PyBpod Alyx Module

Alyx is a database designed for storage and retrieval of all data in an experimental neuroscience laboratory - from subject management through data acquisition, raw data file tracking and storage of metadata resulting from manual analysis.

Alyx is currently used in production at the Cortexlab at UCL and at the International Brain Lab.

The PyBpod Alyx Module allows communication with Alyx databases inside the PyBpod environment. The goal is to use PyBpod to manage Alyx information such as subjects and users, and associate PyBpod experiments with those users and subjects.

Installation

PyBpod Alyx Module is available through PyPI and you can install it using the following command in your Python environment:

pip install pybpod-gui-plugin-alyx

Usage

As with any other plugin for PyBpod, just add pybpod_alyx_module to your GENERIC_EDITOR_PLUGINS_LIST in your project's user_settings.py, as shown below:

GENERIC_EDITOR_PLUGINS_LIST = [
                                ...
                                'pybpod_alyx_module',
                                ...
                              ]

After opening PyBpod, you can right click in your Project and select the Sync to Alyx option.

A new window will show up where you need to add the Alyx server's web address, your username and password.

Afterwards, press the Connect button and if everything went well with the connection the Status message will change to CONNECTED.

At that point, when you press the Get Subjects button, the Alyx subjects will be downloaded and added to the project. If there are subjects that already exist in your project, PyBpod will present a message asking if you want to override them.

Note: Subjects that aren't alive and already exist in your project will be automatically removed from the project.

To get details of a specific Subject, right click on its name and select the Alyx details option. This option only shows up on Alyx subjects as it would be expected.

Configuration extras

The PyBpod Alyx Module also has some configuration options to simplify its usage.

You can add the following options to your user_settings.py if you want.

ALYX_PLUGIN_ADDRESS = 'https://alyxserver.com/'
ALYX_PLUGIN_USERNAME = 'my_username'
ALYX_PLUGIN_PASSWORD = 'my_password'

Note: The configuration options expect strings. The dummy information provided should be changed according to your settings.

Warning: Although available to add through the configuration file, the password is saved as clear text. Use this option carefully.