This guide is a resource for using the Allen SDK package. It is maintained by the Allen Institute for Brain Science.
Quick Start Using Pip¶
First ensure you have pip installed. It is included with the Anaconda distribution.
pip install allensdk
To uninstall the SDK:
pip uninstall allensdk
Other Distribution Formats¶
The Allen SDK is also available from the Github source repository.
Installation with Docker (Optional)¶
Docker is an open-source technology for building and deploying applications with a consistent environment including required dependencies. The AllenSDK is not distributed as a Docker image, but example Dockerfiles are available.
Ensure you have Docker installed.
Use Docker to build one of the images.
Anaconda:docker pull alleninsitute/allensdk
Other docker configurations are also available under docker directory in the source repository.
Run the docker image:docker run -i -t -p 8888:8888 -v /data:/data alleninstitute/allensdk /bin/bash cd allensdk make test
Start a Jupyter Notebook:cd allensdk/doc_template/examples/nb jupyter-notebook --ip=* --no-browser