The Allen Institute Github organization hosts software packages that support public access to Institute resources and data sets.
The Allen Institute for Brain Science has published the Allen Software Development Kit (SDK), which houses source code for reading and processing Allen Brain Atlas data. The Allen SDK focuses primarily on the Allen Cell Types Database, Mouse Connectivity Atlas, and Brain Observatory. Functionality relevant to other atlases is planned for future releases.
DiPDE (dipde) is a simulation platform for numerically solving the time evolution of coupled networks of neuronal populations. Instead of solving the subthreshold dynamics of individual model leaky-integrate-and-fire (LIF) neurons, dipde models the voltage distribution of a population of neurons with a single population density equation. In this way, dipde can facilitate the fast exploration of mesoscale (population-level) network topologies, where large populations of neurons are treated as homogeneous with random fine-scale connectivity.
The NWB API is a Python libary that was used to write Allen Cell Types Database experiments' details to the Neurodata Without Borders: Neurophysiology (NWB) file format. This API is designed to work with a variety of neurophysiology data, including intracellular and extracellular electrophysiology experiments, optical physiology experiments, as well as tracking and stimulus data.