Microbial Strain Management

Use Labii as Microbial Strain Management to manage microbial strains, including bacteria, yeast, and fungi. It allows you to track the strains, their characteristics, and their usage in experiments.

Overview

Labii Microbial Strain Management provides a unified platform to document, track, and manage microbial strains from acquisition to experimental use. Whether your strains come from ATCC, DSMZ, or in-house isolation, Labii captures every detail—taxonomy, growth requirements, storage conditions, and usage history—in one secure, searchable system.

This comprehensive application serves as a centralized repository for managing bacteria, yeast, and fungi throughout their lifecycle in a laboratory environment. The system enables laboratories to maintain detailed records of strain provenance, genetic modifications, phenotypic characteristics, and optimal growth conditions. By integrating strain management with batch tracking, container management, and consumption logging, Labii ensures complete traceability from strain acquisition through experimental use.

Key Features

• Complete Strain Profiles: Comprehensive records including scientific classification, source information, biosafety level, hazard notes, certificates, genome sequences, and reference links

• Standardized Growth Conditions: Document and manage all growth conditions including media type, incubation temperature, atmosphere, and duration with multiple profiles per strain

• Vial-Level Tracking: Precise records of every vial with barcodes, storage format, temperature, and exact freezer location

• Automatic Generation Tracking: Automated lineage visualization with dynamic tree maps showing ancestry and propagation history

• Storage Management: Track every aliquot with precise location data, storage format, and temperature requirements

• Usage History: Detailed audit trails logging who used the strain, how much, purpose, and linked experiment entries

• ELN Integration: Seamless integration with Labii's Electronic Lab Notebook for connected workflows from inventory to analysis

Target Users

This application is designed for:

• Microbiology researchers managing bacterial, yeast, or fungal collections

• Culture collection curators maintaining institutional repositories

• Quality control laboratories tracking strain usage for compliance

• Biotech and pharmaceutical companies managing production strains

• Academic research groups collaborating on microbial studies

• Contract research organizations (CROs) requiring full audit trails

Prerequisites

• Active Labii ELN/LIMS account with appropriate permissions

• Microbial Strain Management application enabled in your workspace

• Basic understanding of microbial culture techniques

• Defined laboratory naming conventions for strains and storage locations

Learn more about Labii Microbial Strain Management at https://www.labii.com/products/microbial-strain-management.

Use Cases

Research Laboratory Strain Management

• Catalog and track experimental strains including bacteria, yeast, and fungi

• Maintain detailed records of genetic modifications and phenotypic characteristics

• Document strain provenance from acquisition through experimental use

• Link strain usage directly to experiments in the electronic lab notebook

• Generate reproducibility reports with complete material traceability

Culture Collection Administration

• Manage institutional repositories with thousands of strain entries

• Track biosafety levels, hazard classifications, and handling requirements

• Maintain certificates, genome sequences, and reference documentation

• Facilitate external sharing with complete strain information packages

• Monitor collection health with automated maintenance scheduling

Quality Control and Compliance

• Implement audit trails for regulatory compliance (GLP, GMP, FDA)

• Document chain of custody from receipt through usage and disposal

• Track passage numbers and generation history for quality assurance

• Schedule periodic verification testing to ensure strain integrity

• Generate compliance reports for regulatory submissions and audits

Biotech and Pharmaceutical Production

• Manage production strains with strict version control

• Track master and working cell banks with automated lineage visualization

• Document storage conditions and environmental monitoring

• Implement multi-level approval workflows for strain modifications

• Link strains to batch production records for full traceability

Academic and Collaborative Research

• Share strain information with collaborators while maintaining access controls

• Track material transfers for intellectual property management

• Document strain usage across multiple research projects

• Facilitate teaching and training with standardized strain protocols

• Enable student researchers to access established strain collections safely

Getting Started

1

Navigate to Microbial Strain Management from the applications menu in your Labii workspace

2

Configure your storage infrastructure:

• Map all physical storage locations (freezers, incubators, refrigerators)

• Create hierarchical storage structure in the core_storage table

• Assign location codes or barcode labels to physical locations

3

Set up your strain catalog:

• Import existing strain inventory or create new strain records

• Assign unique strain identifiers following your naming convention

• Document taxonomy, characteristics, and biosafety levels

4

Document growth conditions:

• Create growth condition records for each strain

• Include media recipes, temperature, and atmosphere requirements

• Link to standard protocol documents where available

5

Inventory your physical containers:

• Create batch records for existing lots

• Generate container entries for each vial, tube, or plate

• Link containers to storage locations

• Apply barcode labels if using a scanning system

For first-time setup, we recommend starting with a small subset of your most frequently used strains to familiarize your team with the workflows before scaling to your entire collection.

