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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 upgrade to version
1.0
How to save and load cells and networks
How to choose a solver
How to set the number of compartments (d_lambda rule)
How to edit morphologies
How to import
NMODL
channels from
NEURON
How to define custom stimuli
How to connect synapses to pre-defined spike trains
How to implement ion diffusion
Examples
Fitting an L5PC with gradient descent
Fitting an SNN to do a Classification Task
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.Na
jaxley.channels.K
jaxley.channels.Leak
jaxley.channels.Izhikevich
jaxley.channels.Rate
jaxley.channels.Fire
jaxley.pumps.Pump
jaxley.pumps.CaFaradayConcentrationChange
jaxley.pumps.CaNernstReversal
jaxley.pumps.CaPump
jaxley.synapses.Synapse
jaxley.synapses.CurrentSynapse
jaxley.synapses.ConductanceSynapse
jaxley.synapses.DynamicSynapse
jaxley.synapses.IonotropicSynapse
jaxley.synapses.SpikeSynapse
jaxley.synapses.AlphaSynapse
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
jaxley.solver_gate.save_exp
jaxley.solver_gate.solve_gate_implicit
jaxley.solver_gate.solve_gate_exponential
jaxley.solver_gate.exponential_euler
jaxley.solver_gate.heaviside
About the Project
Developer notes
Contributing
Contributor Covenant Code of Conduct
Changelog
Credits
FAQ
FAQ
#
What kinds of models can be implemented in Jaxley?
What units does Jaxley use?
