About the NMODL transpiler

Introduction:

• The NMODL Transpiler
  • About NMODL
  • Installation
  • Try NMODL
  • Using the Python API
  • High Level Analysis and Code Generation
  • Documentation
  • Citation
  • Support / Contribuition
  • Examples / Benchmarks
  • Funding & Acknowledgment
• The NEURON MODeling language

Contents:

• Visitors
  • Parsing Model and constructing AST
  • Querying AST objects with Visitors
• Currents
  • NMODL Keywords
• Ions
  • NDMOL Keywords
  • Storage
  • Concentrations
  • Special Case: zero-area nodes
• NMODL “pointers”
  • Integer Variables
• Cable Equation
• Global Variables
  • GLOBAL variables
  • Top-LOCAL variables
  • Thread Variables
  • PARAMETER variables
  • CONSTANT variables
  • What Does CoreNEURON support?
• Longitudinal Diffusion
  • Implementation in NMODL
• Variable timestep integration (CVODE)
  • Implementation in NMODL

Jupyter Notebooks:

• The NMODL Jupyter notebooks
  • About the notebooks
• NMODL Python Interface Tutorial
  • Introduction
  • Parsing Model And Constructing AST
  • Querying AST object with Visitors
    • Lookup visitor
    • Symbol Table Visitor
    • Custom AST visitor
  • Easy code generation using AST visitors
  • Example of CURIE information parsing
• NMODL integration of ODEs
  • KINETIC block
  • DERIVATIVE block
  • LINEAR block
  • NONLINEAR block
• NMODL Kinetic Scheme
  • Reaction Kinetics
  • Law of Mass Action
  • KINETIC block format
  • Other types of reaction statement
  • f_flux / b_flux variables
  • [TODO] CONSERVE
  • Examples
    • Ex. 1
    • Ex. 2
    • Ex. 3
    • Ex. 4
    • Ex. 5
• NMODL SympySolver - cnexp
  • Implementation
  • Pade approximant
  • Implementation Tests
  • Examples
    • Ex. 1
    • Ex. 2
    • Ex. 3
    • Ex. 4
    • Ex. 5
    • Ex. 6
• NMODL SympySolver - sparse
  • Implementation
  • Implementation Tests
  • Examples
    • Ex. 1
    • Ex. 2
• NMODL SympySolver - derivimplicit
  • Implementation
  • Implementation Tests
  • Examples
    • Ex. 1
    • Ex. 2
• NMODL LINEAR solver
• NMODL NONLINEAR solver
  • Newton solver
  • Fall-back solver
• NMODL CONDUCTANCE
  • Introduction
  • Implementation
  • Implementation Tests
  • Examples
    • Ex. 1
    • Ex. 2
    • Ex. 3
    • Ex. 4
    • Ex. 5
    • Ex. 6
    • Ex. 7

Contributing:

• Contributing to the NMODL transpiler
  • Got a Question?
  • Found a Bug?
  • Missing a Feature?
  • Submission Guidelines
  • Development Conventions

Reference:

• Python package
  • Module contents
  • Submodules