Tables and Their Roles

The Microbial Strain Management application uses six interconnected tables to provide complete traceability from strain catalog to experimental usage:

strain

Primary Use: Master catalog of all microbial strains maintained by the laboratory

Key Information Stored:

• Strain identifiers (names, catalog numbers, lab codes)

• Scientific classification (genus, species, strain designation)

• Genetic markers and phenotypic characteristics

• Source information (vendor, collaborator, isolation details)

• Biosafety level and special handling requirements

• Certificates, genome sequences, and reference links

Key Relationships: Parent table linked to strain_growth_condition (one-to-many); referenced by core_batch for lot tracking

Example: Cataloging Escherichia coli BL21(DE3) strain from a commercial supplier with antibiotic resistance markers and expression system capabilities

strain_growth_condition

Primary Use: Documents optimal and acceptable growth parameters for each strain

Key Information Stored:

• Growth media composition and formulation

• Temperature ranges and optimal conditions

• Oxygen requirements (aerobic, anaerobic, microaerophilic)

• pH preferences and acceptable ranges

• Growth rate and typical doubling time

• Special additives or supplements required

• Alternative or backup growth conditions

Key Relationships: Child table of strain (multiple growth conditions can be documented per strain)

Example: Recording that Saccharomyces cerevisiae strain ABC123 grows optimally in YPD medium at 30°C aerobically, but can also grow in synthetic complete media at 25-37°C

core_batch

Primary Use: Tracks specific batches/lots of strains with unique identifiers for traceability

Key Information Stored:

• Batch/lot numbers with standardized naming

• Receipt or preparation dates

• Source information (vendor, in-house preparation)

• Expiration dates or stability limits

• Passage numbers and generation tracking

• Quality control status and test results

Key Relationships: Links strain (parent) to core_container (child); enables lot-level traceability

Example: Creating batch "BATCH-2026-001" when receiving a new shipment of strain XYZ from ATCC, or generating "SC-2026-02-17-A" when subculturing an existing strain

core_container

Primary Use: Manages individual physical containers (tubes, plates, cryovials) holding strain aliquots

Key Information Stored:

• Container IDs or barcode identifiers

• Container types (cryovial, slant, stab, plate)

• Volumes or quantities (CFU, OD, weight)

• Status (available, in-use, depleted, quarantine)

• Quality indicators and viability assessments

• Creation and last-modified dates

Key Relationships: Belongs to core_batch; linked to core_storage for location; referenced in core_consumption for usage tracking

Example: Registering 20 cryovials (CV-001 through CV-020) each containing 1mL aliquots of a newly prepared glycerol stock at -80°C

core_consumption

Primary Use: Logs all usage events when strains are withdrawn from inventory for experiments or other purposes

Key Information Stored:

• Date and time of usage

• User or researcher who accessed the strain

• Purpose and experiment reference numbers

• Quantity consumed or withdrawn

• Source container identifier

• Project codes or grant numbers

• Return status (if applicable)

Key Relationships: References core_container (what was used); can link to experiments, projects, or protocols

Example: Recording that researcher John Doe used cryovial CV-005 (0.1mL) on 2026-02-17 for experiment EXP-2026-042 studying antibiotic resistance mechanisms

core_storage

Primary Use: Maintains the physical storage hierarchy and locations for all containers

Key Information Stored:

• Storage equipment identifiers (freezer names, incubator numbers)

• Hierarchical position details (building, room, equipment, rack, box, position)

• Temperature and environmental conditions

• Access restrictions and security levels

• Maintenance schedules and temperature logs

• Capacity and utilization metrics

Key Relationships: Linked to core_container (containers are stored in locations); supports hierarchical storage structures

Example: Organizing containers in a storage hierarchy like "Building A > Room 101 > -80°C Freezer #3 > Rack B > Box 12 > Position A5"

Core Workflows

New Strain Acquisition and Cataloging

When receiving new strains from vendors or collaborators, proper documentation ensures complete traceability and accessibility.

