This program is a PDE simulator for SBML models. By using this program, users may simulate their spatially extended SBML models. There is also an image that runs on docker, so please refer to that as well.
% git clone /path/to/spatial_simulator
% cd Spatial_Simulator
% make% ./spatialsimulator -t 0.1 -d 0.001 -o 10 /path/to/sampledfield_model.xml
% ./spatialsimulator -x 100 -y 100 -z 100 -m 0.1 -t 10 -d 0.001 -o 500 -c 0 -C 5 -s z30 /path/to/analytic_model.xmlSimulation results will be generated under result/${model_name} directory.
| Options | Definitions |
|---|---|
| -h | display usage |
| -x #(int) | the number of points at x coordinate (for analytic geometry only) (ex. -x 200 (default:100)) |
| -y #(int) | the number of points at y coordinate (for analytic geometry only) (ex. -y 200 (default:100)) |
| -z #(int) | the number of points at z coordinate (for analytic geometry only) (ex. -z 200 (default:100)) |
| -m #(double) | mesh size between {x,y,z} coordinate (ex. -m 0.15) |
| -t #(double) | simulation time (ex. -t 10) (default:1.0) |
| -d #(double) | delta t (ex. -d 0.1) (default:0.01) |
| -o #(int) | output results every # steps (ex. -o 10) (default:1) |
| -c #(double) | min of color bar range (ex. -c 1) (default:0.0) |
| -C #(double) | max of color bar range (ex. -C 10) (default:Max value of InitialConcentration or InitialAmount) |
| -s char#(int) | select which dimension {x,y,z} and the number of slice to output (only 3D) (ex. -s z10 means output xy plane where z = 10) |
| -O outDir | path to output directory (default:"result") |
| model.xml | Target SBML Model |
This software is released under the MIT License, see LICENSE.txt.