10.1145/3219104.3219152},
  isbn = {9781450364461},
  title = {{TERRA-REF data processing infrastructure}},
  year = {2018}
}
@misc{babaeian2020,
  author = {Babaeian, Ebrahim and Gonzalez-Cena, Juan R. and Gohardoust, Mohammad and Hou, Xiaobo and White, Scott A. and Tuller, Markus},
  title = {Physicochemical and Hydrologic Characterization TERRA-REF South Field},
  doi = {},
  year = {2020},
  journal = "\texit{in prep}"
}
@article{brenton2016,
author = {Brenton, Zachary W. and Cooper, Elizabeth A. and Myers, Mathew T. and Boyles, Richard E. and Shakoor, Nadia and Zielinski, Kelsey J. and Rauh, Bradley L. and Bridges, William C. and Morris, Geoffrey P. and Kresovich, Stephen},
  doi = {10.1534/genetics.115.183947},
  issn = {19432631},
  journal = {Genetics},
  keywords = {Bioenergy Association Panel,Biomass composition,Carbon partitioning,MPP,Multiparent Advanced Generation Inter-Cross (MAGIC),Multiparental populations,Nonstructural sugars},
  pmid = {27356613},
  title = {{A genomic resource for the development, improvement, and exploitation of sorghum for bioenergy}},
  year = {2016}
}
@software{david_lebauer_2020_3661373,
  author       = {David LeBauer and
                  Craig Willis and
                  Rachel Shekar and
                  Max Burnette and
                  Ting Li and
                  Scott Rohde and
                  Yan Liu and
                  JD Maloney and
                  Noah Fahlgren and
                  Charlie Zender and
                  Rob Kooper and
                  JeromeMao and
                  harshagrawal28 and
                  Xingchen Hong and
                  Shannon Bradley and
                  Samy Pessé and
                  Katrin Leinweber and
                  Justin Manzo and
                  Jeff Terstriep and
                  Abby Stylianou},
  title        = {{terraref/documentation: Season 6 Data Publication 
                   (2019)}},
  month        = feb,
  year         = 2020,
  publisher    = {Zenodo},
  version      = {v0.9},
  doi          = {10.5281/zenodo.3661373},
  url          = {https://doi.org/10.5281/zenodo.3661373}
}
@software{david_lebauer_2020_3635863,
  author       = {David LeBauer and
                  Nick Heyek and
                  Rachel Shekar and
                  Katrin Leinweber and
                  JD Maloney and
                  Tino Dornbusch},
  title        = {{terraref/reference-data: Season 4 \& 6 Data 
                   Publication (2019)}},
  month        = feb,
  year         = 2020,
  publisher    = {Zenodo},
  version      = {S46\_Pub\_2019},
  doi          = {10.5281/zenodo.3635863},
  url          = {https://doi.org/10.5281/zenodo.3635863}
}
@software{craig_willis_2020_3635853,
  author       = {Craig Willis and
                  David LeBauer and
                  Max Burnette and
                  Rachel Shekar},
  title        = {{terraref/sensor-metadata: Season 4 \& 6 Data 
                   Publication (2019)}},
  month        = feb,
  year         = 2020,
  publisher    = {Zenodo},
  version      = {S46\_Pub\_2019},
  doi          = {10.5281/zenodo.3635853},
  url          = {https://doi.org/10.5281/zenodo.3635853}
}
@software{max_burnette_2020_3635849,
  author       = {Max Burnette and
                  Charlie Zender and
                  JeromeMao and
                  David LeBauer and
                  Rachel Shekar and
                  Noah Fahlgren and
                  Craig Willis and
                  hmb1 and
                  Xingchen Hong and
                  ZongyangLi and
                  Fengling Wang and
                  TinoDornbusch and
                  JD Maloney and
                  Wei Qin and
                  Stuart Marshall and
                  Abby Stylianou and
                  Ting Li},
  title        = {{terraref/computing-pipeline: Season 4 \& 6 Data 
                   Publication (2019)}},
  month        = feb,
  year         = 2020,
  publisher    = {Zenodo},
  version      = {S46\_Pub\_2019},
  doi          = {10.5281/zenodo.3635849},
  url          = {https://doi.org/10.5281/zenodo.3635849}
}
@software{max_burnette_2019_3406335,
  author       = {Max Burnette and
                  Craig Willis and
                  Chris Schnaufer and
                  David LeBauer and
                  Nick Heyek and
                  Wei Qin and
                  Solmaz Hajmohammadi and
