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Changes for page BluePyOpt

Last modified by abonard on 2025/06/13 16:05
From version 53.1
edited by abonard
on 2025/06/13 16:05
Change comment: There is no comment for this version
To version 57.1
edited by abonard
on 2025/06/13 16:05
Change comment: There is no comment for this version

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4 4  
5 5  * ((( ==== **[[Intermediate >>||anchor = "HIntermediate-1"]]** ==== )))
6 6  
7 +* ((( ==== **[[Advanced >>||anchor = "HAdvanced-1"]]** ==== )))
8 +
7 7  === **Beginner** ===
8 8  
9 9  === [[Creating a simple cell optimisation>>https://github.com/BlueBrain/BluePyOpt/blob/master/examples/simplecell/simplecell.ipynb||rel=" noopener noreferrer" target="_blank"]] ===
... ... @@ -43,4 +43,26 @@
43 43  **Level**: intermediate(%%) **Type**: interactive tutorial
44 44  
45 45  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).
48 +=== [[Optimization of burst and tonic firing in thalamo-cortical neurons>>https://github.com/BlueBrain/BluePyOpt/blob/master/examples/thalamocortical-cell/thalamocortical-cell_opt.ipynb||rel=" noopener noreferrer" target="_blank"]] ===
46 46  
50 +**Level**: intermediate(%%) **Type**: interactive tutorial
51 +
52 +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.
53 +=== **Advanced** ===
54 +
55 +=== [[Optimisation of a Neocortical Layer 5 Pyramidal Cell>>https://github.com/BlueBrain/BluePyOpt/blob/master/examples/l5pc/L5PC.ipynb||rel=" noopener noreferrer" target="_blank"]] ===
56 +
57 +**Level**: advanced(%%) **Type**: interactive tutorial
58 +
59 +This notebook shows you how to optimise the maximal conductance of Neocortical Layer 5 Pyramidal Cell as used in Markram et al. 2015.
60 +=== [[Optimisation of a Neocortical Layer 5 Pyramidal Cell in Arbor>>https://github.com/BlueBrain/BluePyOpt/blob/master/examples/l5pc/L5PC_arbor.ipynb||rel=" noopener noreferrer" target="_blank"]] ===
61 +
62 +**Level**: advanced(%%) **Type**: interactive tutorial
63 +
64 +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.
65 +=== [[Simulating optimized cell models in Arbor and cross-validation with Neuron>>https://github.com/BlueBrain/BluePyOpt/blob/master/examples/l5pc/l5pc_validate_neuron_arbor.ipynb||rel=" noopener noreferrer" target="_blank"]] ===
66 +
67 +**Level**: advanced(%%) **Type**: interactive tutorial
68 +
69 +This notebook demonstrates how to run a simulation of a simple single compartmental cell with fixed/optimized parameters in Arbor. We follow the standard BluePyOpt flow of setting up an electrophysiological experiment and export the cell model to a mixed JSON/ACC-format. We then cross-validate voltage traces obtained with Arbor with those from a Neuron simulation.
70 +