Programmatic Model Specification

• Topology
  • Conceptual Overview of Sections
    • Geometry
  • Defining the 3D Shape
  • Reading 3D Data from NEURON
  • Section and Segment Selection
    • Dot notation
    • Stack of sections
    • Default section
  • SectionList
  • SectionRef
• Ions
• Dynamics (Channels, etc…)
  • HOC-based Mechanisms
  • KSChan
  • LinearMechanism
  • StateTransitionEvent
  • Point Processes and Artificial Cells
    • General
  • Mechanisms
  • NMODL
    • NEURON Extension to NMODL
    • Model Description Language
• Basic Reaction-Diffusion
  • Overview
  • Specifying the domain
    • Intracellular regions and regions in Frankenhauser-Hodgkin space
  • Extracellular regions
  • Defining proteins, ions, etc
  • Defining reactions
    • Mathematical functions for rate expressions
  • Manipulating nodes
  • Membrane potential
  • Synchronization with segments
  • Numerical options
  • Error handling
• Networks
  • ParallelContext
    • Implementation Notes
    • MPI
    • SubWorld
    • Parallel Network
    • Parallel Transfer
  • ParallelNetManager
  • NetCon
• Electrode
• MechanismType
• Obsolete Stimuli