Behavioral assay model

Table of contents

  1. Introduction
  2. Fields
  3. How it fits together
  4. Example
  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.

This model with its direct connections only: drag to pan, Ctrl + scroll to zoom, click a model to select it, use the chevron to see its fields.

Fields

FieldDescription
Behavioral assay 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; string; maximum length: 50 characters).
Setup categoryForm-only filter for the setup type field (e.g., Freely Moving Awake, Head-Fixed Awake). Not stored.
Setup typeThe preparation condition under which this assay is run — a setup type encodes both the physiological state of the subject (e.g., Freely Moving Awake) and the class of apparatus (e.g., “Elevated Plus Maze”). This constrains which physical setups can be used when recording a behavior (required). Must reference an existing setup type.
Behavioral categoryForm-only filter for the paradigm field (e.g., “Learning & Memory”). Not stored.
Behavioral paradigmThe shared paradigm this assay implements (required). Must reference an existing behavioral paradigm.
LicensesLicenses that authorize this method, relevant where the task involves food or water restriction, aversive stimuli or anything else your license governs. Can include multiple licenses.
DescriptionHow the task is actually run: stages, durations, reinforcement, criteria. A behavior stores no task parameters of its own, so whatever is not here is not recorded anywhere.
Authenticated groupsGroups given access when the assay is created (create only). Recording a behavior requires Contributor on the assay, so include the people who will run it. After creation, access is managed from the assay’s own page, where individual people can also be invited.
Public accessDesignates if the behavioral assay is publicly available (boolean; default: False). It makes the assay readable on the public portal, not usable. Only owners can modify this setting.

A behavioral assay cannot be deleted while behaviors point to it.

How it fits together

The behavioral track and the setup track: behavioral categories group paradigms, and an assay is your lab's version of a paradigm on a setup type; a setup is your rig of a setup type, with its equipment. A behavior in a session runs one assay on one setup with its subjects. The behavioral track (left) and the setup track (right) run from the shared taxonomies through your lab’s personal attributes and meet in a behavior recorded in a session. This page describes the behavioral assay, drawn solid. The setup type category is a field of the setup type, not a separate record.

BrainSTEM organizes behavioral experiments through a hierarchy that separates shared scientific knowledge from lab-specific implementation details:

  • Behavioral category — The broad domain (e.g., “Anxiety & Affect” → “Anxiety”)
  • Behavioral paradigm — The standardized task shared across the field (e.g., “Elevated Plus Exploration”)
  • Behavioral assay (this page) — Your lab’s specific implementation of a paradigm under a specific preparation condition, linking a paradigm to a setup type (e.g., “EPM 5-min test”)
  • 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 (Freely Moving Awake)
BehaviorRat #7, Session 2024-06-01, ran assay “EPM 5-min test” on setup “EPM Rig B, Room 108”

Permissions

Behavioral assays have four roles: Member (read), Contributor (can record a behavior that uses the assay), Manager (also manages access) and Owner (also edits the assay’s own fields and deletes it). You manage permissions through the management tab. Assays are shared with people and groups, never through a project.

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.