1

Create a new strain record in the strain table:

• Assign a unique strain identifier following your naming convention

• Enter complete taxonomy (genus, species, strain designation)

• Document ATCC/DSMZ catalog number if applicable

• Record source information and acquisition date

• Set biosafety level and handling requirements

2

Document growth conditions in strain_growth_condition:

• Select or create media type (LB, YPD, custom formulations)

• Specify temperature range and optimal incubation temperature

• Indicate oxygen requirements (aerobic, anaerobic, etc.)

• Add special requirements (light, CO2, shaking speed)

• Link to detailed protocol documents if available

3

Create a batch record in core_batch:

• Generate batch/lot number (e.g., BATCH-2026-02-17-001)

• Enter receipt date and source details

• Set expiration date based on stability data

• Record initial passage number (typically P0 for new acquisitions)

• Attach certificate of analysis or vendor documentation

4

Aliquot and create container records:

• Prepare working aliquots (glycerol stocks, lyophilized vials)

• Create a core_container entry for each physical vial/tube

• Apply barcode labels if using a tracking system

• Record volume/quantity in each container

• Set initial status as "Available"

5

Assign storage locations:

• Select appropriate storage equipment based on requirements (-80°C, -20°C, 4°C)

• Navigate storage hierarchy in core_storage

• Assign specific positions for each container

• Update storage location records

• Verify container placement matches system records

Best Practice: Photograph colony morphology or microscopic images and attach them to the strain record for future reference and verification.

Retrieving and Using Strains in Experiments

Efficient strain retrieval with complete documentation maintains audit trails and prevents inventory errors.

1

Search for the desired strain:

• Use the strain table search function

• Filter by strain name, species, characteristics, or catalog number

• Review strain details, biosafety level, and handling requirements

• Check growth condition requirements for your experiment

2

Check container availability:

• View linked core_container records

• Filter by status (show only "Available" containers)

• Review quantities and passage numbers

• Verify storage conditions match requirements

3

Locate the physical container:

• Note the storage location from core_storage

• Navigate to the physical freezer/storage unit

• Use barcode scanner if available for verification

• Retrieve the correct container

4

Log the consumption event:

• Create a new core_consumption record

• Link to the source container

• Enter quantity used or withdrawn

• Reference your experiment ID or project code

• Specify the purpose (inoculation, subculture, distribution)

• Record the date and your name

5

Update container status:

• If partially used, update remaining quantity

• If depleted, change status to "Empty" or "Depleted"

• If returning unused portion, update status and location

• Add notes about condition (viability, contamination, etc.)

Always log consumption events immediately after retrieval to maintain accurate real-time inventory tracking and prevent discrepancies.

Strain Maintenance and Subculturing

Regular subculturing maintains strain viability and provides fresh working stocks while tracking passage history.

1

Identify strains requiring maintenance:

• Review strain records for scheduled maintenance dates

• Check passage numbers in core_batch records

• Query core_consumption for last usage dates

• Prioritize strains approaching expiration or high passage numbers

2

Review growth conditions:

• Access strain_growth_condition for the target strain

• Verify media requirements and formulation

• Confirm incubation temperature and atmosphere

• Note any special requirements or additives

3

Retrieve source material:

• Locate an appropriate source container in core_container

• Choose containers with low passage numbers when possible

• Log retrieval in core_consumption with purpose "Subculture"

• Record source container ID for lineage tracking

4

Create new batch record:

• Generate a new core_batch entry for the subcultured generation

• Increment passage number (e.g., P3 to P4)

• Use date-based naming (SC-2026-02-17-A)

• Link to parent batch for lineage tracking

• Record preparation date and personnel

5

Prepare and register new aliquots:

• Create fresh glycerol stocks, slants, or plates

• Generate core_container entries for each new aliquot

• Apply sequential container IDs

• Apply barcode labels

• Record preparation date and initial quantities

6

Assign storage and update inventory:

• Store new containers in appropriate locations

• Update core_storage assignments

• Consider retiring old high-passage containers

• Flag original containers for disposal if no longer needed

• Update maintenance schedule for next subculture

Labii automatically tracks generation lineage, allowing you to visualize the complete ancestry from original stock to current working vials through the dynamic lineage tree map.

