Best practices

Do NOT manually edit files inside inputs.

If parameter values need to be changed, use variations as shown in scripts/GenerateData.jl. Let PhysiCellModelManager.jl manage the databases that track simulation parameters.

If you need to change the structure of an input file, e.g., adding a new rule or editing custom code, create an entire new subdirectory within the relevant inputs subdirectory. If you anticipate doing a lot of this, consider using PhysiCell Studio for your first round of model development and refinement. <!– PhysiCellModelDeveloper.jl could be made to address this though... –>

Suggested practices

Use createProject to create a new PCMM project.

createProject will create a new PCMM project directory with the necessary structure and files. Note: This is a distinct folder from a PhysiCell sample project or user project. If you do not want the template PhysiCell project copied over, use the keyword argument template_as_default=false, i.e.,

createProject("MyNewProject"; template_as_default=false)

Be slow to delete simulations and scripts.

PhysiCellModelManager.jl tracks simulations in a database so that it does not have to re-run simulations that have already been run. This means that adding new simulations to a script and re-running the entire script, including on an HPC, will not run extraneous simulations. Thus, the script can serve as a record of the simulations that have been run, and can be used to reproduce the results at a later date.

If you do need to manually delete simulations–for example, because of an error that prevented the simulation entry in the database updating its record–use the deleteSimulations function to ensure that the database is updated appropriately.

Use version control on inputs and scripts directories.

Alone, these two directories along with the version of PhysiCell can be used to reproduce the results of a project. The createProject function will create a .gitignore file in the data directory to make sure the appropriate files are tracked.