dishtiny

DISHTINY: A Platform for Studying Open-Ended Evolutionary Transitions in Individuality

https://github.com/mmore500/dishtiny

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
  • Committers with academic emails
  • Institutional organization owner
  • JOSS paper metadata
  • Scientific vocabulary similarity
    Low similarity (9.3%) to scientific vocabulary

Keywords

artificial-life emergence evolution evolutionary-computation evolutionary-transitions open-ended-evolution scientific-computing

Keywords from Contributors

standardization meshing pipeline-testing pde pinn interpretability datacleaner data-profilers dynamics sequences
Last synced: 6 months ago · JSON representation ·

Repository

DISHTINY: A Platform for Studying Open-Ended Evolutionary Transitions in Individuality

Basic Info
  • Host: GitHub
  • Owner: mmore500
  • License: mit
  • Language: C++
  • Default Branch: master
  • Homepage: https://osf.io/g58xk/
  • Size: 2.32 GB
Statistics
  • Stars: 31
  • Watchers: 2
  • Forks: 5
  • Open Issues: 46
  • Releases: 1
Topics
artificial-life emergence evolution evolutionary-computation evolutionary-transitions open-ended-evolution scientific-computing
Created almost 8 years ago · Last pushed 6 months ago
Metadata Files
Readme Contributing License Code of conduct Citation Authors

README.md

dishtiny

version Codacy Badge continuous integration Documentation Status documentation coverage code coverage status DockerHub link dotos GitHub stars Binder

Framework for digital multicellularity research.

Check out the live in-browser web app at https://mmore500.com/dishtiny.

Owner

  • Name: Matthew Andres Moreno
  • Login: mmore500
  • Kind: user
  • Location: East Lansing, MI
  • Company: @devosoft

doctoral student, Computer Science and Engineering at Michigan State University

Citation (CITATION.cff)

type: article
abstract: >-
  The emergence of new replicating entities from the union of simpler entities
  characterizes some of the most profound events in natural evolutionary
  history. Such transitions in individuality are essential to the evolution of
  the most complex forms of life. Thus, understanding these transitions is
  critical to building artificial systems capable of open-ended evolution. Alas,
  these transitions are challenging to induce or detect, even with computational
  organisms. Here, we introduce the DISHTINY (Distributed Hierarchical
  Transitions in Individuality) platform, which provides simple cell-like
  organisms with the ability and incentive to unite into new individuals in a
  manner that can continue to scale to subsequent transitions. The system is
  designed to encourage these transitions so that they can be studied: Organisms
  that coordinate spatiotemporally can maximize the rate of resource harvest,
  which is closely linked to their reproductive ability. We demonstrate the
  hierarchical emergence of multiple levels of individuality among simple
  cell-like organisms that evolve parameters for manually designed strategies.
  During evolution, we observe reproductive division of labor and close
  cooperation among cells, including resource-sharing, aggregation of resource
  endowments for propagules, and emergence of an apoptosis response to somatic
  mutation. Many replicate populations evolved to direct their resources toward
  low-level groups (behaving like multicellular individuals), and many others
  evolved to direct their resources toward high-level groups (acting as
  larger-scale multicellular individuals).
date-released: 2021-07-28
license: MIT
version: 2.0.0
authors:
  - affiliation: Michigan State University
    family-names: Moreno
    given-names: Matthew Andres
    orcid: 'https://orcid.org/0000-0003-4726-4479'
  - affiliation: Michigan State University
    family-names: Ofria
    given-names: Charles
    orcid: 'https://orcid.org/0000-0003-2924-1732'
publisher:
  name: MIT Press
  city: Cambridge
  region: MA
  country: USA
journal: Artificial Life
volume: 25
issue: 2
pages: 17
url: 'https://doi.org/10.1162/artl_a_00284'
doi: 10.1162/artl_a_00284
start: 117
end: 133
year: 2019
issn: 1064-5462
cff-version: 1.1.0
message: 'Please consult docs/citing.md to cite this software.'
title: Toward Open-Ended Fraternal Transitions in Individuality

