Data

Tools

Indexes

Applications

Experiments

Open Source Science

phytooracle

Distributive pipelines for phenomic data analysis

https://github.com/lyonslab/phytooracle

Science Score: 44.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (11.1%) to scientific vocabulary
Last synced: 7 months ago · JSON representation ·

Repository

Distributive pipelines for phenomic data analysis

Basic Info
Statistics
  • Stars: 13
  • Watchers: 8
  • Forks: 27
  • Open Issues: 2
  • Releases: 0
Created over 6 years ago · Last pushed over 4 years ago
Metadata Files
Readme License Citation

README.md

PhytoOracle

PhytoOracle is a scalable, distributed workflow manager for analyzing highthroughput phenotyping data.
It is designed to process data from the UA Gantry, but can be adapted to work on data coming from other platforms.
PhytoOracle uses a master-worker framework for distributed computing (HPC, Cloud, etc.) and can run jobs on nearly all unix-like environments.

Documentation

See detailed documentation here for instruction manuals.

Supported Sensors and Pipelines

For more information on types and description of each camera used, access the documentation above.

Resources

License

PhytoOracle is licensed under the MIT License.

Issues and Questions

Need help? Found a bug? Raise an issue on our github page here.

For specific workflows and adapting a pipeline for your own work contact:

  • Emmanuel Gonzalez: emmanuelgonzalez [at] email.arizona.edu

  • Michele Cosi: cosi [at] email.arizona.edu

For plant detection and plant clustering:

  • Travis Simmons: travis.simmons [at] ccga.edu

For the orthomosaicing algorithm:

  • Ariyan Zarei: ariyanzarei [at] email.arizona.edu

Acknowledgements

This project partially built on code initially developed by the TERRA-REF project and AgPipeline team. We thank the University of Arizona Advanced Cyberinfrastrcture Concept class of 2019 for additional work.

This material based upon work supported by Cyverse & CCTools. Cyverse is based upon work supported by the National Science Foundation under Grant Numbers: DBI-0735191, DBI-1265383, DBI-1743442. CCTools is based upon work supported by the National Science Foundation under Grant Numbers: CCF-0621434 and CNS-0643229.

Owner

  • Name: Lyons Lab @ University of Arizona
  • Login: LyonsLab
  • Kind: organization
  • Email: coge.genome@gmail.com
  • Location: Tucson, AZ

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Gonzalez"
  given-names: "Emmanuel"
  orcid: "https://orcid.org/0000-0002-3021-9842"
- family-names: "Zarei"
  given-names: "Ariyan"
  orcid: "https://orcid.org/0000-0000-0000-0000"
- family-names: "Hendler"
  given-names: "Nathanial"
  orcid: "https://orcid.org/0000-0000-0000-0000"
- family-names: "Simmons"
  given-names: "Travis"
  orcid: "https://orcid.org/0000-0000-0000-0000"
- family-names: "Demieville"
  given-names: "Jeffrey"
  orcid: "https://orcid.org/0000-0000-0000-0000"
- family-names: "Lyons"
  given-names: "Eric"
  orcid: "https://orcid.org/0000-0000-0000-0000"
- family-names: "Pauli"
  given-names: "Duke"
  orcid: "https://orcid.org/0000-0000-0000-0000"
title: "PhytoOracle: Scalable, Modular Phenomic Data Processing Pipelines"
date-released: 2021-09-28
url: "https://github.com/LyonsLab/PhytoOracle"

GitHub Events

Total
Last Year