Command Line Interface
A Command Line Interface (CLI) is also provided for running long simulations:
Use
It can be used to simulate a sbml model and save the results. For example, this would simulate the model from the file filename.xml for ten units of time, with 1 unit of time between images, and store the results in results.sme:
./spatial-cli filename.xml 10 1 -o results.sme
The file results.sme can be opened in the GUI to see the simulation results.
An existing simulation can also be continued, for example this would simulate 5 more steps of length 1 and append the results to the existing simulation results in results.sme:
./spatial-cli results.sme 5 1
If the output file is not specified it defaults to overwriting the input file.
Multiple time intervals can be specified as semicolon delimited lists, the same as in the GUI. For example:
./spatial-cli results.sme 5;25;10 1;2.5;0.1
Command line parameters
Spatial Model Editor CLI v1.6.0
Usage: ./cli/spatial-cli [OPTIONS] file times image-intervals
Positionals:
file TEXT:FILE REQUIRED The spatial SBML model to simulate
times TEXT REQUIRED The simulation time(s) (in model units of time)
image-intervals TEXT REQUIRED
The interval(s) between saving images (in model units of time)
Options:
-h,--help Print this help message and exit
-s,--simulator ENUM:value in {dune->0,pixel->1} OR {0,1}=0
The simulator to use: dune or pixel
-o,--output-file TEXT The output file to write the results to. If not set, then the input file is used.
-n,--nthreads UINT:NONNEGATIVE=0
The maximum number of CPU threads to use (0 means unlimited)
-v,--version Display program version information and exit
-d,--dump-config Dump the default config ini file and exit
-c,--config Read an ini file containing simulation options
Using a config file
To create an ini file with the default options
./spatial-cli -d > config.ini
You can then edit this file as desired, and use it when running a simulation
./spatial-cli filename.xml -c config.ini