Strain Distribution and Material Transfer

Sharing strains with collaborators or external institutions requires complete documentation for compliance and intellectual property tracking.

1

Verify strain availability and permissions:

• Locate requested strain in strain table

• Review intellectual property restrictions

• Check material transfer agreement (MTA) requirements

• Verify biosafety and export control compliance

• Obtain necessary approvals if required

2

Prepare strain information package:

• Export strain details from strain record

• Include growth conditions from strain_growth_condition

• Attach certificates or relevant documentation

• Provide safety data and handling instructions

• Generate strain data sheet for recipient

3

Prepare shipment:

• Identify suitable containers for distribution in core_container

• Create new batch if preparing fresh cultures specifically for sharing

• Prepare appropriate packaging for shipping requirements

• Include necessary documentation and labels

4

Log the distribution:

• Create core_consumption record with purpose "Distribution"

• Enter recipient organization and contact information

• Record MTA reference numbers

• Link to project or collaboration agreement

• Note quantity and format shipped

• Document shipping date and tracking information

5

Update inventory and follow up:

• Update container status (depleted if fully shipped)

• Track shipment delivery confirmation

• Maintain distribution records for audit purposes

• Schedule follow-up communication with recipient

Quality Control and Strain Verification

Periodic verification ensures stored strains maintain expected characteristics and remain viable.

1

Schedule QC testing:

• Review strain records for QC schedule

• Identify strains requiring periodic verification

• Check last verification dates in historical records

• Prioritize critical production or master strains

• Generate QC work list

2

Retrieve test samples:

• Select representative containers from core_container

• Choose containers across different storage locations

• Log retrieval in core_consumption with purpose "QC Testing"

• Record source container IDs for traceability

3

Perform verification testing:

• Culture strains according to documented growth conditions

• Perform identity confirmation (colony morphology, microscopy)

• Verify phenotypic characteristics (antibiotic resistance, markers)

• Conduct genetic testing if required (PCR, sequencing)

• Document all observations and test results

4

Compare results with specifications:

• Review original strain record characteristics

• Compare current results against documented specifications

• Identify any deviations or unexpected changes

• Assess viability and growth performance

• Evaluate contamination status

5

Update records and take action:

• Document QC results in strain records

• Update pass/fail status

• Flag problematic strains for investigation

• Quarantine or dispose of contaminated materials

• Update core_container status as needed

• Schedule next QC verification

Regular QC verification prevents experimental failures caused by strain drift, contamination, or degradation, ensuring reproducibility and data integrity.

Quick Usage Guide

Day-to-Day Operations

Typical Daily Workflow

Morning Check:

• Review scheduled maintenance tasks for strains requiring subculture

• Check low-stock alerts for strains needing replenishment

• Verify any pending distribution requests

During Experiments:

• Search strain table to identify required strains

• Check core_container availability and storage locations

• Retrieve containers and log in core_consumption immediately

• Update container status after usage

End of Day:

• Verify all consumption events were logged

• Update storage locations for any relocated containers

• Process any new strain receipts or batch preparations

• Review QC schedule for upcoming verification tasks

Common Search and Filter Operations

Finding Strains by Characteristics:

• Filter by species, genus, or specific genetic markers

• Search by biosafety level or handling requirements

• Query by source (ATCC, DSMZ, in-house isolation)

• Filter by project or research area tags

Checking Inventory Status:

• View all containers for a specific strain

• Filter by storage location (specific freezer or room)

• Search for containers by barcode or ID

• Query available vs. depleted containers

Tracking Usage History:

• View consumption records by date range

• Filter by researcher or project code

• Track usage frequency for specific strains

• Generate reports for specific experiments

Integration with Other Labii Features

ELN Integration:

• Link consumption records directly to experiment entries

• Embed strain details into protocol templates

• Auto-populate materials lists from strain selections

• Navigate from experiment to strain provenance with one click

Protocol Management:

• Reference standardized growth protocols from strain records

• Link standard operating procedures for handling

• Attach media preparation recipes to growth conditions

• Version control for protocol updates

Project Tracking:

• Associate strain consumption with specific projects

• Track project-specific strain usage for budgeting

• Generate project-level material summaries

• Link to grant numbers for reporting

Inventory Ordering:

