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README.md

CellSim

Installation and first run

  • Install Julia 1.0 or newer
  • Clone this repository:

    $ git clone https://gitea.oknaj.eu/gjankowiak/CellSim
    
  • Switch directories and branch:

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

and

    (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.

Troubleshooting

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
    julia>