Setting Up Lab Infrastructure in BrainSTEM

Table of contents

  1. Introduction
  2. Understanding Lab Infrastructure Components
  3. Behavioral Paradigms
  4. Planning Your Infrastructure
  5. Creating Setups
  6. Adding Equipment to Setups
  7. Setting Up Inventories
  8. Adding Consumable Stocks
  9. Permission Management
  10. Best Practices
  11. Integration with Experimental Workflows
  12. Troubleshooting
  13. Next Steps

Introduction

Before conducting experiments in BrainSTEM, we recommend you establish your lab’s infrastructure. This tutorial covers creating and configuring the foundational elements that support your research workflows: setups with equipment and inventories with consumable stocks. Proper infrastructure setup ensures smooth experiment creation and maintains consistency across your lab.

Understanding Lab Infrastructure Components

BrainSTEM’s lab infrastructure consists of four interconnected components:

  1. Setups: Physical experimental environments (behavioral setup, recording rigs, surgical stations)
  2. Equipment: Hardware devices used in your setups
  3. Inventories: Organizational systems for tracking lab resources
  4. Consumable Stocks: Specific items and materials in your inventories

These components work together to provide the foundation for documenting procedures, behaviors, data acquisition, and manipulations.

Behavioral Paradigms

Behavioral paradigms are standardized experimental protocols (such as T-maze alternation, open field exploration, etc.) that are performed within a specific setup environment. In BrainSTEM, these are managed under Personal Attributes → Behavioral Paradigms.

For detailed instructions on creating, managing, and best practices for behavioral paradigms, see the dedicated tutorial: Behavioral Paradigms.

When planning your infrastructure, ensure that your setups have the correct environment type for the behavioral paradigms you intend to use.

Planning Your Infrastructure

Before You Begin

  1. Audit your physical spaces: List experimental environments in your lab
  2. Inventory your equipment: Document devices, instruments, and tools
  3. Catalog your supplies: Identify consumables, probes, drugs, and other materials
  4. Define access permissions: Determine which group members need access to what resources

Infrastructure Hierarchy

Understanding the relationships between components:

Setup (Physical Environment)
├── Equipment (Devices in that environment)
│   ├── Hardware devices (specific models/brands)
│   └── Coordinates systems (for positioning)
└── Associated with → Procedures, Behaviors, Data acquisition

Inventory (Storage/Organization System)
└── Consumable Stocks (Specific items)
    └── Associated with → Procedures

Creating Setups

Setups represent your physical experimental environments. Each setup corresponds to a specific location or configuration where experiments are conducted.

Step 1: Navigate to Setups

  1. Go to Personal AttributesSetups in the left navigation menu
  2. Click the Add setup button

Step 2: Configure Basic Setup Information

Fill in the essential details:

FieldInstructions
NameUse descriptive, standardized names (e.g., “Behavior Room A”, “Surgery Station 1”, “2P Imaging Rig”, “Head-fixed Linear Track”)
Environment TypeSelect appropriate category: Behavioral environments (T-maze, Open field, Barnes maze, Linear track), Recording environments (Head-fixed disc, Homecage, Custom rigs), or Surgical environments (Surgical table)
Authenticated GroupsSelect groups that should have access to this setup
DescriptionProvide comprehensive details including: Physical location (room number, building), Setup purpose and capabilities, Special requirements or restrictions, Contact person for technical issues

Step 3: Define Specifications

Add relevant specifications for your setup. Specifications can be a string or a number. Common examples:

Behavioral mazes: Arm lengths, corridor widths, platform sizes
Recording rigs: Stage dimensions, working distances
Surgical stations: Table dimensions, reach distances

Example specification:

DimensionValue
Length“20 cm”
Width“50 cm”

Step 4: Setup Example

Behavioral Setup: “T-maze Behavior Room”

FieldValue
NameT-maze Behavior Room
Setup TypeT-maze
DescriptionBehavioral testing room with automated T-maze system for spatial memory tasks. Located in Room 302B, Neuroscience Building
Public AccessNo
SpecificationsArmLength: “45 cm”, StemLength: “50 cm”, CorridorWidth: “10 cm”

Use consistent naming conventions across your lab. This makes setups easier to find and select during experiment creation.

Adding Equipment to Setups

Equipment represents the devices and instruments within your setups. Each piece of equipment belongs to a specific setup and can be used in procedures, data acquisition, and manipulations.

Step 1: Navigate to Equipment

  1. Go to ModulesEquipment
  2. Click the Add equipment button

Step 2: Configure Equipment Basics

FieldInstructions
NameUse specific, identifiable names (Good: “Intan RHD2000 #1”, “Behavior Camera Main”, “LED Driver Ch1-4”; Avoid: “Recording device”, “Camera”, “Light”)
SetupSelect the setup where this equipment is located
Hardware DeviceChoose from the resources database or submit new devices
Coordinates SystemDefine how this equipment’s position is measured (Common: “External_XYZ_Absolute”)

Step 3: Common Equipment Types

Data Acquisition: Recording systems (Intan, Plexon), imaging systems (two-photon microscopes, miniscopes), behavioral cameras, motion tracking systems

Stimulation: Optogenetic systems (LED drivers, lasers), electrical stimulation equipment (stimulus isolators, function generators)

Surgical: Stereotaxic systems, micromanipulators, injection pumps, drill systems

Step 4: Equipment Configuration Example

FieldValue
NameIntan RHD2000 System #1
SetupSelect: Open Field Arena
Hardware DeviceIntan RHD2000 USB interface board
TypeDataAcquisitionSystem

Link equipment to appropriate hardware devices in the resources database. If your specific model isn’t available, submit it for approval first.

Setting Up Inventories

Inventories help organize and track consumable resources in your lab. They provide structure for managing supplies and ensure proper accounting of materials used in experiments.