• Monitor container levels for reorder triggers

• Generate purchase requests for commercial strains

• Track vendor information and catalog numbers

• Maintain reorder history and costs

Best Practices

Best Practices

Naming Conventions and Standardization

Strain Naming:

• Use systematic format: Genus_species_Lab#_Characteristics (e.g., Ecoli_BL21_L001_KanR)

• Include key genetic markers in abbreviated form

• Maintain consistency across all strain entries

• Document naming convention in laboratory SOPs

Batch Numbering:

• Implement date-based format: BATCH-YYYY-MM-DD-### or SC-YYYYMMDD-A

• Use sequential counters for same-day batches

• Include passage number prefix for subcultures (e.g., P4-BATCH-2026-02-17)

• Never reuse batch numbers

Container Identification:

• Apply sequential IDs within each batch (CV-001, CV-002, etc.)

• Use barcodes for high-throughput operations

• Include batch reference in container labels

• Pre-print labels before aliquoting to save time

Storage Location Coding:

• Design 5-7 level hierarchy: Building > Room > Equipment > Rack > Box > Position

• Use alphanumeric codes for easy navigation (e.g., BldgA-R101-F3-RB-B12-A5)

• Label physical locations with matching codes

• Photograph storage layouts for reference

Data Entry Guidelines

Required vs. Optional Fields:

• Configure mandatory fields: strain name, species, biosafety level, source

• Require growth temperature and media type at minimum

• Make batch and container linkages required for traceability

• Set storage location as required before container activation

Streamlining Entry:

• Create templates for common media types (LB, TSA, YPD, etc.)

• Use dropdown menus for standardized values (biosafety levels, oxygen requirements)

• Implement autocomplete for researcher names and project codes

• Enable bulk container creation for batch aliquoting operations

Photo Documentation:

• Attach colony morphology images to strain records

• Photograph microscopic features for reference

• Document packaging and labeling for distribution

• Capture storage box layouts for visual navigation

Operational Workflows

Daily Consumption Logging:

• Log all retrievals immediately—don't wait until end of day

• Use mobile devices or tablets at storage locations for real-time entry

• Implement barcode scanning to reduce manual entry errors

• Set up automated reminders for incomplete consumption records

Maintenance Scheduling:

• Configure automated alerts for strains requiring subculture

• Schedule based on passage number, age, or last usage date

• Assign maintenance tasks to specific personnel

• Track completion and reschedule next maintenance event

Quality Assurance:

• Perform random QC checks monthly on 5-10% of collection

• Verify high-value or critical strains quarterly

• Document all QC results even when results are normal

• Investigate and resolve any deviations immediately

Inventory Audits:

• Conduct physical counts quarterly for high-use strains

• Reconcile system records with physical inventory

• Flag discrepancies for investigation

• Update records to match verified counts

Common Pitfalls to Avoid

Data Integrity Issues:

• ❌ Avoid: Ad-hoc strain naming that doesn't follow conventions

• ✅ Instead: Enforce naming standards with validation rules

• ❌ Avoid: Removing containers without logging consumption

• ✅ Instead: Make consumption logging mandatory before removal

• ❌ Avoid: Vague storage locations like "freezer in corner"

• ✅ Instead: Use specific hierarchical location codes

• ❌ Avoid: Skipping growth condition documentation

• ✅ Instead: Require minimum growth parameters for all strains

Traceability Gaps:

• ❌ Avoid: Reusing batch numbers for different preparations

• ✅ Instead: Generate unique batch numbers with timestamps

• ❌ Avoid: Creating containers without linking to batches

• ✅ Instead: Require batch association before container creation

• ❌ Avoid: Failing to track passage numbers during subculture

• ✅ Instead: Auto-increment passage numbers in batch records

Operational Inefficiencies:

• ❌ Avoid: Manual data entry when barcoding is available

• ✅ Instead: Implement barcode scanning for containers and locations

• ❌ Avoid: Delayed consumption logging causing backlogs

• ✅ Instead: Log usage at point of retrieval using mobile access

• ❌ Avoid: Cluttered inventory with expired or duplicate strains

• ✅ Instead: Regular reviews to archive or dispose of unused strains

Security and Compliance

Access Controls:

• Implement role-based permissions (curator, manager, user, read-only)

• Restrict deletion privileges to collection managers only

• Require authentication for all system access

• Log all data modifications with user attribution

Audit Trail Maintenance:

