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Feat: Improve readme #55

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26 changes: 23 additions & 3 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -6,17 +6,37 @@ Generalisation of neuronal electrical models on a morphological population with

This code accompanies the paper:

[Arnaudon, A., Reva, M., Zbili, M., Markram, H., Van Geit, W., & Kanari, L. (2023). Controlling morpho-electrophysiological variability of neurons with detailed biophysical models. iScience, 2023.](https://www.cell.com/iscience/fulltext/S2589-0042(23)02299-X)
[Arnaudon, A., Reva, M., Zbili, M., Markram, H., Van Geit, W., & Kanari, L. (2023). Controlling morpho-electrophysiological variability of neurons with detailed biophysical models. iScience, 2023.](https://www.cell.com/iscience/fulltext/S2589-0042%2823%2902299-X)

## Installation

This code can be installed via [pip](https://pip.pypa.io/en/stable/) with
This code can be installed via [pip](https://pip.pypa.io/en/stable/) from pypi with

```
pip install emodel-generalisation
```

or from github with

```
git clone git@github.com:BlueBrain/emodel-generalisation.git
pip install .
```

## Documentation

The documentation can be found here: https://emodel-generalisation.readthedocs.io/en/latest/

## Code structure

This code contains several modules, the most important are:
* [model](emodel_generalisation/model) contains an adapted version of BlueBrain/BluePyEmodel core functionalities for evaluating electrical models, built on top of BlueBrain/BluePyOpt
* [tasks](emodel_generalisation/tasks) contains the luigi workflows to run MCMC, adapt and generalise electrical model
* [bluecellulab_evaluator](emodel_generalisation/bluecellulab_evaluator.py) contains functions to compute currents with BlueBrain/BlueCelluLab and hoc files of models
* [mcmc](emodel_generalisation/mcmc.py) contains the code to run MCMC sampling of electrical models
* [information](emodel_generalisation/information.py) contains some WIP code to compute information theory measures on sampled electrical models


## Examples

We provide several examples of the main functionalities of the ```emodel-generalisation``` code:
Expand All @@ -28,7 +48,7 @@ We provide several examples of the main functionalities of the ```emodel-general

## Citation

When you use the ``emodel-generalisation`` code or method for your research, we ask you to [cite](https://www.cell.com/iscience/fulltext/S2589-0042(23)02299-X):
When you use the ``emodel-generalisation`` code or method for your research, we ask you to [cite](https://www.cell.com/iscience/fulltext/S2589-0042%2823%2902299-X):

> Arnaudon, A., Reva, M., Zbili, M., Markram, H., Van Geit, W., & Kanari, L. (2023). Controlling morpho-electrophysiological variability of neurons with detailed biophysical models. iScience, 2023.

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