tk2-growth-and-decay

https://github.com/jeremyworsfold/tk2-growth-and-decay

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 (8.0%) to scientific vocabulary

Last synced: 6 months ago · JSON representation ·

Repository

Basic Info

Host: GitHub
Owner: jeremyworsfold
License: mit
Language: Julia
Default Branch: main
Size: 18.1 MB

Statistics

Stars: 0
Watchers: 1
Forks: 0
Open Issues: 0
Releases: 0

Created about 1 year ago · Last pushed 8 months ago

Metadata Files

Readme License Citation

Stochastically bistable growth and decay in the Togashi-Kaneko model

Contains a package and scripts written in Julia used to generate the figures for the article located at:

Structure

If you want to just see how the figures have been created at a high level, look at the scripts directory to see the scripts used to create each figure. This also contains formatting presets and functions for the figure aesthetics.

To see how the Gillespie simulations have been done, look at the package TK2.jl in src.

The timeseries figure is made using Catalyst.jl's implementation of the Gillespie algorithm.

For longer simulations a specific Gillespie was written for this system in custom_gillespie.jl with the aggregated values collected inoutputhist.jl. This was done to greatly save on memory and time over the Catalyst implementation by only saving binned histogram information of interest on the molecular counts.

parameters contains the simulation specifications for each figure. The simulations will likely take a long time so T_end can be reduced to obtain results more quickly.

Stochastically bistable growth and decay in the Togashi-Kaneko model figure

Owner

Name: Jeremy Worsfold
Login: jeremyworsfold
Kind: user

Website: https://jeremyworsfold.github.io/
Repositories: 1
Profile: https://github.com/jeremyworsfold

Citation (CITATION.cff)

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
  - family-names: Worsfold
    given-names: Jeremy
    orcid: https://orcid.org/0000-0003-3252-9454
title: "Stochastically bistable growth and decay in the Togashi-Kaneko model"
version: 1.0.0
date-released: 2025-07-09

ecosyste.ms

Data

Tools

Indexes

Applications

Experiments

Open Source Science