VertexModel.jl

Open a Julia REPL at the project root directory.

Activate environment with using Pkg; Pkg.activate("."), or ] activate..

(If running for the first time) Run Using Pkg; Pkg.instantiate() or ] instantiate.

Load package by running using VertexModel

Once VertexModel.jl has been precompiled, run function vertexModel using default parameters by entering: vertexModel()

Input parameters are optional; use different values other than defaults by running eg. vertexModel(realTimetMax=12345.0)

Possible input parameters: |Variable name: | Default value:| Explanation: | |:----------------------|:--------------|:---------------------------------------------------------------------------------------| |initialSystem | "large" | String specifying initial system state | |nCycles | 1 | Number of cell cycles in run time | |realCycleTime | 86400.0 | Cell cycle time in seconds | |realTimetMax | nCycles*realCycleTime | Total simulation time, overriding specified number of cell cycles | |γ | 0.2 | Parameter in energy relaxation | |L₀ | 0.75 | Preferred cell perimeter length | |A₀ | 1.0 | Cell preferred area | |viscousTimeScale | 1000.0 | Relaxation rate | |pressureExternal | 0.0 | External pressure applied isotropically to system boundary | |peripheralTension | 0.0 | Tension applied to system boundary | |t1Threshold | 0.05 | Edge length at which a T1 transition is triggered | |solver | Tsit5() | Name of integration algorithm to use | |nBlasThreads | 1 | Number of threads used by calls to BLAS functions | |subFolder | "" | Name of subfolder within data directory in which to store results | |outputTotal | 100 | Number of data output instances per simulation | |outputToggle | 1 | Controls whether data are saved from simulation | |frameDataToggle | 1 | Controls whether system data are produced at intermediate time points | |frameImageToggle | 1 | Controls whether images are produced at intermediate time points | |printToggle | 1 | Controls whether updates are printed to command line during runs | |videoToggle | 1 | Controls whether a movie of the simulation is produced at the end | |plotCells | 1 | Plot cell polygons in visualisation | |scatterEdges | 0 | Plot scatter points showing cell edge midpoints in visualisation | |scatterVertices | 0 | Plot scatter points showing vertex locations in visualisation | |scatterCells | 0 | Plot scatter points showing cell centroids in visualisation | |plotForces | 0 | Plot arrows showing resultant internal forces on vertices in visualisation | |plotEdgeMidpointLinks| 0 | If non-zero, use this value to set random seed for simulation | |setRandomSeed | 0 | If non-zero, use this value to set random seed for simulation |