Skip to main content
Ctrl+K
 - Home

Getting started

  • Installation
  • Tutorials
    • Basics of Jaxley
    • Network simulations in Jaxley
    • Speeding up simulations
    • Building ion channels and synapses
    • Training biophysical models
  • FAQ
    • What kinds of models can be implemented in Jaxley?
    • What units does Jaxley use?

More guides

  • Advanced tutorials
    • Key concepts in Jaxley
    • Defining groups
    • Customizing synaptic parameters
    • Working with morphologies
    • The graph backend
    • Ion dynamics
    • Simplified models
    • Synaptic parameter sharing
  • How-to guide
    • How to save and load cells and networks
    • How to define custom stimuli
    • How to import NMODL channels from NEURON
    • How to set the number of compartments (d_lambda rule)
    • How to edit morphologies
    • How to implement ion diffusion
    • How to choose a solver
  • Examples
    • Fitting an L5PC with gradient descent
  • API reference
    • jaxley.Compartment
    • jaxley.Branch
    • jaxley.Cell
    • jaxley.Network
    • jaxley.integrate
    • jaxley.integrate.build_init_and_step_fn
    • jaxley.utils.dynamics.build_dynamic_state_utils
    • jaxley.read_swc
    • jaxley.morphology.distance_direct
    • jaxley.morphology.distance_pathwise
    • jaxley.morphology.morph_delete
    • jaxley.morphology.morph_connect
    • jaxley.channels.Channel
    • jaxley.channels.HH
    • jaxley.channels.Izhikevich
    • jaxley.channels.Rate
    • jaxley.channels.Fire
    • jaxley.channels.Na
    • jaxley.channels.K
    • jaxley.channels.Leak
    • jaxley.channels.Km
    • jaxley.channels.CaL
    • jaxley.channels.CaT
    • jaxley.pumps.Pump
    • jaxley.pumps.CaFaradayConcentrationChange
    • jaxley.pumps.CaNernstReversal
    • jaxley.pumps.CaPump
    • jaxley.synapses.Synapse
    • jaxley.synapses.IonotropicSynapse
    • jaxley.synapses.TanhRateSynapse
    • jaxley.synapses.TanhConductanceSynapse
    • jaxley.connect.connect
    • jaxley.connect.connectivity_matrix_connect
    • jaxley.connect.fully_connect
    • jaxley.connect.sparse_connect
    • jaxley.optimize.transforms.SigmoidTransform
    • jaxley.optimize.transforms.SoftplusTransform
    • jaxley.optimize.transforms.NegSoftplusTransform
    • jaxley.optimize.transforms.AffineTransform
    • jaxley.optimize.transforms.ChainTransform
    • jaxley.optimize.transforms.MaskedTransform
    • jaxley.optimize.transforms.CustomTransform
    • jaxley.optimize.optimizer.TypeOptimizer
    • jaxley.io.graph.to_swc_graph
    • jaxley.io.graph.build_compartment_graph
    • jaxley.io.graph.vis_compartment_graph
    • jaxley.io.graph.from_graph
    • jaxley.modules.base.to_graph

About the Project

  • Developer notes
    • Contributing
    • Contributor Covenant Code of Conduct
  • Changelog
  • Credits

Advanced tutorials

Navigation

  • General features
  • Morphologies
  • Channels and models
  • Training and optimization

Advanced tutorials#

Our advanced tutorials provide a detailed explanation of different features of Jaxley. If you are looking for brief answers to specific questions, check our how-to guide.

General features#

  • Key concepts in Jaxley
  • Defining groups
  • Customizing synaptic parameters

Morphologies#

  • Working with morphologies
  • The graph backend

Channels and models#

  • Ion dynamics
  • Simplified models

Training and optimization#

  • Synaptic parameter sharing

previous

What units does Jaxley use?

next

Key concepts in Jaxley

Navigation
  • General features
  • Morphologies
  • Channels and models
  • Training and optimization

By Jaxleyverse team

© Copyright 2024, Jaxleyverse team.