semtor.jl
Julia simulation for epithelial-to-mesenchymal transitions (EMT).
Science Score: 41.0%
This score indicates how likely this project is to be science-related based on various indicators:
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✓CITATION.cff file
Found CITATION.cff file -
○codemeta.json file
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○.zenodo.json file
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✓DOI references
Found 1 DOI reference(s) in README -
✓Academic publication links
Links to: biorxiv.org -
○Academic email domains
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (17.4%) to scientific vocabulary
Repository
Julia simulation for epithelial-to-mesenchymal transitions (EMT).
Basic Info
- Host: GitHub
- Owner: SteffenPL
- License: mit
- Language: Julia
- Default Branch: main
- Size: 226 KB
Statistics
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 3
- Releases: 1
Metadata Files
README.md
SEMTor
Julia implementation for a computational model for epithelial-to-mesenchymal transitions-like events in a pseudostratified epithelium.
See the preprint for more details:
S. Plunder, C. Danesin, B. Glise, M. A. Ferreira, S. Merino-Aceituno, E. Theveneau, Modelling variability and heterogeneity of EMT scenarios highlights nuclear positioning and protrusions as main drivers of extrusion. (2023) bioRxiv.
Stand-alone EMT simulator (sEMTor)
For trying the model, one can use the JavaScript version of the simulator: semtor.github.io.
The JavaScript variant implements the same model, but without abilities for data collection. For running scientific simulations and performing parameter studies, please this the Julia version instead.
Installation
The simulator is written in Julia, and can be installed as a Julia package. We recommend to install Julia via juliaup.
We recommend to clone this repository for usage, as it contains also input files.
bash
git clone https://github.com/SteffenPL/sEMTor.jl
julia --project
and then
julia
using Pkg
Pkg.activate(".")
Pkg.instantiate()
This will create a new environment and install all required packages.
Installation as a package
The package can be installed via the Julia package manager via:
julia
using Pkg
Pkg.add("github.com/SteffenPL/sEMTor.jl")
Usage as a GitHub Codespace
This repository is also configured to be used within a GitHub codespace. Just click
on the webpage of the repository on the button Code and select Open with Codespaces.
Example
```julia using SEMTor
p = StaticParameters() # load default parameters (no EMT) ens = simulate_ensemble(p) # run 50 simulations
plot_state(ens[1][end], p) # plot the last state of the first simulation
st = compute_statistics(ens, p)
plot statistical results
using CairoMakie df = st.stats_mean["tissue"]
T = df.time # time X = df.apicalheightmean # mean tissue height Xstd = df.apicalheight_std # standard deviation of tissue height
lines(T, X, axis = (xlabel = "time [hr]", ylabel = "tissue height [5µm]")) band!(T, X - Xstd, X + Xstd, color=(:gray, 0.3)) current_figure() ```
Owner
- Name: Steffen
- Login: SteffenPL
- Kind: user
- Repositories: 4
- Profile: https://github.com/SteffenPL
Citation (CITATION.bib)
@misc{sEMTor.jl,
author = {Steffen Plunder <steffen.plunder@web.de> and contributors},
title = {sEMTor.jl},
url = {https://github.com/SteffenPL/sEMTor.jl},
version = {v1.0.0-DEV},
year = {2024},
month = {2}
}
GitHub Events
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Last Year
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Last synced: 10 months ago
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- Total pull requests: 6
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- Total pull request authors: 1
- Average comments per issue: 0
- Average comments per pull request: 0.0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 6
Past Year
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Top Authors
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