EXAMPLE_DIRECTORY.md

Example Directory

This file contains a directory to all GillesPy2 and SpatialPy example notebooks.

GillesPy2

"Start Here" Model

Starting Models

• Michaelis Menten

  • SSA C Solver
  • SSA NumPy Solver
  • Tau Leaping NumPy
  • Tau Hybrid NumPy

• Vilar Oscillator

  • SSA
  • Tau Leaping
  • Tau Hybrid

Results Management

• Basic Results Management
• Single Trajectory to CSV
• Multiple Trajectories to CSV
• Using Pickle

Data Visualization

• Data Visualization
• Live Output

Advanced Features

• Events
• Kinetic Model for Styrene Polymerization
• Photosynthesis
• GillesPy2 in Parallel
• SBML Import
• Variable Inputs (SSA)
• Volume Test
• Hybrid Continuous Species
• Hybrid Switching
• Parameter Changing

Extra Models

• Brusselator
• Genetic Toggle Switch
• Opioid Model
• Oregonator
• Tyson Oscillator
• Degradation Model
• Dimer Model
• Tyson Oscillator

SpatialPy

General Examples

• Bistable Elf Ehrenberg
• Boundary Conditions
• SpatialPy Gravity
• Coral Reef
• 3D Cylinder Diffusion
• hes1
• Lid Driven Cavity
• MinCDE
• Turing Pattern (Old)
• Turing Pattern (New)
• Weir
• Yeast Polarization
  • G-Protein 1D
  • Polarisome 1D
  • cdc42

Tests

• Diffusion Validation
• Spatial Birth-Death
• Compile Time Test
• Read Meshes