No Description
You can not select more than 25 topics Topics must start with a letter or number, can include dashes ('-') and can be up to 35 characters long.
Gaspard Jankowiak b8a2d6b3f1 [results] save results from before recompute 1 year ago
configs pre/post initialization 1 year ago
configs_metrics no nucleus configs for metrics 1 year ago
initial_conditions config + init torino 1 year ago
plot_data [results] save results from before recompute 1 year ago
src fix config parsing + dir creation 1 year ago
.gitignore add gitignore 1 year ago
Manifest.toml update manifest 1 year ago
Project.toml fix parameters parsing + clean up plotting 1 year ago Debugging nucleus again 1 year ago add 1 year ago add 1 year ago
example_config.yaml add example configuration 1 year ago
go.jl add go file 1 year ago
metrics_nonuc_beta.jl metrics: typo 1 year ago
metrics_nonuc_width.jl add batch files 1 year ago
plot_all_the_plots.jl [results] save results from before recompute 1 year ago
plot_metrics.jl metrics 1 year ago
run.jl project structure 1 year ago


Installation and first run

  • Install Julia 1.0 or newer
  • Clone this repository:

    $ git clone
  • Switch directories and branch:

    $ cd CellSim
    $ git checkout nucleus
  • Download necessary packages: on the Julia prompt, hit ], you should get a prompt:
  • You can now do
    pkg> activate .


    (CellSim) pkg> instantiate
  • At this point you should be able to run the code with
    $ julia --project run.jl configs/straight.yaml

It can take a really long time (30 seconds or more) to start because of the initial loading required.

Configuration files

The models parameters are defined in YAML files located in the configs directory. You can of course copy and edit those. There are a large number of parameters, which are explained in short comments.


If you get an error like the following:

[NSApplication _setup:]
: unrecognized selector sent to instance 0x7f9183705170
2019-01-30 17:23:30.788 julia[2002:154898] *** Terminating app due to uncaught exception 'NSInvalidArgumentException', reason: '-[NSApplication _setup:]: unrecognized selector sent to instance 0x7f9183705170'

in expression starting at /Users/chiaragiverso/CellSim/run.jl:5
__pthread_kill at /usr/lib/system/libsystem_kernel.dylib (unknown line)
Allocations: 104904598 (Pool: 104879133; Big: 25465); GC: 227
Abort trap: 6

you can try installing PyPlot via julia directly:

    julia> ]
    pkg> add Conda