libCellML Hodgkin-Huxley Tutorials

This set of tutorials takes the user progressively through different aspects of the libCellML functionality while building towards a model of Hodgkin and Huxley’s squid axon activation. It is aimed at users who are already familiar with the concept of CellML and modelling.

For more information on the theoretical background behind these steps, please see the Theory pages.

• Hodgkin-Huxley 1: Creating a model using the API
  • Overview
  • Step 1: Set up the model
  • Step 2: Create the gateEquations component
  • Step 3: Validate the model
  • Step 4: Add the variables
  • Step 5: Add the units
  • Step 6: Analyse the mathematical construction of the model
  • Step 7: Sanity check
  • Step 8: Serialise and output the model
• Hodgkin-Huxley 2: Creating a model which uses imports
  • Step 1: Create the model
  • Step 2: Create a potassium channel equations component
  • Step 3: Create the nGate and its child components
  • Step 4: Specify imports for the generic gate components
  • Step 5: Specify imports for the controller component
  • Step 6: Analyse the model
  • Step 7: Define the constants
  • Step 8: Connect the input variables
  • Step 9: Connect the calculated variables
  • Step 10: Connect to imported components
  • Step 11: Output the model
• Hodgkin-Huxley 3: Debugging a model
  • Overview
  • Step 1: Parse the existing sodium channel model
  • Step 2: Validate the parsed model
  • Step 3: Repair the parsed model
  • Step 4: Resolve the model’s imports
  • Step 5: Validate the imported dependencies
  • Step 6: Analyse the model(s)
  • Step 7: Serialise and print the repaired model
• Hodgkin-Huxley 4: Generating code from a model
  • Step 1: Parse the existing membrane model
  • Step 2: Resolve the imports and flatten
  • Step 3: Validate and analyse the flattened model
  • Step 4: Generate code and output
• Hodgkin-Huxley 5: Interact with generated code
  • Step 1: Link to the generated code
  • Step 2: Access the variables in the generated files
  • Step 3: Access the functions in the generated files
  • Step 4: Iterate through the solution
  • Step 5: Sanity check