                  Kristina Riemer},
  title        = {{terraref/terrautils: Season 6 Data Publication 
                   (2019)}},
  month        = sep,
  year         = 2019,
  publisher    = {Zenodo},
  version      = {S6\_Pub\_2019},
  doi          = {10.5281/zenodo.3406335},
  url          = {https://doi.org/10.5281/zenodo.3406335}
}
@software{max_burnette_2019_3406332,
  author       = {Max Burnette and
                  ZongyangLi and
                  Solmaz Hajmohammadi and
                  David LeBauer and
                  Nick Heyek and
                  Craig Willis},
  title        = {{terraref/extractors-3dscanner: Season 6 Data 
                   Publication (2019)}},
  month        = sep,
  year         = 2019,
  publisher    = {Zenodo},
  version      = {S6\_Pub\_2019},
  doi          = {10.5281/zenodo.3406332},
  url          = {https://doi.org/10.5281/zenodo.3406332}
}
@software{max_burnette_2019_3406329,
  author       = {Max Burnette and
                  David LeBauer and
                  Wei Qin and
                  Yan Liu},
  title        = {{terraref/extractors-metadata: Season 6 Data 
                   Publication (2019)}},
  month        = sep,
  year         = 2019,
  publisher    = {Zenodo},
  version      = {S6\_Pub\_2019},
  doi          = {10.5281/zenodo.3406329},
  url          = {https://doi.org/10.5281/zenodo.3406329}
}
@software{max_burnette_2019_3406318,
  author       = {Max Burnette and
                  Jerome Mao and
                  David LeBauer and
                  Charlie Zender and
                  Harsh Agrawal},
  title        = {{terraref/extractors-environmental: Season 6 Data 
                   Publication (2019)}},
  month        = sep,
  year         = 2019,
  publisher    = {Zenodo},
  version      = {S6\_Pub\_2019},
  doi          = {10.5281/zenodo.3406318},
  url          = {https://doi.org/10.5281/zenodo.3406318}
}
@software{jeromemao_2019_3406312,
  author       = {Jerome Mao and
                  Max Burnette and
                  Henry Butowsky and
                  Charlie Zender and
                  David LeBauer and
                  Sidke Paheding},
  title        = {{terraref/extractors-hyperspectral: Season 6 Data 
                   Publication (2019)}},
  month        = sep,
  year         = 2019,
  publisher    = {Zenodo},
  version      = {S6\_Pub\_2019},
  doi          = {10.5281/zenodo.3406312},
  url          = {https://doi.org/10.5281/zenodo.3406312}
}
@software{max_burnette_2019_3406311,
  author       = {Max Burnette and
                  David LeBauer and
                  Solmaz Hajmohammadi and
                  Zongyang Li and
                  Craig Willis and
                  Wei Qin and
                  Patrick and
                  JD Maloney},
  title        = {{terraref/extractors-multispectral: Season 6 Data 
                   Publication (2019)}},
  month        = sep,
  year         = 2019,
  publisher    = {Zenodo},
  version      = {S6\_Pub\_2019},
  doi          = {10.5281/zenodo.3406311},
  url          = {https://doi.org/10.5281/zenodo.3406311}
}
@software{max_burnette_2019_3406304,
  author       = {Max Burnette and
                  David LeBauer and
                  Zongyang Li and
                  Wei Qin and
                  Solmaz Hajmohammadi and
                  Craig Willis and
                  Sidke Paheding and
                  Nick Heyek},
  title        = {{terraref/extractors-stereo-rgb: Season 6 Data 
                   Publication (2019)}},
  month        = sep,
  year         = 2019,
  publisher    = {Zenodo},
  version      = {S6\_Pub\_2019},
  doi          = {10.5281/zenodo.3406304},
  url          = {https://doi.org/10.5281/zenodo.3406304}
}
@software{scott_rohde_2016_48661,
  author       = {Scott Rohde and
                  Carl Crott and
                  Patrick Mulroony and
                  Jeremy Kemball and
                  David LeBauer and
                  Rob Kooper and
                  Jimmy Chen and
                  Andrew Shirk and
                  Zhengqi Yang and
                  Max Burnette and
                  Uday Saraf and
                  Michael Dietze},
  title        = {bety: BETYdb 4.6},
  month        = mar,
  year         = 2016,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.48661},
  url          = {https://doi.org/10.5281/zenodo.48661}
}
@url{Brown1996azmet,
	Author = {Brown, P. W. and Russell, B. },
