A behavioral assay is your lab's specific implementation of a behavioral paradigm. While paradigms describe the shared conceptual task (e.g., "Morris Water Navigation Task"), an assay captures how your lab actually runs it — the specific protocol, parameters, and setup type used.
How It Fits Together
BrainSTEM organizes behavioral experiments through a hierarchy that separates shared scientific knowledge from lab-specific implementation details:
- Behavioral Category — The broad domain (e.g., "Learning & Memory" → "Spatial Learning")
- Behavioral Paradigm — The standardized task shared across the field (e.g., "Morris Water Navigation Task")
- Behavioral Assay (this page) — Your lab's specific implementation of a paradigm, linking it to a setup type (e.g., "MWM 4-day acquisition, 60s trials, probe on day 5")
- Behavior — The actual execution of an assay within a session, tied to specific subjects and a physical setup
Categories and paradigms are shared taxonomies available to everyone. Assays are lab-specific — they belong to your groups and capture exactly how you run a paradigm.
Example
| Level |
Example |
| Paradigm |
Elevated Plus Exploration |
| Assay |
"EPM 5-min test" — single 5-min session, 300 lux open arms, setup type: Elevated Plus Maze |
| Behavior |
Rat #7, Session 2024-06-01, ran assay "EPM 5-min test" on setup "EPM Rig B" |
Fields
- Name: A descriptive name for this assay, ideally indicating the paradigm and key protocol details (e.g., "MWM 4-day acquisition" or "EPM 5-min test") (required).
- Setup type: The standardized apparatus type (e.g., "Elevated Plus Maze", "Open Field Arena"). Each setup type has a category describing the experimental condition (Freely Moving Awake, Head-Fixed Awake, etc.) (required).
- Behavioral paradigm: The shared paradigm this assay implements (required).
- Description: Protocol details — trial structure, timing, parameters, and any lab-specific variations.
- Authenticated groups: Assign one or more groups during the creation process. Assigned groups will have change permissions. You can adjust permissions later on the "Manage permissions" page (required).
- Public access: Determines if the assay is publicly available or accessible only through the private portal.
Permissions
Behavioral assays have four permission levels: membership (read access), change permissions, managers, and owners. You manage permissions through the management tab. For more information on permissions, please see the documentation.
API Access
The API allows for programmable access to behavioral assays, enabling you to read, edit, and delete assays through the API. For details about the fields and data structure, refer to the documentation.