• Ensure all consumption events are logged with user, date, and purpose

• Link strain usage to experiment IDs or project codes

• Maintain chain of custody for material transfers

• Generate compliance reports for regulatory inspections

Backup and Disaster Recovery:

• Enable automatic daily backups of all strain data

• Export critical strain catalog quarterly to external storage

• Maintain paper backup of master strain list

• Document recovery procedures for system failures

Biosafety Compliance:

• Flag all BSL-2 and higher strains with appropriate warnings

• Require training documentation for handling restricted agents

• Implement approval workflows for select agents if applicable

• Maintain Material Safety Data Sheets (MSDS) linked to strains

Implementation Guide

Prerequisites and Requirements

Before implementing Microbial Strain Management, ensure you have the following in place:

Technical Requirements:

• Labii ELN/LIMS platform access with appropriate subscription level

• Microbial Strain Management application enabled in your workspace

• User accounts created with role-based permissions assigned

• Barcode scanner hardware (optional but recommended for high-throughput labs)

• Label printer for container identification

• Mobile device or tablet for storage location data entry (optional but recommended)

Data Requirements:

• Complete inventory list of existing strains (if migrating from another system)

• Storage location map showing freezer layouts and hierarchies

• Standard operating procedures for strain handling and maintenance

• Biosafety level classifications for all strains

• Vendor catalog information and source documentation

• Historical usage data (if available from previous system)

Organizational Requirements:

• Designated strain collection manager or curator

• Defined naming conventions for strains, batches, and containers

• Established protocols for subculturing intervals and conditions

• Regular maintenance schedule for strain verification

• Training materials and documentation for all users

Initial Setup Process

1

Configure Storage Infrastructure (Week 1)

Map all physical storage locations throughout your laboratory:

• Document all freezers (-80°C, -20°C), refrigerators (4°C), and ambient storage

• Photograph each storage unit and its internal organization

• Create hierarchical structure in core_storage table

• Assign unique location codes matching physical labels

• Test the storage structure by searching for sample locations

2

Establish Naming Conventions (Week 1)

Define and document standardized naming schemes:

• Strain identifiers format (e.g., Genus_species_Lab#_Markers)

• Batch numbering pattern (e.g., BATCH-YYYY-MM-DD-###)

• Container ID format (e.g., CV-### for cryovials)

• Storage location coding system

• Create style guide document for reference

3

Populate Strain Catalog (Week 1-2)

Build your master strain repository:

• Prepare strain inventory spreadsheet with required fields

• Import existing strain data using bulk upload tool

• Manually verify and complete any missing information

• Assign unique identifiers following naming convention

• Document taxonomy, source, and biosafety levels

• Review entries with senior scientists for accuracy

4

Document Growth Conditions (Week 2)

Create growth condition records for reliable reproducibility:

• Create strain_growth_condition entries for each strain

• Include complete media formulations and preparation notes

• Specify temperature, oxygen, and pH requirements

• Link to detailed protocol documents where available

• Flag strains with unusual or critical requirements

• Validate conditions with experienced laboratory staff

5

Inventory Physical Containers (Week 2-3)

Systematically catalog all existing physical inventory:

• Schedule time to access each storage location

• Create core_batch records for existing lots with current information

• Generate core_container entries for every vial, tube, or plate

• Apply barcode labels to containers during cataloging

• Link containers to precise storage locations

• Record current quantities and status assessments

6

Configure User Access and Permissions (Week 3)

Set up role-based access controls:

• Create user groups (Collection Manager, Lab Manager, Researcher, Read-Only)

• Assign appropriate permissions for each role

• Configure approval workflows if required for your organization

• Set up notification preferences for each user

• Test access controls with sample users

7

Develop Training Materials (Week 3)

Prepare comprehensive user documentation:

• Create quick reference guides for common tasks

• Record video tutorials for key workflows

• Write standard operating procedures

• Develop troubleshooting guides

• Prepare FAQ document based on anticipated questions

8

Conduct User Training (Week 4)

Train all laboratory personnel on the new system:

• Schedule 2-hour hands-on training sessions by user group

• Cover searching, retrieval, and consumption logging workflows

• Practice batch creation and container management

• Demonstrate reporting capabilities

• Provide time for Q&A and hands-on practice

• Distribute training materials and contact information

9

Pilot and Validate (Week 4)

Test the system with real-world operations:

• Enforce mandatory system use for all strain transactions

• Monitor first week of operations closely

• Collect user feedback through surveys and interviews

• Validate data accuracy with physical spot checks

• Identify and address any workflow bottlenecks

• Refine processes based on user experience

Implementation Tip: Start with a pilot group of 3-5 experienced users who can provide valuable feedback before rolling out to the entire laboratory. This helps identify issues early and creates internal champions for system adoption.

