Add simplecell example #165
Conversation
Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## main #165 +/- ##
==========================================
- Coverage 60.07% 52.45% -7.63%
==========================================
Files 109 124 +15
Lines 7838 10436 +2598
==========================================
+ Hits 4709 5474 +765
- Misses 3129 4962 +1833 ☔ View full report in Codecov by Sentry. |
examples/simplecell/LICENSE.txt
Outdated
There was a problem hiding this comment.
I don't think you have any of these mod files in this example.
There was a problem hiding this comment.
If true, then this file can be removed.
There was a problem hiding this comment.
Good catch, I removed the mod files part but I think we should still keep the part about the morphology, right?
examples/simplecell/final.json
Outdated
There was a problem hiding this comment.
The gpfs pdfs paths can be removed form the file.
There was a problem hiding this comment.
Good catch. Removed in the last commit
| " - `optimisation_params`: Additional optimisation parameters, such as `offspring_size` set to `20`, indicating the number of solutions generated per generation. \n", | ||
| " - `validation_protocols`: Lists protocols used for validation, e.g., `[\"IDrest_0.4\"]`. \n", | ||
| " - `morph_modifiers`: Set to an empty list `[]`, meaning no specific modifications to morphologies are applied by default.\n", | ||
| " - `plot_currentscape`: We set this to False because we are using NEURON's built-in HH mechanism, where the currents are not defined as RANGE variables. As a result, Currentscape is unable to access and plot these currents." |
There was a problem hiding this comment.
It would be nice to add a warning in BPEM when plot_currentscape is True, but we have hh mechanism. This can be done in another PR
There was a problem hiding this comment.
added on in the last commit, let me know if it is alright
examples/simplecell/simplecell.ipynb
Outdated
| "source": [ | ||
| "We can now define the targets which contains the protocols (ecodes) and the features. We define two protocols, `IDrest` and `IV` protocols.\n", | ||
| "\n", | ||
| "For the `IDrest` protocol with an amplitude of 0.2 nA (and 0.4 nA for validation), we select the `Spikecount`, `mean_frequency`, and `voltage_base` capture the neuron's spiking activity and resting potential. In the `IV` protocol, at an amplitude of -0.1 nA, `voltage_base` and `ohmic_input_resistance_vb_ssse` assess the neuron's baseline potential and input resistance. \n", |
There was a problem hiding this comment.
Fixed in the last commit
| " \"validated\": false,\n", | ||
| " \"seed\": 1,\n", | ||
| " \"pdfs\": [\n", | ||
| " \"/gpfs/bbp.cscs.ch/home/ikilic/workspace/BluePyEModel/examples/simplecell/figures/simplecell/optimisation/emodel=simplecell__etype=cADpyr__species=rat__brain_region=SSCX__seed=1__optimisation.pdf\",\n", |
There was a problem hiding this comment.
Can also remove /gpfs paths here after removing them from final.json
There was a problem hiding this comment.
Removed in the last commit
No description provided.