PhysiCellModelManager.jl

Check out Getting started for a quick guide to using PhysiCellModelManager.jl. Make sure you are familiar with the Best practices section before using PhysiCellModelManager.jl.

Quick start

See Getting started for more details.

1. Install Julia.
2. Ensure the general registry is added:

pkg> registry add General

3. Add the BergmanLabRegistry:

pkg> registry add https://github.com/drbergman-lab/BergmanLabRegistry

4. Install PhysiCellModelManager.jl:

pkg> add PhysiCellModelManager

5. Create a new project:

julia> using PhysiCellModelManager
julia> createProject()

6. Import a project:

julia> initializeModelManager()
julia> importProject("path/to/project_folder") # replace with the path to your project folder

7. Check the output of Step 5 and record your input folders:

julia> config_folder = "my_project" # replace these with the name from the output of Step 5
julia> custom_code_folder = "my_project"
julia> rules_folder = "my_project" 
julia> inputs = InputFolders(config_folder, custom_code_folder; rulesets_collection = rules_folder) # also add ic_cell and ic_substrate if used

8. Run the model:

julia> out = run(inputs; n_replicates = 1)

9. Check the output:

julia> using Plots # make sure to install Plots first
julia> plot(out)
julia> plotbycelltype(out)

10. Vary parameters:

julia> xml_path = configPath("some_cell_type", "apoptosis", "death_rate") # replace with a cell type in your model
julia> new_apoptosis_rates = [1e-5, 1e-4, 1e-3]
julia> dv = DiscreteVariation(xml_path, new_apoptosis_rates)
julia> out = run(inputs, dv; n_replicates = 3) # 3 replicates per apoptosis rate => 9 simulations total