Step 1: Create Inventory Categories

Navigate to Personal AttributesInventories and create logical groupings:

Common Inventory Categories

Organize inventories by material type (Neural Probes, Viral Vectors, Pharmacological Agents), storage location (Freezer -80°C, Refrigerator 4°C), or experiment type (Electrophysiology Supplies, Optogenetics Materials).

Step 2: Configure Inventory Details

For each inventory:

FieldInstructions
NameClear, descriptive identification (Examples: “Silicon Probe Storage”, “AAV Virus Stocks”, “Behavioral Supplies RT”)
DescriptionInclude important details: Physical location and access requirements, Storage conditions and handling notes, Responsible person or contact, Special safety considerations
Authenticated GroupsGroups that can access and modify this inventory
Public AccessUsually False for lab inventories

Step 3: Inventory Setup Example

FieldValue
NameNeural Electrode Inventory
DescriptionStorage for all neural recording electrodes and probes. Located in Room 302, Cabinet B. Handle with anti-static precautions. Contact: Lab Manager for restocking.
Authenticated GroupsElectrophysiology Team, Lab Managers

Adding Consumable Stocks

Consumable stocks are the specific items within your inventories. These are the actual materials that get used in procedures and need to be tracked for experimental documentation.

Step 1: Navigate to Consumable Stocks

  1. Go to ModulesConsumable stocks
  2. Click Add consumable stock

Step 2: Configure Stock Information

Field CategoryFieldDescription
Basic InformationNameSpecific, identifiable descriptions
 InventorySelect the appropriate inventory category
 ConsumableChoose from resources database or submit new items
Tracking DetailsLot numberManufacturer’s batch identifier
 SupplierWhere the item was purchased
 CostFor budget tracking and planning
Storage InformationStorage locationSpecific location within the inventory
 Storage conditionsTemperature, humidity, special requirements
 Expiration dateIf applicable
Usage InformationIntended useSpecific experimental applications
 NotesSpecial handling, preparation, or usage instructions

Step 3: Consumable Stock Example

FieldValue
TypeSiliconProbe
InventorySelect: Neural Electrode Inventory
ConsumableNeuroNexus A1x32-Poly2
Acquisition Date2024-01-15
Storage LocationCabinet B, Slot 15, Anti-static tube #A1x32-15
Storage ConditionsRoom temperature, anti-static protection
Intended UseChronic hippocampal recordings in behaving mice
Cost$1,200
NotesPre-cleaned with 70% ethanol. Handle with non-magnetic forceps only. Sterilize with EtO gas before implantation.

Permission Management

Proper permission management ensures that the right people have access to the right resources while maintaining security and organization.

BrainSTEM infrastructure uses four permission levels for setups and inventories and therby inherited to equipment and consumable stocks:

Permission LevelCapabilities
MembersView details
Read-only access
Cannot modify or create infrastructure
ContributorsAll Member permissions
Create and modify associated equipment and consumable stocks.
Select setups and equipment when creating experiments
Select inventory and consumable stocks when creating experiments
Cannot modify setup settings or manage permissions
ManagersAll Contributor permissions
Manage permissions for others
Configure setup specifications
Cannot delete infrastructure or transfer ownership
OwnersAll Manager permissions
Full control over setups and equipment
Delete infrastructure components
Transfer ownership to other users
Complete administrative control

Best Practices for Assigning Permissions:

  • Owners: PI, lab manager, or senior lab members with equipment responsibility
  • Managers: Postdocs or experienced graduate students who primarily use specific rigs
  • Contributors: Lab members who regularly use the equipment for their research
  • Members: All lab members who might occasionally need read access

Group-Based Access

Recommended Group Structure:

Lab Members (Basic access to most lab resources)
├── Graduate Students (Access to setups and equipment for their projects)
├── Postdocs (Broader access, can manage equipment in their research areas)
├── Lab Manager (Administrative access, inventory management)
├── PI and Senior Staff (Full ownership and administrative control)
└── Technique-Specific Groups (Optional, for specialized equipment)
    ├── Electrophysiology Users (Access to recording equipment and probes)
    ├── Imaging Users (Access to microscopes and imaging supplies)
    └── Behavior Users (Access to behavioral setups and paradigms)

Best Practices

Naming Conventions

  • Setups: Include location and be specific (e.g., “Room302_TmazeBehavior”, “HeadFixed_2P_VR”)
  • Equipment: Include model and serial number (e.g., “IntanRHD2000_SN1234”)
  • Inventories: Include storage info (e.g., “Probes_RoomTemp”, “Viruses_Minus80”)
  • Consumable Stocks: Include lot numbers and concentrations where applicable

Documentation and Maintenance

  • Include technical specifications, calibration status, and safety considerations in descriptions
  • Specify physical locations, storage conditions, and responsible contacts
  • Update consumable stock levels monthly, review equipment quarterly, audit permissions annually
  • Document modifications, update permissions when roles change, and archive rather than delete old equipment

Integration with Experimental Workflows

Using Infrastructure in Procedures

When creating procedures, your infrastructure components become available:

  • Setups provide the location context
  • Equipment specifies tools used (stereotaxic frames, injection systems)
  • Consumable stocks track materials consumed (probes, viruses, drugs)

Using Infrastructure in Sessions

Your setup determines available:

  • Equipment for data acquisition modules
  • Behavioral paradigms compatible with the environment type

Troubleshooting

Setup not available: Verify authentication permissions and environment type compatibility

Equipment missing from dropdowns: Confirm correct setup assignment, equipment type alignment, and permission matching

Consumable stock access issues: Check group membership and owner/manager permissions

Next Steps

With your lab infrastructure in place, you’re ready to move on to experimental workflows: