cellular_raza

cellular_raza: Cellular Agent-based Modeling from a Clean Slate - Published in JOSS (2025)

https://github.com/jonaspleyer/cellular_raza

Science Score: 100.0%

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
Found 2 DOI reference(s) in README and JOSS metadata
✓
Academic publication links
Links to: joss.theoj.org
✓
Committers with academic emails
1 of 2 committers (50.0%) from academic institutions
○
Institutional organization owner
✓
JOSS paper metadata
Published in Journal of Open Source Software

Keywords

agent-based agent-based-modeling biology cellular rust rust-library simulation

Last synced: 4 months ago · JSON representation ·

Repository

Cellular Agent-based Modeling from a Clean Slate

Basic Info

Host: GitHub
Owner: jonaspleyer
License: gpl-2.0
Language: Rust
Default Branch: master
Homepage: https://cellular-raza.com
Size: 141 MB

Statistics

Stars: 17
Watchers: 2
Forks: 0
Open Issues: 0
Releases: 0

Topics

agent-based agent-based-modeling biology cellular rust rust-library simulation

Created over 3 years ago · Last pushed 5 months ago

Metadata Files

Readme Contributing License Citation

cellular_raza

Cellular Agent-based Modeling from a Clean Slate

| | stable | beta | nightly | |---|---|---|---| | ubuntu-22.04 | stable-ubuntu-22.04 | beta-ubuntu-22.04 | nightly-ubuntu-22.04 | | ubuntu-24.04 | stable-ubuntu-24.04 | beta-ubuntu-24.04 | nightly-ubuntu-24.04 | | macos-13 | stable-macos-13 | beta-macos-13 | nightly-macos-13 | | macos-14 | stable-macos-14 | beta-macos-14 | nightly-macos-14 | | windows-latest | stable-windows-latest | beta-windows-latest | nightly-windows-latest |

Documentation

The documentation at cellular-raza.com provides an introduction, examples, the most recent technical documentation, submission guidelines and much more.

Getting Started

The "getting-started" guide at cellular-raza.com/guides/getting-started is a good entry point to learn how to use cellular_raza.

Contributing

Please use github to write a pull-request. Also have a look at the coding guidelines.

License

Download the GNU GENERAL PUBLIC LICENSE Version 2.0.

Owner

Name: Jonas Pleyer
Login: jonaspleyer
Kind: user
Location: Freiburg

Website: https://jonas.pleyer.org
Repositories: 79
Profile: https://github.com/jonaspleyer

Doctoral Student - Agent-Based Modelling in Cellular Systems

JOSS Publication

cellular_raza: Cellular Agent-based Modeling from a Clean Slate

Published

June 10, 2025

DOI

10.21105/joss.07723

Volume 10, Issue 110, Page 7723

Authors

Jonas Pleyer

Freiburg Center for Data Analysis and Modelling and AI (FDMAI), University of Freiburg, Freiburg, Germany

Christian Fleck

Freiburg Center for Data Analysis and Modelling and AI (FDMAI), University of Freiburg, Freiburg, Germany

Editor

AHM Mahfuzur Rahman

Citation (CITATION.cff)

cff-version: "1.2.0"
authors:
- family-names: Pleyer
  given-names: Jonas
  orcid: "https://orcid.org/0009-0001-0613-7978"
- family-names: Fleck
  given-names: Christian
  orcid: "https://orcid.org/0000-0002-6371-4495"
doi: 10.5281/zenodo.15095966
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Pleyer
    given-names: Jonas
    orcid: "https://orcid.org/0009-0001-0613-7978"
  - family-names: Fleck
    given-names: Christian
    orcid: "https://orcid.org/0000-0002-6371-4495"
  date-published: 2025-06-10
  doi: 10.21105/joss.07723
  issn: 2475-9066
  issue: 110
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 7723
  title: "cellular_raza: Cellular Agent-based Modeling from a Clean
    Slate"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.07723"
  volume: 10
title: "cellular_raza: Cellular Agent-based Modeling from a Clean Slate"

