# Biologically Detailed Brain Cell Modeling in JAX
<p align="center">
<img alt="Header image of BrainCell." src="https://raw.githubusercontent.com/chaobrain/braincell/main/docs/_static/braincell.png" width=50%>
</p>
<p align="center">
<a href="https://pypi.org/project/braincell/"><img alt="Supported Python Version" src="https://img.shields.io/pypi/pyversions/braincell"></a>
<a href="https://github.com/chaobrain/braincell/blob/main/LICENSE"><img alt="LICENSE" src="https://img.shields.io/badge/License-Apache%202.0-blue.svg"></a>
<a href='https://braincell.readthedocs.io/en/latest/?badge=latest'>
<img src='https://readthedocs.org/projects/braincell/badge/?version=latest' alt='Documentation Status' />
</a>
<a href="https://badge.fury.io/py/braincell"><img alt="PyPI version" src="https://badge.fury.io/py/braincell.svg"></a>
<a href="https://github.com/chaobrain/braincell/actions/workflows/CI.yml"><img alt="Continuous Integration" src="https://github.com/chaobrain/braincell/actions/workflows/CI.yml/badge.svg"></a>
<a href="https://doi.org/10.5281/zenodo.14969987"><img src="https://zenodo.org/badge/825447742.svg" alt="DOI"></a>
</p>
[braincell](https://github.com/chaobrain/braincell) provides a unified interface for modeling single-compartment and multi-compartment Hodgkin-Huxley-styled neuron models.
It is built on top of [JAX](https://github.com/jax-ml/jax) and [brainstate](https://github.com/chaobrain/brainstate), offering a highly parallelized and efficient simulation
of biophysically detailed brain cell models.
## Quick start
Here is an example to model the **single-compartment** thalamus neuron model by using the interface of `braincell.SingleCompartment`:
```python
import braincell
import brainstate
import brainunit as u
class HTC(braincell.SingleCompartment):
def __init__(self, size, solver: str = 'ind_exp_euler'):
super().__init__(size, V_initializer=brainstate.init.Constant(-65. * u.mV), V_th=20. * u.mV, solver=solver)
self.na = braincell.ion.SodiumFixed(size, E=50. * u.mV)
self.na.add(INa=braincell.channel.INa_Ba2002(size, V_sh=-30 * u.mV))
self.k = braincell.ion.PotassiumFixed(size, E=-90. * u.mV)
self.k.add(IKL=braincell.channel.IK_Leak(size, g_max=0.01 * (u.mS / u.cm ** 2)))
self.k.add(IDR=braincell.channel.IKDR_Ba2002(size, V_sh=-30. * u.mV, phi=0.25))
self.ca = braincell.ion.CalciumDetailed(size, C_rest=5e-5 * u.mM, tau=10. * u.ms, d=0.5 * u.um)
self.ca.add(ICaL=braincell.channel.ICaL_IS2008(size, g_max=0.5 * (u.mS / u.cm ** 2)))
self.ca.add(ICaN=braincell.channel.ICaN_IS2008(size, g_max=0.5 * (u.mS / u.cm ** 2)))
self.ca.add(ICaT=braincell.channel.ICaT_HM1992(size, g_max=2.1 * (u.mS / u.cm ** 2)))
self.ca.add(ICaHT=braincell.channel.ICaHT_HM1992(size, g_max=3.0 * (u.mS / u.cm ** 2)))
self.kca = braincell.MixIons(self.k, self.ca)
self.kca.add(IAHP=braincell.channel.IAHP_De1994(size, g_max=0.3 * (u.mS / u.cm ** 2)))
self.Ih = braincell.channel.Ih_HM1992(size, g_max=0.01 * (u.mS / u.cm ** 2), E=-43 * u.mV)
self.IL = braincell.channel.IL(size, g_max=0.0075 * (u.mS / u.cm ** 2), E=-70 * u.mV)
```
Here is an example to model the **multi-compartment** neuron model by using the interface of `braincell.MultiCompartment`:
```python
import braincell
import brainstate
import brainunit as u
class HTC(braincell.MultiCompartment):
def __init__(self, size, solver: str = 'staggered'):
morphology = braincell.Morphology.from_swc(...)
