Software for computational neuroscience
Upstream packages
The following tools are among the software currently tested in NeuroFedora and can be installed directly from upstream forges (e.g. PyPi). You can see the tests results here.
Python packages
| Software | Summary | pip (PyPi) | Notes |
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Blue Brain Python Optimisation Library (bluepyopt). |
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A clock-driven simulator for spiking neural networks. |
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A module for modeling extracellular potentials of multicompartment neuron models built on NEURON. |
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A Python library for working with NeuroML descriptions of neuronal models. |
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Does not currently install on Python 3.13. https://github.com/nest/NEAT/issues/183 |
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A Python package to develop, simulate and analyse biological neuronal networks in NEURON. |
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NeuroM: a light-weight neuron morphology analysis package. |
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A common JSON/YAML based format for compact network specification, closely tied to NeuroML v2. |
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Empirically-based simulator for modeling neurons and networks of neurons. |
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A Python library for optimising neuronal models. |
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A Python library for working with the Low Entropy Model Specification language (LEMS). |
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Python scripting interface of MOOSE Simulator (https://moose.ncbs.res.in). |
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Python utilities for NeuroML. |
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A Python package for simulator-independent specification of neuronal network models. |
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A test-driven framework for formally validating scientific models against data. |
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System packages
The following general purpose utilties are included in the repositories:
| Software | Install with | Notes |
|---|---|---|
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A high-performance library for Computational Neuroscience simulations |
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A package to simulate recurrent spiking neural networks with spike timing dependent plasticity (STDP). |
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Common interfaces for neuronal simulators |
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Systems Biology Markup Language library |
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A Python and C++ interface to the SONATA format |
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Multiscale Neuroscience and Systems Biology Simulator |
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The NEST simulator |
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