GitHub Events

Total
  • Release event: 1
  • Watch event: 1
Last Year
  • Release event: 1
  • Watch event: 1

Committers

Last synced: 10 months ago

All Time
  • Total Commits: 3,157
  • Total Committers: 7
  • Avg Commits per committer: 451.0
  • Development Distribution Score (DDS): 0.125
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Matthew Andres Moreno m****t@g****m 2,762
Matthew Andres Moreno m****o@g****m 226
rodsan0 r****0 159
github-actions 4****] 7
perryk12 5****2 1
mmore100 7****0 1
dependabot[bot] 4****] 1

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 95
  • Total pull requests: 34
  • Average time to close issues: 19 days
  • Average time to close pull requests: 30 days
  • Total issue authors: 2
  • Total pull request authors: 3
  • Average comments per issue: 0.44
  • Average comments per pull request: 0.41
  • Merged pull requests: 28
  • Bot issues: 0
  • Bot pull requests: 2
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Top Authors
Issue Authors
  • mmore500 (93)
  • rodsan0 (2)
Pull Request Authors
  • mmore500 (20)
  • rodsan0 (12)
  • dependabot[bot] (2)
Top Labels
Issue Labels
Pull Request Labels
dependencies (2) Merge: Ready (1) enhancement (1) Merge: Not Ready (1) python (1)

Dependencies

package.json npm
  • express 4.16.3 development
  • puppeteer 1.20.0 development
tests/dish2/viz/artists/package.json npm
  • canvas 2.6.1
  • fs 0.0.1-security
  • jquery 3.5.1
  • jsdom 16.4.0
tests/dish2/viz/renderers/package.json npm
  • canvas 2.6.1
  • fs 0.0.1-security
  • jquery 3.5.1
  • jsdom 16.4.0
tests/dish2/web/package.json npm
  • canvas 2.6.1
  • fs 0.0.1-security
  • jquery 3.5.1
  • jsdom 16.4.0
binder/requirements.txt pypi
  • 125 dependencies
third-party/requirements.in pypi
  • aiobotocore ==1.1.2
  • boto3 ==1.14.44
  • breathe ==4.19.2
  • coverxygen ==1.5.0
  • deprecation ==2.1.0
  • exdown ==0.7.0
  • exhale ==0.2.3
  • frozendict ==1.2
  • fsspec ==0.8.5
  • gitpython ==3.1.14
  • idna ==2.8
  • image-slicer ==2.1.1
  • ipykernel ==5.5.3
  • ipython ==7.16.1
  • iterdub ==0.2.0
  • iterpop ==0.3.4
  • j2cli ==0.3.10
  • jupyter_client ==6.1.12
  • jupyter_core ==4.7.1
  • keyname ==0.4.1
  • markdown-it-py ==0.6.2
  • markdown2 ==2.3.9
  • matplotlib ==3.3.2
  • myst-parser ==0.13.5
  • nb-clean ==2.0.2
  • nbconvert ==5.6.1
  • nbmetalog ==0.2.6
  • networkx ==2.5
  • nose ==1.3.7
  • numpy ==1.19.5
  • opencv-python ==4.5.1.48
  • osfclient ==0.0.5
  • pandas ==1.1.2
  • python-slugify ==4.0.1
  • s3fs ==0.5.1
  • scipy ==1.5.4
  • seaborn ==0.11.0
  • sphinx ==3.1.2
  • sphinx-rtd-theme ==0.5.0
  • sphinxemoji ==0.1.8
  • statsmodels ==0.12.2
  • teeplot ==0.2.0
  • toml ==0.10.1
  • tqdm ==4.50.2
  • traitlets ==4.3.3
  • tweepy ==3.10.0
third-party/requirements.txt pypi
  • 125 dependencies
.github/workflows/CI.yml actions
  • JamesIves/github-pages-deploy-action 4.0.0 composite
  • actions/checkout v2 composite
  • codecov/codecov-action v1 composite
  • docker/build-push-action v1 composite
  • fregante/setup-git-user v1 composite
Dockerfile docker
  • mmore500/conduit sha-785924c@sha256 build