Brian2

Python astronomy tools

MEG and EEG.

Deep learning with spiking neural networks in Python, providing gradient-based training of SNNs via PyTorch autodifferentiation for brain-inspired computing and neuromorphic research, with online learning capabilities and extensive tutorials (1.9K+ stars, actively maintained)

Python Materials Genomics: robust materials analysis library defining classes for structures and molecules with support for many electronic structure codes; foundational toolkit powering the Materials Project (Berkeley Lab, 1.8K+ stars)

Molecular dynamics analysis

Simulation of large-scale brain models