super().__init__(size,
morphology=morphology, # the only difference from SingleCompartment
V_initializer=brainstate.init.Constant(-65. * u.mV),
V_th=20. * u.mV,
solver=solver)
self.na = braincell.ion.SodiumFixed(size, E=50. * u.mV)
self.na.add(INa=braincell.channel.INa_Ba2002(size, V_sh=-30 * u.mV))
self.k = braincell.ion.PotassiumFixed(size, E=-90. * u.mV)
self.k.add(IDR=braincell.channel.IKDR_Ba2002(size, V_sh=-30. * u.mV, phi=0.25))
```
## Installation
You can install ``braincell`` via pip:
```bash
pip install braincell --upgrade
```
Alternatively, you can install `BrainX`, which bundles `braincell` with other compatible packages for a comprehensive brain modeling ecosystem:
```bash
pip install BrainX -U
```
## Documentation
The official documentation is hosted on Read the Docs: [https://braincell.readthedocs.io](https://braincell.readthedocs.io)
## See also the brain modeling ecosystem
We are building the brain modeling ecosystem: https://brainmodeling.readthedocs.io/
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"description": "\r\n\r\n# Biologically Detailed Brain Cell Modeling in JAX\r\n\r\n<p align=\"center\">\r\n \t<img alt=\"Header image of BrainCell.\" src=\"https://raw.githubusercontent.com/chaobrain/braincell/main/docs/_static/braincell.png\" width=50%>\r\n</p> \r\n\r\n\r\n\r\n<p align=\"center\">\r\n\t<a href=\"https://pypi.org/project/braincell/\"><img alt=\"Supported Python Version\" src=\"https://img.shields.io/pypi/pyversions/braincell\"></a>\r\n\t<a href=\"https://github.com/chaobrain/braincell/blob/main/LICENSE\"><img alt=\"LICENSE\" src=\"https://img.shields.io/badge/License-Apache%202.0-blue.svg\"></a>\r\n <a href='https://braincell.readthedocs.io/en/latest/?badge=latest'>\r\n <img src='https://readthedocs.org/projects/braincell/badge/?version=latest' alt='Documentation Status' />\r\n </a> \t\r\n <a href=\"https://badge.fury.io/py/braincell\"><img alt=\"PyPI version\" src=\"https://badge.fury.io/py/braincell.svg\"></a>\r\n <a href=\"https://github.com/chaobrain/braincell/actions/workflows/CI.yml\"><img alt=\"Continuous Integration\" src=\"https://github.com/chaobrain/braincell/actions/workflows/CI.yml/badge.svg\"></a>\r\n <a href=\"https://doi.org/10.5281/zenodo.14969987\"><img src=\"https://zenodo.org/badge/825447742.svg\" alt=\"DOI\"></a>\r\n</p>\r\n\r\n\r\n\r\n[braincell](https://github.com/chaobrain/braincell) provides a unified interface for modeling single-compartment and multi-compartment Hodgkin-Huxley-styled neuron models. \r\nIt is built on top of [JAX](https://github.com/jax-ml/jax) and [brainstate](https://github.com/chaobrain/brainstate), offering a highly parallelized and efficient simulation \r\nof biophysically detailed brain cell models.\r\n\r\n\r\n\r\n\r\n\r\n\r\n## Quick start\r\n\r\n\r\nHere is an example to model the **single-compartment** thalamus neuron model by using the interface of `braincell.SingleCompartment`:\r\n\r\n```python\r\nimport braincell\r\nimport brainstate\r\nimport brainunit as u\r\n\r\nclass HTC(braincell.SingleCompartment):\r\n def __init__(self, size, solver: str = 'ind_exp_euler'):\r\n super().