	Date-Added = {2020-04-21 08:41:20 -0700},
	Date-Modified = {2020-04-21 08:43:28 -0700},
	Lastchecked = {2020-03-20},
	Title = {{AZMET, The Arizona Meteorological Network. Arizona Cooperative Extension.}},
	Url = {https://cals.arizona.edu/AZMET/},
	Year = {1996}}
@article{Selby2019,
   author = {Selby, Peter and Abbeloos, Rafael and Backlund, Jan Erik and Basterrechea Salido, Martin and Bauchet, Guillaume and Benites-Alfaro, Omar E and Birkett, Clay and Calaminos, Viana C and Carceller, Pierre and Cornut, Guillaume and Vasques Costa, Bruno and Edwards, Jeremy D and Finkers, Richard and Yanxin Gao, Star and Ghaffar, Mehmood and Glaser, Philip and Guignon, Valentin and Hok, Puthick and Kilian, Andrzej and König, Patrick and Lagare, Jack Elendil B and Lange, Matthias and Laporte, Marie-Angélique and Larmande, Pierre and LeBauer, David S and Lyon, David A and Marshall, David S and Matthews, Dave and Milne, Iain and Mistry, Naymesh and Morales, Nicolas and Mueller, Lukas A and Neveu, Pascal and Papoutsoglou, Evangelia and Pearce, Brian and Perez-Masias, Ivan and Pommier, Cyril and Ramírez-González, Ricardo H and Rathore, Abhishek and Raquel, Angel Manica and Raubach, Sebastian and Rife, Trevor and Robbins, Kelly and Rouard, Mathieu and Sarma, Chaitanya and Scholz, Uwe and Sempéré, Guilhem and Shaw, Paul D and Simon, Reinhard and Soldevilla, Nahuel and Stephen, Gordon and Sun, Qi and Tovar, Clarysabel and Uszynski, Grzegorz and Verouden, Maikel and The BrAPI consortium},
    title = "{BrAPI—an application programming interface for plant breeding applications}",
    journal = {Bioinformatics},
    volume = {35},
    number = {20},
    pages = {4147-4155},
    year = {2019},
    month = {03},
    abstract = "{Modern genomic breeding methods rely heavily on very large amounts of phenotyping and genotyping data, presenting new challenges in effective data management and integration. Recently, the size and complexity of datasets have increased significantly, with the result that data are often stored on multiple systems. As analyses of interest increasingly require aggregation of datasets from diverse sources, data exchange between disparate systems becomes a challenge.To facilitate interoperability among breeding applications, we present the public plant Breeding Application Programming Interface (BrAPI). BrAPI is a standardized web service API specification. The development of BrAPI is a collaborative, community-based initiative involving a growing global community of over a hundred participants representing several dozen institutions and companies. Development of such a standard is recognized as critical to a number of important large breeding system initiatives as a foundational technology. The focus of the first version of the API is on providing services for connecting systems and retrieving basic breeding data including germplasm, study, observation, and marker data. A number of BrAPI-enabled applications, termed BrAPPs, have been written, that take advantage of the emerging support of BrAPI by many databases.More information on BrAPI, including links to the specification, test suites, BrAPPs, and sample implementations is available at https://brapi.org/. The BrAPI specification and the developer tools are provided as free and open source.}",
    issn = {1367-4803},
    doi = {10.1093/bioinformatics/btz190},
    url = {https://doi.org/10.1093/bioinformatics/btz190},
    eprint = {https://academic.oup.com/bioinformatics/article-pdf/35/20/4147/30148301/btz190.pdf}
}
@inproceedings{Marini2018cos,
author = {Marini, Luigi and Gutierrez-Polo, Indira and Kooper, Rob and Satheesan, Sandeep Puthanveetil and Burnette, Maxwell and Lee, Jong and Nicholson, Todd and Zhao, Yan and McHenry, Kenton},
title = {Clowder: Open Source Data Management for Long Tail Data},
year = {2018},
isbn = {9781450364461},
publisher = {Association for Computing Machinery},
address = {New York, NY, USA},
url = {https://doi.org/10.1145/3219104.3219159},
doi = {10.1145/3219104.3219159},
booktitle = {Proceedings of the Practice and Experience on Advanced Research Computing},
articleno = {40},
numpages = {8},
keywords = {data management, data curation, linked data, scientific gateways, metadata management},
location = {Pittsburgh, PA, USA},
series = {PEARC ’18}
}
@software{luigi_marini_2019_3300953,
  author       = {Luigi Marini and
                  Rob Kooper and
                  Indira Gutierrez and
