Programmatic Model Specification

• Topology
  • Conceptual Overview of Sections
    • Geometry
  • Defining the 3D Shape
    • pt3dclear()
    • pt3dadd()
    • pt3dconst()
    • pt3dstyle()
    • pt3dinsert()
    • pt3dremove()
    • pt3dchange()
  • Reading 3D Data from NEURON
    • n3d()
    • x3d()
    • y3d()
    • z3d()
    • diam3d()
    • arc3d()
    • spine3d()
    • setSpineArea()
    • getSpineArea()
    • define_shape()
    • area()
    • ri()
    • distance()
    • diam_changed
    • L
    • diam
    • Ra
  • Section and Segment Selection
    • Dot notation for properties
    • sec= for functions
    • Default section
  • SectionList
    • SectionList
  • SectionRef
    • SectionRef
  • Section
    • Section.connect()
    • Section.disconnect()
    • Section.nseg
    • Section.orientation()
    • Section.parentseg()
    • Section.cell()
    • Section.hname()
    • Section.name()
    • Section.subtree()
    • Section.wholetree()
  • topology()
  • delete_section()
  • section_exists()
  • section_owner()
  • disconnect()
  • issection()
  • ismembrane()
  • sectionname()
  • secname()
  • psection()
  • parent_section()
  • parent_node()
  • parent_connection()
  • section_orientation()
• Ions
  • ion_style()
  • ion_register()
  • ion_charge()
• Dynamics (Channels, etc…)
  • HOC-based Mechanisms
    • make_pointprocess()
    • make_mechanism()
  • KSChan
    • KSChan
    • KSState
    • KSGate
    • KSTrans
  • LinearMechanism
    • LinearMechanism
  • Point Processes and Artificial Cells
    • General
  • Mechanisms
  • NMODL
    • NEURON Extension to NMODL
    • Model Description Language
• Basic Reaction-Diffusion
  • Overview
    • Related resources
  • Specifying the domain
    • Intracellular regions and regions in Frankenhauser-Hodgkin space
  • Extracellular regions
    • rxd.Extracellular
  • Defining proteins, ions, etc
    • rxd.Species
    • rxd.State
    • rxd.Parameter
  • Defining reactions
    • rxd.Reaction
    • rxd.Rate
    • rxd.MultiCompartmentReaction
    • Mathematical functions for rate expressions
  • Manipulating nodes
    • rxd.nodelist.NodeList
    • rxd.node.Node
    • rxd.node.Node1D
    • rxd.node.Node3D
    • rxd.node.NodeExtracellular
  • Membrane potential
    • rxd.v
  • Synchronization with segments
    • rxd.re_init()
  • Numerical options
    • rxd.nthread()
    • rxd.set_solve_type()
  • SBML Export
    • rxd.export.sbml()
  • Saving and restoring state
  • Error handling
    • rxd.RxDException
• Networks
  • ParallelContext
    • ParallelContext
    • Implementation Notes
    • MPI
    • SubWorld
    • Parallel Network
    • Parallel Transfer
  • ParallelNetManager
    • ParallelNetManager
  • NetCon
    • NetCon
• Electrode
  • Electrode
    • Electrode.IClamp()
    • Electrode.del()
    • Electrode.dur()
    • Electrode.amp()
    • Electrode.VClamp()
    • Electrode.dur0()
    • Electrode.amp0()
    • Electrode.VClampigraph()
    • Electrode.VClampFamily()
    • Electrode.Testlevel()
    • Electrode.Holding()
    • Electrode.Returnlevel()
    • Electrode.Location()
• MechanismType
  • MechanismType
    • MechanismType.select()
    • MechanismType.selected()
    • MechanismType.remove()
    • MechanismType.make()
    • MechanismType.count()
    • MechanismType.menu()
    • MechanismType.action()
    • MechanismType.is_netcon_target()
    • MechanismType.has_net_event()
    • MechanismType.is_artificial()
    • MechanismType.pp_begin()
    • MechanismType.pp_next()
    • MechanismType.internal_type()
    • MechanismType.file()
    • MechanismType.code()
• StateTransitionEvent
  • StateTransitionEvent
    • StateTransitionEvent.state()
    • StateTransitionEvent.transition()
• Obsolete Stimuli
  • fstim()
  • fstimi()
  • fclamp()
  • fclampi()
  • fclampv()
  • prstim()