13. Original STEPS API guides

These guides use the original STEPS API (‘API_1’, see Python interfaces to STEPS).

Contents:

• 13.1. Well-Mixed Reaction Systems
  • 13.1.1. Model Specification
    • 13.1.1.1. Model container
    • 13.1.1.2. Species
    • 13.1.1.3. Volume System
    • 13.1.1.4. Reactions
  • 13.1.2. Preparing geometry for well-mixed simulation
  • 13.1.3. Simulation with Wmdirect
  • 13.1.4. Controlling the simulation
• 13.2. Surface-Volume Reactions (Example: IP3 Model)
  • 13.2.1. Model specification
    • 13.2.1.1. Model container
    • 13.2.1.2. Species
    • 13.2.1.3. Surface System
    • 13.2.1.4. Reactions
  • 13.2.2. Geometry specification
  • 13.2.3. Simulation with Wmdirect
• 13.3. Simulating Diffusion in Volumes
  • 13.3.1. Analytical solution
  • 13.3.2. Modelling solution
    • 13.3.2.1. Organisation of code
    • 13.3.2.2. Model specification
    • 13.3.2.3. Geometry specification
    • 13.3.2.4. Simulation with Tetexact
    • 13.3.2.5. Plotting simulation output
    • 13.3.2.6. Simulation with TetOpSplit
• 13.4. Simulating Diffusion on Surfaces
  • 13.4.1. Analytical solution
  • 13.4.2. Modelling solution
    • 13.4.2.1. Organisation of code
    • 13.4.2.2. Model specification
    • 13.4.2.3. Geometry specification
    • 13.4.2.4. Simulation with Tetexact
    • 13.4.2.5. Plotting simulation output
    • 13.4.2.6. Simulation with TetODE
• 13.5. Diffusion Boundary
  • 13.5.1. Modeling solution
    • 13.5.1.1. Organisation of code
    • 13.5.1.2. Model specification
    • 13.5.1.3. Geometry specification
    • 13.5.1.4. Simulation with Tetexact
    • 13.5.1.5. Plotting simulation output
• 13.6. Surface Diffusion Boundary
  • 13.6.1. Modelling solution
    • 13.6.1.1. Organisation of code
    • 13.6.1.2. Model specification
    • 13.6.1.3. Geometry specification
    • 13.6.1.4. Simulation with Tetexact
    • 13.6.1.5. Plotting simulation output
• 13.7. Simulating Membrane Potential
  • 13.7.1. Markov gating scheme
  • 13.7.2. Modelling solution
    • 13.7.2.1. Organisation of code
    • 13.7.2.2. Model specification
    • 13.7.2.3. Geometry specification
    • 13.7.2.4. Simulation with Tetexact
    • 13.7.2.5. Plotting simulation output
    • 13.7.2.6. Simulation with TetOpSplit
    • 13.7.2.7. Simulation with TetODE
• 13.8. Stochastic Calcium Burst model with GHK currents
  • 13.8.1. Modelling solution
    • 13.8.1.1. extra/constants.py file
    • 13.8.1.2. Command line execution
  • 13.8.2. Model specification
    • 13.8.2.1. Calcium dynamics
    • 13.8.2.2. P-type Calcium channel
    • 13.8.2.3. T-type Calcium channel
    • 13.8.2.4. BK-type Calcium-activated Potassium channel
    • 13.8.2.5. SK-type Calcium-activated Potassium channel
    • 13.8.2.6. Leak channel
  • 13.8.3. Geometry specification
  • 13.8.4. Simulation with Tetexact
    • 13.8.4.1. Initialization
    • 13.8.4.2. Running the simulation
• 13.9. From Serial to Parallel (Parallel TetOpSplit Solver)
  • 13.9.1. Reaction-Diffusion Simulation
    • 13.9.1.1. Replace the modules
    • 13.9.1.2. Partition the mesh
    • 13.9.1.3. Create files for recording
    • 13.9.1.4. Create solver and run the simulation
    • 13.9.1.5. Simulation execution
  • 13.9.2. Complex Mesh Partitioning
  • 13.9.3. Parallel EField Simulation
• 13.10. Visualization Toolkit
  • 13.10.1. Prerequisites
  • 13.10.2. Installation
  • 13.10.3. Examples
    • 13.10.3.1. Visualization of Spatial IP3 Receptor Model
  • 13.10.4. Showcase: Plots and Visual Components
    • 13.10.4.1. Plots
    • 13.10.4.2. Visual Component
• 13.11. SBML support
  • 13.11.1. Introduction
  • 13.11.2. Level of support
    • 13.11.2.1. Supported
    • 13.11.2.2. Not Supported
    • 13.11.2.3. SBML Test Suite
    • 13.11.2.4. Support for MathML
  • 13.11.3. Other considerations
    • 13.11.3.1. Units
    • 13.11.3.2. Default volume
  • 13.11.4. SBML file import solution
    • 13.11.4.1. Structure of code
    • 13.11.4.2. SBML file import
    • 13.11.4.3. Biochemical model and Geometry description
    • 13.11.4.4. Simulation with well-mixed solver
    • 13.11.4.5. Complete code
    • 13.11.4.6. SBML Interface methods
    • 13.11.4.7. Example import function usage
• 13.12. Preliminary Functionalities
  • 13.12.1. meshio: Mesh Input/Output Module
  • 13.12.2. Checkpointing
• 13.13. STEPS for Matlab
  • 13.13.1. Major differences between STEPS and Matlab Simbiology:
  • 13.13.2. Limitations:
  • 13.13.3. Reaction rate units supported:
  • 13.13.4. Compartment volume units supported:
  • 13.13.5. Installation
  • 13.13.6. Dimerisation-decay model
  • 13.13.7. Diffusion between compartments and events
• 13.14. STEPS-CUBIT Geometry Preparation Toolkit
  • 13.14.1. Prerequisites
  • 13.14.2. Installation
    • 13.14.2.1. Independent Installation
    • 13.14.2.2. Integrative Installation
  • 13.14.3. Examples
    • 13.14.3.1. Spatial IP3 Receptor Model
  • 13.14.4. Advanced Topic: Element Selection
    • 13.14.4.1. Direct Selection from Component Panel
    • 13.14.4.2. Direct Box/Polygon Selection with Mouse
    • 13.14.4.3. Indeirect Bounding Object Selection
  • 13.14.5. Other Supporting Functions