Award Abstract # 1208912
Collaborative Research: Arbor: Comparative Analysis Workflows for the Tree of Life

NSF Org: DEB
Division Of Environmental Biology
Recipient: REGENTS OF THE UNIVERSITY OF IDAHO
Initial Amendment Date: May 7, 2012
Latest Amendment Date: March 1, 2016
Award Number: 1208912
Award Instrument: Standard Grant
Program Manager: Simon Malcomber
smalcomb@nsf.gov  (703)292-8227
DEB  Division Of Environmental Biology
BIO  Directorate for Biological Sciences
Start Date: May 1, 2012
End Date: April 30, 2019 (Estimated)
Total Intended Award Amount: $2,299,244.00
Total Awarded Amount to Date: $2,860,659.00
Funds Obligated to Date: FY 2012 = $2,299,244.00
FY 2014 = $542,969.00
FY 2016 = $18,446.00
History of Investigator:
  • Luke Harmon (Principal Investigator)
     lukeh@uidaho.edu
  • Charles Hughes (Co-Principal Investigator)
  • Jeffrey Baumes (Co-Principal Investigator)
  • Wesley Turner (Former Co-Principal Investigator)
Recipient Sponsored Research Office: Regents of the University of Idaho
 875 PERIMETER DR
 MOSCOW
 ID  US  83844-9803
(208)885-6651
Sponsor Congressional District: 01
Primary Place of Performance: University of Idaho
 Campus Box 3051
 Moscow
 ID  US  83844-3051
Primary Place of Performance
Congressional District:
Unique Entity Identifier (UEI): QWYKRJH5NNJ3
Parent UEI:
NSF Program(s): GoLife,
ASSEMBLING THE TREE OF LIFE
Primary Program Source: 01001213DB NSF RESEARCH & RELATED ACTIVIT
01001415DB NSF RESEARCH & RELATED ACTIVIT
01001617DB NSF RESEARCH & RELATED ACTIVIT
Program Reference Code(s): 6133, 9150
Program Element Code(s): 613300, 768900
Award Agency Code: 4900
Fund Agency Code: 4900
Assistance Listing Number(s): 47.074

ABSTRACT

Our understanding of the tree of life, a tree that summarizes the evolutionary relationships of living organisms, has grown rapidly in recent years. However, interpreting and analyzing large evolutionary trees has proven difficult. This project will create visual workflow software, "Arbor", to help scientists and the general public understand the tree of life. Arbor will be easy to use: anyone will be able to carry out analyses by creating a specific workflow of their methods. Users will be able to easily obtain data over the internet and share their Arbor workflows with others, promoting collaborative efforts. Finally, Arbor will be easily expandable and able to grow as new methods are invented.

Arbor will enable "tree-thinking" to permeate scientific research, while also providing extensive educational outreach to classrooms and museums. Students and the general public benefit tremendously from a better understanding of the relationships among all species. Likewise, the visual workflows and user interfaces developed by this project will be freely available to the programming community, stimulating additional software development. Finally, enabling the scientific community to analyze the dynamic tree of life will enable new research across a tremendous range of fields, including medicine, public health, agriculture, ecology, and genetics.

PUBLICATIONS PRODUCED AS A RESULT OF THIS RESEARCH

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(Showing: 1 - 10 of 120)
Anderson, Carlos J R and Harmon, Luke "Ecological and mutation-order speciation in digital organisms" Am. Nat. , v.183 , 2014 , p.257--268 http://dx.doi.org/10.1086/674359
Anderson, Carlos J R and Harmon, Luke "Ecological and mutation-order speciation in digital organisms" Am. Nat. , v.183 , 2014 , p.257--268
Anderson, Carlos JR and Harmon, Luke "Ecological and mutation-order speciation in digital organisms" The American Naturalist , v.183 , 2014 , p.257--268
Andrew R. Deans , Suzanna E. Lewis, Eva Huala, Salvatore S. Anzaldo, Michael Ashburner, James P. Balhoff, David C. Blackburn, Judith A. Blake, J. Gordon Burleigh, Bruno Chanet, Laurel D. Cooper, Mélanie Courtot, Sándor Csösz, Hong Cui, Wasila Dahdul, Sand "Finding our way through phenotypes" PLoS Biology , v.13 , 2015 , p.e1002033
Botero, C. A., L. J. Harmon, and Q. Atkinson "The promise and limits of eco-evolutionary studies of human culture: a comment on Sloan Wilson et al." Religion, Brain, and Behavior. , 2016 10.1080/2153599X.2015.1132249
Botero, Carlos A and Harmon, Luke J and Atkinson, Quentin "The promise and limits of eco-evolutionary studies of human culture" Religion Brain Behav. , v.7 , 2016 , p.153--155 https://doi.org/10.1080/2153599X.2015.1132249
Botero, Carlos A and Harmon, Luke J and Atkinson, Quentin "The promise and limits of eco-evolutionary studies of human culture" Religion Brain Behav. , v.7 , 2016 , p.153--155
Boucher, Florian C and D{\'e}mery, Vincent and Conti, Elena and Harmon, Luke J and Uyeda, Josef "A General Model for Estimating Macroevolutionary Landscapes" Syst. Biol. , v.67 , 2018 , p.304--319 https://doi.org/10.1093/sysbio/syx075
Boucher, Florian C and D{\'e}mery, Vincent and Conti, Elena and Harmon, Luke J and Uyeda, Josef "A General Model for Estimating Macroevolutionary Landscapes" Syst. Biol. , v.67 , 2018 , p.304--319
Caetano, Daniel S and Harmon, Luke J "Estimating correlated rates of trait evolution with uncertainty" bioRxiv , 2017 , p.102939 https://doi.org/10.1093/sysbio/syy067
Caetano, Daniel S and Harmon, Luke J "Estimating correlated rates of trait evolution with uncertainty" bioRxiv , 2017 , p.102939
(Showing: 1 - 10 of 120)

PROJECT OUTCOMES REPORT

Disclaimer

This Project Outcomes Report for the General Public is displayed verbatim as submitted by the Principal Investigator (PI) for this award. Any opinions, findings, and conclusions or recommendations expressed in this Report are those of the PI and do not necessarily reflect the views of the National Science Foundation; NSF has not approved or endorsed its content.

Our project has developed a new web tool for analyzing biodiversity. This tool, called Arbor Workflows, allows users to access, analyze, and understand the diversity of life on Earth. Built on a base that encourages reuse and sharing of data over the web, Arbor enables scientists to work together on projects spanning a wide range of applications.

The tools that we have built focus on understanding how species are related to one another, and how they differ from one another in the traits that they have and where they live. Our tools are visual and work over the web, allowing researchers to gather data from many sources in a visual and intuitive way.

For example, researchers can obtain data from the Encyclopedia of Life, a huge online database of the Earth's species, and combine it with data from the Open Tree of Life, an NSF-funded database on species relationships. They can then use Arbor to visualize patterns of similarity and differences across species, and test hypothesis about how the traits of those species are related to their environment.

Our planet faces an unprecidented biodiversity crisis. Arbor uses tools from computational biology to help understand the Earth's species, how they came to be, the factors influencing their distribution, and the threats that they face in the future. 


Last Modified: 09/13/2019
Modified by: Luke Harmon

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