__init__(size, V_initializer=brainstate.init.Constant(-65. * u.mV), V_th=20. * u.mV, solver=solver)\r\n\r\n self.na = braincell.ion.SodiumFixed(size, E=50. * u.mV)\r\n self.na.add(INa=braincell.channel.INa_Ba2002(size, V_sh=-30 * u.mV))\r\n\r\n self.k = braincell.ion.PotassiumFixed(size, E=-90. * u.mV)\r\n self.k.add(IKL=braincell.channel.IK_Leak(size, g_max=0.01 * (u.mS / u.cm ** 2)))\r\n self.k.add(IDR=braincell.channel.IKDR_Ba2002(size, V_sh=-30. * u.mV, phi=0.25))\r\n\r\n self.ca = braincell.ion.CalciumDetailed(size, C_rest=5e-5 * u.mM, tau=10. * u.ms, d=0.5 * u.um)\r\n self.ca.add(ICaL=braincell.channel.ICaL_IS2008(size, g_max=0.5 * (u.mS / u.cm ** 2)))\r\n self.ca.add(ICaN=braincell.channel.ICaN_IS2008(size, g_max=0.5 * (u.mS / u.cm ** 2)))\r\n self.ca.add(ICaT=braincell.channel.ICaT_HM1992(size, g_max=2.1 * (u.mS / u.cm ** 2)))\r\n self.ca.add(ICaHT=braincell.channel.ICaHT_HM1992(size, g_max=3.0 * (u.mS / u.cm ** 2)))\r\n\r\n self.kca = braincell.MixIons(self.k, self.ca)\r\n self.kca.add(IAHP=braincell.channel.IAHP_De1994(size, g_max=0.3 * (u.mS / u.cm ** 2)))\r\n\r\n self.Ih = braincell.channel.Ih_HM1992(size, g_max=0.01 * (u.mS / u.cm ** 2), E=-43 * u.mV)\r\n self.IL = braincell.channel.IL(size, g_max=0.0075 * (u.mS / u.cm ** 2), E=-70 * u.mV)\r\n\r\n```\r\n\r\n\r\nHere is an example to model the **multi-compartment** neuron model by using the interface of `braincell.MultiCompartment`:\r\n\r\n\r\n```python\r\nimport braincell\r\nimport brainstate\r\nimport brainunit as u\r\n\r\n\r\nclass HTC(braincell.MultiCompartment):\r\n def __init__(self, size, solver: str = 'staggered'):\r\n morphology = braincell.Morphology.from_swc(...)\r\n super().__init__(size, \r\n morphology=morphology, # the only difference from SingleCompartment\r\n V_initializer=brainstate.init.Constant(-65. * u.mV), \r\n V_th=20. * u.mV, \r\n solver=solver)\r\n \r\n self.na = braincell.ion.SodiumFixed(size, E=50. * u.mV)\r\n self.na.add(INa=braincell.channel.INa_Ba2002(size, V_sh=-30 * u.mV))\r\n\r\n self.k = braincell.ion.PotassiumFixed(size, E=-90. * u.mV)\r\n self.k.add(IDR=braincell.channel.IKDR_Ba2002(size, V_sh=-30. * u.mV, phi=0.25))\r\n\r\n```\r\n\r\n\r\n\r\n## Installation\r\n\r\nYou can install ``braincell`` via pip:\r\n\r\n```bash\r\npip install braincell --upgrade\r\n```\r\n\r\n\r\nAlternatively, you can install `BrainX`, which bundles `braincell` with other compatible packages for a comprehensive brain modeling ecosystem:\r\n\r\n```bash\r\npip install BrainX -U\r\n```\r\n\r\n\r\n## Documentation\r\n\r\nThe official documentation is hosted on Read the Docs: [https://braincell.readthedocs.io](https://braincell.readthedocs.io)\r\n\r\n\r\n\r\n## See also the brain modeling ecosystem\r\n\r\nWe are building the brain modeling ecosystem: https://brainmodeling.readthedocs.io/\r\n\r\n",
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