Welcome to SiNAPS’s documentation!

Sinaps is a Python package providing a fast, flexible and expressive tool to model signal propagation and ionic electrodiffusion in neurons. It is an efficient framework to build computational models of voltage and calcium dynamics. It is based on the Cable theory for voltage propagation, and the Nernst-Plank equation for the electrodiffusion of ions.

Figure 1 : Voltage propagation in neuron triggered by synaptic action potential.

Contributing

Please ask questions and submit bugs or feature requests on the git-hub issue tracker or contact claire.guerrier@univ-cotedazur.fr.

Credits

Sinaps is currently developped in the LJAD, Université Côte d’Azur, Nice, France.

Site map

GETTING STARTED

• Installation
  • Via Python Package
  • Installation troubleshooting
• Conventions
  • Units
• Overview
  • Object creation
  • Running simulation
  • Viewing results

TUTORIALS

• Reaction Diffusion
  • Initialization
  • Chemical reactions
  • Running electro diffusion simulatiom
  • Plotting results
• Complex Geometry
  • Creating Neuron structure from swc file
  • Accessing data
  • Modeling synapses
  • Running the simulation
  • Plotting

IN DEPTH

• Data structure
  • Section
  • Channels
  • Neuron
  • Simulation
  • Species
• Plotting
  • Neuronal geometry
  • Potential
  • Plotting the currents
  • Plotting the species dynamics
• Customizing channels
  • Setting up the channels
  • Running the simu
  • Plots
  • Running the calcium dynamics
  • Plots
• Model Description
  • Notations
  • Derivation of the discretized Cable equation in branches
  • Derivation of the discretized Cable equation at junctions
  • Derivation of the discretized Nernst-Planck equation
  • Implementation of chemical reactions
  • Bibliography
• API Reference
  • Section
  • Neuron
  • Simulation
  • Channels
  • I/O
• GitHub