GitHub Events

Total

Issues event: 15
Watch event: 8
Delete event: 10
Issue comment event: 34
Push event: 179
Pull request event: 21
Create event: 29

Last Year

Issues event: 15
Watch event: 8
Delete event: 10
Issue comment event: 34
Push event: 179
Pull request event: 21
Create event: 29

Committers

Last synced: almost 2 years ago

All Time

Total Commits: 990
Total Committers: 2
Avg Commits per committer: 495.0
Development Distribution Score (DDS): 0.001

Past Year

Commits: 866
Committers: 2
Avg Commits per committer: 433.0
Development Distribution Score (DDS): 0.001

Top Committers

Name	Email	Commits
Jonas Pleyer	j**r@f**e	989
Jonas Pleyer	5****r	1

Committer Domains (Top 20 + Academic)

fdm.uni-freiburg.de: 1

Issues and Pull Requests

Last synced: 4 months ago

All Time

Total issues: 8
Total pull requests: 13
Average time to close issues: about 1 month
Average time to close pull requests: 4 days
Total issue authors: 3
Total pull request authors: 2
Average comments per issue: 3.38
Average comments per pull request: 0.15
Merged pull requests: 9
Bot issues: 0
Bot pull requests: 12

Past Year

Issues: 7
Pull requests: 13
Average time to close issues: 14 days
Average time to close pull requests: 4 days
Issue authors: 2
Pull request authors: 2
Average comments per issue: 3.71
Average comments per pull request: 0.15
Merged pull requests: 9
Bot issues: 0
Bot pull requests: 12

View more stats

Top Authors

Issue Authors

Armavica (4)
finsberg (3)
jonaspleyer (1)

Pull Request Authors

dependabot[bot] (12)
Kevin-Mattheus-Moerman (1)

Top Labels

Issue Labels

documentation (3) publication (3) enhancement (2) bug (1)

Pull Request Labels

dependencies (12) rust (9)

Packages

Total packages: 7
Total downloads:
- cargo 164,176 total

Total dependent packages: 13
(may contain duplicates)
Total dependent repositories: 0
(may contain duplicates)
Total versions: 159
Total maintainers: 1

crates.io: cellular_raza

Cellular Agent-based Modeling from a Clean Slate

Homepage: https://cellular-raza.com/
Documentation: https://docs.rs/cellular_raza/
License: GPL-2.0
Latest release: 0.3.0
published 5 months ago

Versions: 28
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 28,545 Total

Rankings

Dependent repos count: 29.3%

Dependent packages count: 33.8%

Forks count: 37.5%

Average: 47.8%

Stargazers count: 50.6%

Downloads: 88.0%

Maintainers (1)

jonaspleyer

Last synced: 4 months ago

crates.io: cellular_raza-core-proc-macro

Cellular simulation tool

Homepage: https://cellular-raza.com/
Documentation: https://docs.rs/cellular_raza-core-proc-macro/
License: GPL-2.0
Latest release: 0.3.0
published 5 months ago

Versions: 24
Dependent Packages: 1
Dependent Repositories: 0
Downloads: 24,005 Total

Rankings

Dependent repos count: 29.5%

Dependent packages count: 34.8%

Forks count: 39.7%

Stargazers count: 41.5%

Average: 48.4%

Downloads: 96.4%

Maintainers (1)

jonaspleyer

Last synced: 4 months ago

crates.io: cellular_raza-concepts

cellular_raza concepts

Homepage: https://cellular-raza.com/
Documentation: https://docs.rs/cellular_raza-concepts/
License: GPL-2.0
Latest release: 0.3.0
published 5 months ago

Versions: 27
Dependent Packages: 4
Dependent Repositories: 0
Downloads: 28,212 Total

