Wiki source code of LFPykit showcase
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| 5 | = LFPykit showcase = | ||
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| 7 | Demonstration on how to run predictions using LFPykit ([[LFPykit.rtfd.io>>url:https://lfpy.rtfd.io/]], [[github.com/LFPy/LFPkit>>url:https://github.com/LFPy/LFPy]]) on the Collaboratory. | ||
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| 9 | The LFPykit module provides electrostatic models in a manner that facilitates forward-model predictions of extracellular potentials and related measures from multicompartment neuron models, but without explicit dependencies on neural simulation software such as NEURON ([[https:~~/~~/neuron.yale.edu>>https://neuron.yale.edu]], [[https:~~/~~/github.com/neuronsimulator/nrn>>https://github.com/neuronsimulator/nrn]]), Arbor ([[https:~~/~~/arbor.readthedocs.io>>https://arbor.readthedocs.io]], [[https:~~/~~/github.com/arbor-sim/arbor>>https://github.com/arbor-sim/arbor]]), and LFPy ([[https:~~/~~/LFPy.readthedocs.io>>https://LFPy.readthedocs.io]], [[https:~~/~~/github.com/LFPy/LFPy>>https://github.com/LFPy/LFPy]]) | ||
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| 11 | To use this material, create a new collab and clone [[https:~~/~~/github.com/LFPy/LFPykit>>https://github.com/LFPy/LFPykit]] into it. | ||
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| 13 | The LFPykit package can be installed as | ||
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| 15 | {{{!pip install . # or !pip install LFPykit}}} | ||
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| 17 | in a jupyter notebook. Different usage with LFPy, NEURON and Arbor are provided in different notebooks located in the examples directory. Missing packages resulting in ImportError and similar can usually be installed issuing | ||
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| 19 | {{{!pip install <missing-package-name>}}} | ||
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| 21 | which may require a kernel restart to take effect. | ||
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| 23 | Using the **Official EBRAINS Docker image** in the Lab is recommended as LFPykit and neural simulators (Arbor, NEURON, LFPy) is preinstalled. For new notebooks/console sessions use the **EBRAINS_experimental_release** (or select this as a kernel and restart when opening notebooks). | ||
| 24 | ))) | ||
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| 31 | = What can I find here? = | ||
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| 33 | * Notice how the table of contents on the right | ||
| 34 | * is automatically updated | ||
| 35 | * to hold this page's headers | ||
| 36 | |||
| 37 | = Who has access? = | ||
| 38 | |||
| 39 | Describe the audience of this collab. | ||
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| 45 | {{box title="**Contents**"}} | ||
| 46 | {{toc/}} | ||
| 47 | {{/box}} | ||
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| 50 | ))) | ||
| 51 | ))) |