                  Constantinos Sophocleous and
                  Max Burnette and
                  Todd Nicholson and
                  Michal Ondrejcek and
                  Bing Zhang and
                  Inna Zharnitsky and
                  Sandeep Puthanveetil Satheesan and
                  Smruti Padhy and
                  Yan Zhao and
                  Rui Liu and
                  Ashwini Vaidya and
                  Jim Myers and
                  Mario Felarca and
                  Brock Angelo and
                  Gene Roeder and
                  Jong Lee and
                  Will Hennessy and
                  Theerasit Issaranon and
                  Yibo Guo and
                  Xiaocheng Yuan and
                  Varun Kethineedi and
                  Avinash Kumar and
                  Nishant Nayudu and
                  Ward Poelmans and
                  Winston Jansz and
                  Gregory Jansen and
                  Chris Navarro and
                  Michelle Pitcel and
                  Nicholas Tenczar and
                  Chen Wang and
                  Mike Lambert and
                  Kenton McHenry},
  title        = {{Clowder: Open Source Data Management for Long Tail 
                   Data}},
  month        = jul,
  year         = 2019,
  publisher    = {Zenodo},
  version      = {v1.7.1},
  doi          = {10.5281/zenodo.3300953},
  url          = {https://doi.org/10.5281/zenodo.3300953}
}
 
@article{LeBauer2018byt,
author = {LeBauer, David and Kooper, Rob and Mulrooney, Patrick and Rohde, Scott and Wang, Dan and Long, Stephen P. and Dietze, Michael C.},
title = {BETYdb: a yield, trait, and ecosystem service database applied to second-generation bioenergy feedstock production},
journal = {GCB Bioenergy},
volume = {10},
number = {1},
pages = {61-71},
keywords = {bioenergy crops, database, ecosystem services, meta-analysis, open access, plant traits, yields},
doi = {10.1111/gcbb.12420},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/gcbb.12420},
eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1111/gcbb.12420},
abstract = {Abstract Increasing demand for sustainable energy has led to research and development on the cultivation of diverse plant species for biomass production. To support the research and development required to domesticate and cultivate crops for bioenergy, we developed the Biofuel Ecophysiological Traits and Yields database (BETYdb). BETYdb is a centralized open-access repository that facilitates organization, discovery, and exchange of information about plant traits, crop yields, and ecosystem functions. BETYdb provides user interfaces to simplify storage and discovery as well as programming interfaces that support automated and reproducible scientific workflows. Presently, BETYdb contains over forty thousand observations of plant traits, biomass yields, and ecosystem dynamics collected from the published articles and ongoing field studies. Over half of these records represent fewer than ten genera that have been intensively evaluated for biomass production, while the other half represent over two thousand plant species reflecting research on new crops, unmanaged ecosystems, and land use transitions associated with bioenergy. BETYdb has been accessed over twenty-five thousand times and is used in the fields of bioenergy and ecosystem ecology to quantify yield potential and ecosystem functioning of crops and unmanaged systems under present and future climates. Here, we summarize the database contents and illustrate its applications. We show its utility in a new analysis that confirms that Miscanthus is twice as productive as switchgrass over a much wider range of environmental and management conditions than covered in previous analyses. We compare traits related to carbon uptake and water use of these species with each other and with two coppice shrubs, poplar and willow. These examples, along with a growing body of published research that used BETYdb, illustrate the scope of research supported through this open-access database.},
year = {2018}
}
  @Manual{chamberlain2019traits,
    title = {traits: Species Trait Data from Around the Web},
    author = {Scott Chamberlain and Zachary Foster and Ignasi Bartomeus and David LeBauer and Chris Black and David Harris},
    year = {2019},
    note = {R package version 0.4.2},
    url = {https://CRAN.R-project.org/package=traits},
  }