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directed-digital-evolution

Computational model of laboratory directed evolution + experiments.

https://github.com/amlalejini/directed-digital-evolution

Science Score: 54.0%

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
    Links to: zenodo.org
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (8.2%) to scientific vocabulary

Keywords

artificial-selection digital-evolution directed-evolution evolutionary-computation parent-selection-algorithms
Last synced: 6 months ago · JSON representation ·

Repository

Computational model of laboratory directed evolution + experiments.

Basic Info
  • Host: GitHub
  • Owner: amlalejini
  • Language: Python
  • Default Branch: main
  • Homepage:
  • Size: 71 MB
Statistics
  • Stars: 3
  • Watchers: 1
  • Forks: 1
  • Open Issues: 0
  • Releases: 1
Topics
artificial-selection digital-evolution directed-evolution evolutionary-computation parent-selection-algorithms
Created over 4 years ago · Last pushed over 3 years ago
Metadata Files
Readme Contributing License Code of conduct Citation Authors

README.md

Directed digital evolution

supplemental DOI OSF DockerHub link GitHub stars

Click the supplemental material badge (in pink) at the top of this readme to navigate to the supplemental material ebook.

Repository guide:

  • bib/ contains BibTex files with references used in the supplemental material.
  • docs/ contains documentation
  • experiments/ contains the configuration files, HPC submission scripts, and analyses for all preliminary and final (published) experiments
  • include/ contains the C++ header files that implement the model of directed evolution
  • tests/ contains tests for directed digital evolution library functions

Credits

This package was created with Cookiecutter and the devosoft/cookiecutter-empirical-project project template.

This package uses Empirical, a library of tools for scientific software development, with emphasis on also being able to build web interfaces using Emscripten.

Owner

  • Name: Alex Lalejini
  • Login: amlalejini
  • Kind: user
  • Location: Grand Rapids, MI
  • Company: Grand Valley State University

Assistant Professor @ Grand Valley State University

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Lalejini"
  given-names: "Alexander"
  orcid: "https://orcid.org/0000-0003-0994-2718"
- family-names: "Dolson"
  given-names: "Emily"
  orcid: "https://orcid.org/0000-0001-8616-4898"
- family-names: "Vostinar"
  given-names: "Anya E."
  orcid: "https://orcid.org/0000-0001-7216-5283"
- family-names: "Zaman"
  given-names: "Luis"
  orcid: "https://orcid.org/0000-0001-6838-7385"
title: "Directed digital evolution software"
doi: 10.5281/zenodo.6403135
url: "https://github.com/amlalejini/directed-digital-evolution"
# preferred-citation:
#   type: article
#   authors:
#   - family-names: "Lisa"
#     given-names: "Mona"
#     orcid: "https://orcid.org/0000-0000-0000-0000"
#   - family-names: "Bot"
#     given-names: "Hew"
#     orcid: "https://orcid.org/0000-0000-0000-0000"
#   doi: "10.0000/00000"
#   journal: "Journal Title"
#   month: 9
#   start: 1 # First page number
#   end: 10 # Last page number
#   title: "My awesome research software"
#   issue: 1
#   volume: 1
#   year: 2021

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Dependencies

experiments/requirements.txt pypi
  • numpy *
  • pandas *
  • python-dateutil *
  • pytz *
  • pyvarco *
  • scipy *
  • six *