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1D.py
1D_biased_walk.py
README
blender_parameters.py

README

1. To run an example of 1D random walk on a filament:
   $ ecell3-session 1D.py

2. To view the simulation results wth the Spatiocyte Visualizer:
   $ spatiocyte

3. To create a movie of the simulation results generated by matplotlib
   (requires matplotlib and avconv preinstalled):
   $ python ../plot/plotCoordinateLog.py

4. To view the movie, we can use the VLC player (requires VLC preinstalled):
   $ vlc CoordinateLog.csv.mov 

5. To create high quality frames using Blender, warning, this may take a lot of
   computational time (requires Blender preinstalled):
   $ blender --background --python ../blender/blender.py

6. To create a movie of those frames and view it:
   $ avconv -i image%04d.png -vcodec qtrle blender.mov
   $ vlc blender.mov

7. To increase resolution and quality of the rendering, change the following
   lines in blender_parameters.py:
   resolution_percentage = 100
   render_samples = 100
   $ blender --background --python ../blender/blender.py

8. To save a rendered frame session as a Blender file for future modification
   with Blender:
   $ blender --background --python ../blender/save_blender_file.py

9. To run an example of biased 1D random walk on a filament:
   $ ecell3-session 1D_biased_walk.py

10. To view microscopy snapshots of the biased walk with Spatiocyte Visualizer
   $ spatiocyte MicroscopyLog.dat