Rankings

Dependent repos count: 28.4%

Dependent packages count: 33.0%

Forks count: 40.5%

Average: 51.4%

Stargazers count: 55.6%

Downloads: 99.3%

Maintainers (1)

jonaspleyer

Last synced: 4 months ago

crates.io: cellular_raza-core

Cellular simulation tool

Homepage: https://cellular-raza.com/
Documentation: https://docs.rs/cellular_raza-core/
License: GPL-2.0
Latest release: 0.3.0
published 5 months ago

Versions: 26
Dependent Packages: 2
Dependent Repositories: 0
Downloads: 26,943 Total

Rankings

Dependent repos count: 30.7%

Dependent packages count: 36.2%

Forks count: 40.5%

Average: 52.4%

Stargazers count: 56.0%

Downloads: 98.4%

Maintainers (1)

jonaspleyer

Last synced: 4 months ago

crates.io: cellular_raza-core-derive

Cellular simulation tool

Documentation: https://docs.rs/cellular_raza-core-derive/
License: GPL-2.0
Latest release: 0.0.5
published about 2 years ago

Versions: 2
Dependent Packages: 2
Dependent Repositories: 0
Downloads: 2,854 Total

Rankings

Dependent repos count: 30.7%

Dependent packages count: 36.2%

Forks count: 40.5%

Average: 52.4%

Stargazers count: 56.0%

Downloads: 98.4%

Maintainers (1)

jonaspleyer

Last synced: 4 months ago

crates.io: cellular_raza-concepts-derive

Cellular simulation tool

Homepage: https://cellular-raza.com/
Documentation: https://docs.rs/cellular_raza-concepts-derive/
License: GPL-2.0
Latest release: 0.3.0
published 5 months ago

Versions: 26
Dependent Packages: 3
Dependent Repositories: 0
Downloads: 27,093 Total

Rankings

Dependent repos count: 30.7%

Dependent packages count: 36.2%

Forks count: 40.5%

Average: 52.4%

Stargazers count: 56.0%

Downloads: 98.4%

Maintainers (1)

jonaspleyer

Last synced: 4 months ago

crates.io: cellular_raza-building-blocks

cellular_raza Building Blocks

Homepage: https://cellular-raza.com/
Documentation: https://docs.rs/cellular_raza-building-blocks/
License: GPL-2.0
Latest release: 0.3.0
published 5 months ago

Versions: 26
Dependent Packages: 1
Dependent Repositories: 0
Downloads: 26,524 Total

Rankings

Dependent repos count: 30.7%

Dependent packages count: 36.2%

Average: 55.0%

Downloads: 98.1%

Maintainers (1)

jonaspleyer

Last synced: 4 months ago

Dependencies

.github/workflows/test_nightly.yml actions

actions-rs/cargo v1 composite
actions-rs/toolchain v1 composite
actions/checkout v2 composite

.github/workflows/test_stable.yml actions

actions-rs/cargo v1 composite
actions-rs/toolchain v1 composite
actions/checkout v2 composite

Cargo.toml cargo

async-std 1.12
bincode 1.3
chrono 0.4
crossbeam-channel 0.5
hurdles 1.0
indicatif 0.17
itertools 0.10
nalgebra 0.32
ndarray 0.15
num 0.4
ode_integrate 0.0.2
plotters 0.3
rand 0.8
rand_chacha 0.3.1
rayon 1.6
serde 1.0
sled 0.34
typed-sled 0.2
uuid 1.2

