Behavioral Assay model

Table of contents

  1. Introduction
  2. How it fits together
  3. Example
  4. Fields
  5. Permissions
  6. API access

Introduction

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

LevelExample
ParadigmElevated Plus Exploration
Assay“EPM 5-min test” — single 5-min session, 300 lux open arms, setup type: Elevated Plus Maze
BehaviorRat #7, Session 2024-06-01, ran assay “EPM 5-min test” on setup “EPM Rig B”

Fields

FieldDescription
NameA 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 typeThe 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). Must reference an existing setup type.
Behavioral paradigmThe shared paradigm this assay implements (required). Must reference an existing behavioral paradigm.
DescriptionProtocol details — trial structure, timing, parameters, and any lab-specific variations.
Authenticated groupsAssign 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 accessDetermines 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.

Visit the permissions page to learn more.

API access

The API allows for programmable access to behavioral assays, enabling you to read, edit, and delete assays through the API. Learn more about the fields and data structure on the Behavioral assay API page.