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NeuroDynamics-0.1.1
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NeuroDynamics: A Just-In-Time compilation approach for neuronal dynamics simulation.
| ویژگی | مقدار |
|---|---|
| سیستم عامل | OS Independent |
| نام فایل | NeuroDynamics-0.1.1 |
| نام | NeuroDynamics |
| نسخه کتابخانه | 0.1.1 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | Chaoming Wang |
| ایمیل نویسنده | adaduo@outlook.com |
| آدرس صفحه اصلی | https://github.com/PKU-NIP-Lab/BrainPy |
| آدرس اینترنتی | https://pypi.org/project/NeuroDynamics/ |
| مجوز | - |
.. image:: https://github.com/PKU-NIP-Lab/NumpyBrain/blob/master/docs/images/logo.png
:target: https://github.com/PKU-NIP-Lab/NumpyBrain
:align: center
:alt: logo
.. image:: https://readthedocs.org/projects/numpybrain/badge/?version=latest
:target: https://numpybrain.readthedocs.io/en/latest/?badge=latest
:alt: Documentation Status
.. image:: https://anaconda.org/oujago/npbrain/badges/version.svg
:target: https://anaconda.org/oujago/npbrain
.. image:: https://badge.fury.io/py/npbrain.svg
:target: https://badge.fury.io/py/npbrain
**Note**: *BrainPy is a project under development.*
*More features are coming soon. Contributions are welcome.*
Why to use BrainPy
=====================
``BrainPy`` is a microkernel framework for SNN (spiking neural network) simulation
purely based on **native** python. It only relies on `NumPy <https://numpy.org/>`_.
However, if you want to get faster performance,you can additionally
install `Numba <http://numba.pydata.org/>`_. With `Numba`, the speed of C or FORTRAN can
be obtained in the simulation.
``BrainPy`` wants to provide a highly flexible and efficient SNN simulation
framework for Python users. It endows the users with the fully data/logic flow control.
The core of the framework is a micro-kernel, and it's easy to understand (see
`How NumpyBrain works`_).
Based on the kernel, the extension of the new models or the customization of the
data/logic flows are very simple for users. Ample examples (such as LIF neuron,
HH neuron, or AMPA synapse, GABA synapse and GapJunction) are also provided.
Besides the consideration of **flexibility**, for accelerating the running
**speed** of NumPy codes, `Numba` is used. For most of the times,
models running on `Numba` backend is very fast
(see `examples/benchmark <https://github.com/PKU-NIP-Lab/NumpyBrain/tree/master/examples/benchmark>`_).
.. figure:: https://github.com/PKU-NIP-Lab/NumpyBrain/blob/master/docs/images/speed_comparison.png
:alt: Speed comparison with brian2
:figclass: align-center
:width: 350px
More details about BrainPy please see our `document <https://numpybrain.readthedocs.io/en/latest/>`_.
Installation
============
Install ``BrainPy`` using ``pip``::
$> pip install git+https://github.com/PKU-NIP-Lab/BrainPy
Install from source code::
$> python setup.py install
The following packages need to be installed to use ``BrainPy``:
- Python >= 3.5
- NumPy >= 1.13
- Sympy >= 1.2
- Matplotlib >= 2.0
- autopep8
Packages recommended to install:
- Numba >= 0.40.0
- JAX >= 0.1.0
Define a Hodgkin–Huxley neuron model
====================================
.. code-block:: python
import npbrain.numpy as np
import npbrain as nb
def HH(noise=0., E_Na=50., g_Na=120., E_K=-77., g_K=36.,
E_Leak=-54.387, g_Leak=0.03, C=1.0, Vth=20.):
ST = nb.types.NeuState(
{'V': -65., 'm': 0., 'h': 0., 'n': 0., 'sp': 0., 'inp': 0.},
help='Hodgkin–Huxley neuron state.\n'
'"V" denotes membrane potential.\n'
'"n" denotes potassium channel activation probability.\n'
'"m" denotes sodium channel activation probability.\n'
'"h" denotes sodium channel inactivation probability.\n'
'"sp" denotes spiking state.\n'
'"inp" denotes synaptic input.\n'
)
@nb.integrate
def int_m(m, t, V):
alpha = 0.1 * (V + 40) / (1 - np.exp(-(V + 40) / 10))
beta = 4.0 * np.exp(-(V + 65) / 18)
return alpha * (1 - m) - beta * m
@nb.integrate
def int_h(h, t, V):
alpha = 0.07 * np.exp(-(V + 65) / 20.)
beta = 1 / (1 + np.exp(-(V + 35) / 10))
return alpha * (1 - h) - beta * h
@nb.integrate
def int_n(n, t, V):
alpha = 0.01 * (V + 55) / (1 - np.exp(-(V + 55) / 10))
beta = 0.125 * np.exp(-(V + 65) / 80)
return alpha * (1 - n) - beta * n
@nb.integrate(noise=noise / C)
def int_V(V, t, m, h, n, Isyn):
INa = g_Na * m ** 3 * h * (V - E_Na)
IK = g_K * n ** 4 * (V - E_K)
IL = g_Leak * (V - E_Leak)
dvdt = (- INa - IK - IL + Isyn) / C
return dvdt
def update(ST, _t_):
m = np.clip(int_m(ST['m'], _t_, ST['V']), 0., 1.)
h = np.clip(int_h(ST['h'], _t_, ST['V']), 0., 1.)
n = np.clip(int_n(ST['n'], _t_, ST['V']), 0., 1.)
V = int_V(ST['V'], _t_, m, h, n, ST['inp'])
sp = np.logical_and(ST['V'] < Vth, V >= Vth)
ST['sp'] = sp
ST['V'] = V
ST['m'] = m
ST['h'] = h
ST['n'] = n
ST['inp'] = 0.
return nb.NeuType(requires={"ST": ST}, steps=update, vector_based=True)
Define an AMPA synapse model
============================
.. code-block:: python
def AMPA(g_max=0.10, E=0., tau_decay=2.0):
requires = dict(
ST=nb.types.SynState(['s'], help='AMPA synapse state.'),
pre=nb.types.NeuState(['sp'], help='Pre-synaptic state must have "sp" item.'),
post=nb.types.NeuState(['V', 'inp'], help='Post-synaptic neuron must have "V" and "inp" items.')
)
@nb.integrate(method='euler')
def ints(s, t):
return - s / tau_decay
def update(ST, _t_, pre):
s = ints(ST['s'], _t_)
s += pre['sp']
ST['s'] = s
@nb.delayed
def output(ST, post):
post_val = - g_max * ST['s'] * (post['V'] - E)
post['inp'] += post_val
return nb.SynType(requires=requires, steps=(update, output), vector_based=False)
.. _How NumpyBrain works: https://numpybrain.readthedocs.io/en/latest/guides/how_it_works.html
زبان مورد نیاز
| مقدار | نام |
|---|---|
| >=3.5 | Python |
نحوه نصب
نصب پکیج whl NeuroDynamics-0.1.1:
pip install NeuroDynamics-0.1.1.whl
نصب پکیج tar.gz NeuroDynamics-0.1.1:
pip install NeuroDynamics-0.1.1.tar.gz