Beginner
Creating a simple cell optimisation
Level: beginner Type: interactive tutorial
This notebook will explain how to set up an optimisation of simple single compartmental cell with two free parameters that need to be optimised. As this optimisation is for example purpose only, no real experimental data is used in this notebook.
Optimisation using the CMA evolutionary strategy
Level: beginner Type: interactive tutorial
This notebook will explain how to optimise a model using the covariance matrix adaptation (CMA) optimisation strategy. BluePyOpt includes two flavors of CMA: a single objective one and a hybrid single/multi objective one.
Optimising synaptic parameters
Level: beginner Type: interactive tutorial
This notebook shows how the parameters of a NEURON point process (in this case a synapse), can be optimised using BluePyOpt.
Intermediate
Creating an optimisation with meta parameters
Level: intermediate Type: interactive tutorial
This notebook will explain how to set up an optimisation that uses metaparameters (parameters that control other parameters)
Setup of a cell model with multi electrode simulation for local field potential recording
Level: intermediate Type: interactive tutorial
This notebook will demonstrate how to instantiate a cell model and evaluator that include local field potential (LFP) computation and its recording using a simulated multi electrode array (MEA).
Exporting a cell in the neuroml format and running it
Level: intermediate Type: interactive tutorial
In this tutorial we will go over how to export a cell to neuroml, create a LEMS simulation able to run the neuroml cell and then how to run the simulation.
Tsodyks-Markram model of short-term synaptic plasticity
Level: intermediate Type: interactive tutorial
In this notebook we demonstrate how to fit the parameters of the Tsodyks-Markram model to a given in vitro somatic recording. The in vitro trace used here shows a typical L5TTPC-L5TTPC depressing connection, kindly provided by Rodrigo Perin (EPFL).
Optimization of burst and tonic firing in thalamo-cortical neurons
Level: intermediate Type: interactive tutorial
In this tutorial we will go over how to set up the cell model and the cell evaluator, run an optimisation and how to analyse optimisation results.
Advanced
Optimisation of a Neocortical Layer 5 Pyramidal Cell
Level: advanced Type: interactive tutorial
This notebook shows you how to optimise the maximal conductance of Neocortical Layer 5 Pyramidal Cell as used in Markram et al. 2015.
Optimisation of a Neocortical Layer 5 Pyramidal Cell in Arbor
Level: advanced Type: interactive tutorial
This notebook shows you how to optimise the maximal conductance of Neocortical Layer 5 Pyramidal Cell as used in Markram et al. 2015 using Arbor as the simulator.