C Software usage

C.1 Undergraduate research project

This code base is using the R Language and renv to make a reproducible scientific project named undergraduate_research_project.

1. Clone the repository with: git clone https://github.com/jvelezmagic/undergraduate_research_project.
2. Download latest version of R.
3. Open R project.
4. Install the renv package with install.packages('renv').
5. Restore working environment with: renv::restore().
6. Render the book with: bookdown::render_book().
7. Edit documents and render again.

C.2 Cell-viewer

This code base is using the Python Language.

1. Clone the repository with: git clone https://github.com/ccg-esb-lab/uJ.
2. Go to single-channel directory.
3. Inside of MGGT-AMP-Pulse (i.e., chromosome strain) or pBGT-AMP-Pulse (i.e., plasmid strain) enter to 6_Lineages_corrector_napari.ipynb.
4. Change the parameters and use it.

C.3 Filamentation model

This code base is using the Julia Language and DrWatson to make a reproducible scientific project named CellFilamentation.

1. Clone the repository with: git clone https://github.com/jvelezmagic/CellFilamentation.
2. Download latest version of Julia.
3. Open Julia project.
4. Open Julia console and do the following to restore working environment:

using Pkg
Pkg.activate(".") # Path to the project.
Pkg.instantiate()

5. Play with the model.