cellular_raza-benchmarks/Cargo.toml cargo

criterion 0.4 development
nalgebra 0.32 development
cellular_raza 0.0.5

cellular_raza-building-blocks/Cargo.toml cargo

cellular_raza-concepts/Cargo.toml cargo

cellular_raza-concepts-derive/Cargo.toml cargo

cellular_raza-core/Cargo.toml cargo

cellular_raza-examples/bacteria_population/Cargo.toml cargo

cellular_raza-examples/cell_sorting/Cargo.toml cargo

cellular_raza-examples/organoid_turing_growth/Cargo.toml cargo

cellular_raza-examples/pool_model_pyo3/Cargo.toml cargo

cellular_raza-examples/ureter_signalling/Cargo.toml cargo

cellular_raza-examples/pool_model_pyo3/pyproject.toml pypi

cellular_raza-examples/pool_model_pyo3/requirements.txt pypi

Pillow ==10.1.0
Pygments ==2.16.1
asttokens ==2.4.1
certifi ==2023.7.22
charset-normalizer ==3.3.1
comm ==0.1.4
contourpy ==1.1.1
cycler ==0.12.1
debugpy ==1.8.0
decorator ==5.1.1
executing ==2.0.1
fonttools ==4.43.1
idna ==3.4
importlib ==1.0.4
ipykernel ==6.26.0
ipython ==8.17.0
jedi ==0.19.1
jupyter_client ==8.5.0
jupyter_core ==5.5.0
kiwisolver ==1.4.5
matplotlib ==3.8.0
matplotlib-inline ==0.1.6
maturin ==1.1.0
nest-asyncio ==1.5.8
numpy ==1.26.1
packaging ==23.2
pandas ==1.5.3
parso ==0.8.3
pexpect ==4.8.0
platformdirs ==3.11.0
pooch ==1.8.0
prompt-toolkit ==3.0.39
psutil ==5.9.6
ptyprocess ==0.7.0
pure-eval ==0.2.2
pyparsing ==3.1.1
python-dateutil ==2.8.2
pyvista ==0.42.3
pyzmq ==25.1.1
requests ==2.31.0
scooby ==0.9.2
six ==1.16.0
stack-data ==0.6.3
tornado ==6.3.3
traitlets ==5.13.0
urllib3 ==2.0.7
vtk ==9.2.6
wcwidth ==0.2.8

cellular_raza-examples/template/Cargo.toml cargo

cellular_raza-core-proc-macro/Cargo.toml cargo

.github/workflows/test_beta.yml actions

actions-rs/cargo v1 composite
actions-rs/toolchain v1 composite
actions/checkout v2 composite

cellular_raza-examples/diffusion/Cargo.toml cargo

cellular_raza-homepage/go.mod go

github.com/imfing/hextra v0.7.0

cellular_raza-homepage/go.sum go

github.com/imfing/hextra v0.7.0

cellular_raza-examples/immersed_boundary/Cargo.toml cargo

.github/workflows/docs-header.yml actions

actions/checkout v2 composite

cellular_raza-examples/sender-receiver/Cargo.toml cargo

cellular_raza/Cargo.toml cargo

cellular_raza-building-blocks 0.0.8
cellular_raza-concepts 0.0.8
cellular_raza-core 0.0.8

cellular_raza-examples/semi_vertex/Cargo.toml cargo

cellular_raza-examples/cell_sorting_brownian/Cargo.toml cargo

cellular_raza-examples/bacterial_rods/Cargo.toml cargo

cellular_raza

Science Score: 100.0%

Keywords

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

cellular_raza

Documentation

Getting Started

Contributing

License

Owner

JOSS Publication

cellular_raza: Cellular Agent-based Modeling from a Clean Slate

Authors

Editor

Tags

Citation (CITATION.cff)

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

crates.io: cellular_raza

Rankings

Maintainers (1)

crates.io: cellular_raza-core-proc-macro

Rankings

Maintainers (1)

crates.io: cellular_raza-concepts

Rankings

Maintainers (1)

crates.io: cellular_raza-core

Rankings

Maintainers (1)

crates.io: cellular_raza-core-derive

Rankings

Maintainers (1)

crates.io: cellular_raza-concepts-derive

Rankings

Maintainers (1)

crates.io: cellular_raza-building-blocks

Rankings

Maintainers (1)

Dependencies