Tutorials and Examples

Here is a collection of different tutorials to help you learn GAMer.

PyGAMer Jupyter Notebook Tutorials

• Meshing a protein using PyGAMer
  • Conditioning the protein mesh
  • Now let’s construct a bounding box to represent the cytosol around the protein
  • Tetrahedralizing
• Solving a diffusion PDE on a GAMer mesh using FEniCS
  • Generating the mesh using GAMer
  • Setup the model problem in FEniCS

BlendGAMer Tutorials

• Using BlendGAMer to Refine a Subcellular Model
  • Introduction
  • Import OBJ File into Blender
  • Preliminary Work on Imported Mesh
  • Analyze Mesh, Clean-up, and Repeat
  • Using BlendGAMer to Condition the Mesh
  • Add Boundary Box
  • Using Boolean Modifier
  • Refine Cube with GAMer
  • Adding Cytosolic Boundary
  • Adding Other Boundaries
  • Tetrahedralization
• Modeling Diffusion in the Calcium Release Unit
  • Model of Diffusion With Decay (Strong Formulation)
  • Model of Diffusion With Decay (Weak/Variational Formulation)
  • Solving the Linear Problem Using Dolfin/FEniCS