Create, Simulate, Visualize, and Analyze Realistic 3D Cell Models
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META-INF
bng
data_plotters
developer_utilities
icons
io_mesh_mcell_mdl
mdl
test_suite
.gitignore
CHANGELOG.md
README.md
SimControl.c
SimControl.java
__init__.py
cellblender_id.py
cellblender_molecules.py
cellblender_operators.py
cellblender_panels.py
cellblender_properties.py
cellblender_source_info.py
data_model.py
glyph_library.blend
makefile
object_surface_regions.py
parameter_system.py
run_simulations.py
run_wrapper.py
sim_runner_queue.py
utils.py

README.md

CellBlender 1.0.1

Introduction:

CellBlender development is supported by the NIGMS-funded (P41GM103712) National Center for Multiscale Modeling of Biological Systems (MMBioS).

CellBlender is an addon for Blender (2.6x-2.7x) to create computational cell biology models for use in MCell and potentially other cell simulation biophysics engines. In CellBlender 1.0.1 you can define molecules and reactions, create geometric objects, define named surface regions on the objects, assign properties to those regions, run an MCell simulation based off of the CellBlender project, create plots of said simulation, visualize an animation of the molecule trajectories, and render the results. MDL import currently only supports mesh data, but full support will be added in future versions of CellBlender.

One goal for CellBlender is to provide a comprehensive model building and visualization environment which completely encapsulates all of MCell's MDL language in GUI form such that the user need not ever edit an MDL file by hand (or even know that such files exist). CellBlender is already nearly feature complete with respect to MCell, but there may still be a few minor ones missing for now.

Installing CellBlender Addon:

Startup Blender and go to the File->User Preferences menu. In the User Preferences control panel choose the Addons tab. Click the Install from File button at the bottom of the window. Navigate to the unextracted zip file that you downloaded (cellblender_v1.0.1.zip), select it, and click the Install from File button near the upper-right hand corner.

Activating CellBlender Addon in Blender:

In the Addons panel scroll down till you see Cell Modeling: CellBlender and check the check box to enable it. Then click Save as Default to enable the addon permanently in Blender for any future projects you make.

Using CellBlender:

For detailed instructions with images, please see http://mcell.org/tutorials/. If you have any questions about CellBlender, feel free to ask us at http://mmbios.org/index.php/mcell-cellblender-forum/.

Additional notes:

If you are hand-editing MDLs, note that CELLBLENDER mode VIZ_OUTPUT will output molecules but will not output meshes. We assume that your meshes are already present in your CellBlender/Blender project. The philosophy here is that the CellBlender/Blender project IS your MCell project and that the MCell compute kernel is a physics engine driving the dynamics of objects created and visualized in Blender.

Depending on your graphics hardware beware, of exporting more than 10000 molecules or so, if you want good performance (>10 frames per second) in CellBlender playback. But if your goal is to render a movie you should be able to export and render many 100s of thousands of molecules per frame with CellBlender.