Configuration Recommendations

User Permission Levels:

• Collection Manager: Full administrative access to create, edit, and delete all records; manage system configuration

• Lab Manager: Create batches and containers; edit consumption records; view all data; no deletion privileges

• Researcher: View strain catalog; log consumption events; create containers from authorized batches; no editing of master strain records

• Read-Only: View-only access to strain catalog and inventory; suitable for rotation students or external collaborators

Automation Settings:

• Enable automatic batch number generation with timestamp format BATCH-YYYY-MM-DD-001

• Configure container ID auto-increment within each batch for sequential numbering

• Set up low-stock email alerts when container count drops below threshold (recommend 3 containers)

• Schedule automated weekly reports on strain usage summarized by project or researcher

• Enable automatic passage number increment during subculture workflows

Data Validation Rules:

• Require biosafety level classification for all strain entries (BSL-1, BSL-2, etc.)

• Mandate source/origin information for new strain acquisitions

• Enforce batch linkage requirement for all container records

• Require storage location assignment before container status can be set to "Available"

• Validate consumption quantities don't exceed container capacity

Integration Configuration:

• Link strain records to ELN experiment templates for auto-population

• Connect to laboratory procurement system for reordering workflows

• Integrate project codes for automatic cost tracking and allocation

• Enable API access for data export to institutional biorepository systems

• Configure webhooks for real-time notifications to downstream systems

Success Metrics and Validation

Key Performance Indicators:

• 100% of strain usage logged within 24 hours of retrieval

• Zero orphaned containers (all containers linked to valid batches and storage)

• Container location accuracy >98% (verified through random audits)

• Average time to locate strain <2 minutes from search to physical retrieval

• User satisfaction score >4.0/5.0 based on quarterly surveys

• <5% error rate in batch/container linkages

• 95% on-time completion of scheduled maintenance tasks

Validation Activities:

• Weekly spot checks during first month comparing system records to physical inventory

• Monthly full reconciliation of high-value strain inventory

• Quarterly user surveys assessing system usability and training needs

• Annual comprehensive audit of all strain records for data completeness

• Continuous monitoring of consumption logging compliance through system analytics

Advanced Features

Automated Lineage Tracking and Visualization

Labii automatically tracks vial generation lineage, creating dynamic tree maps that visualize the complete ancestry of each strain from original stock to current working vials.

How It Works:

• Each subculture event automatically increments the generation counter

• Parent-child relationships are established when creating new batches from existing containers

• The lineage tree displays graphically with interactive navigation

• Click any node to view detailed information about that generation

Use Cases:

• Verify passage numbers before critical experiments

• Identify the original source for all current working stocks

• Track strain drift patterns across generations

• Support regulatory compliance with complete genealogy

The automatic lineage visualization helps maintain quality control by making it easy to identify high-passage strains that may need replacement from lower-passage stocks.

Scheduled Maintenance and Alerts

Configure intelligent alerting systems to proactively manage strain collection health and prevent stockouts.

Subculture Reminders:

1

Set maintenance intervals based on strain type (e.g., monthly for fastidious organisms, quarterly for hardy strains)

2

System automatically generates work lists of strains requiring subculture

3

Email notifications sent to assigned personnel with strain details and growth conditions

4

Track completion and automatically schedule next maintenance event

Low Stock Alerts:

• Define minimum container thresholds per strain (default: 3 containers)

• Automatic email alerts when inventory falls below threshold

• Auto-generate procurement requests for commercial strains

• Dashboard widget shows all low-stock strains at a glance

Expiration Tracking:

• Set expiration dates based on passage number, age, or stability data

• Flag approaching expiration 30 days in advance

• Generate disposal lists for expired materials

• Prompt QC verification before using near-expiration stocks

Advanced Reporting and Analytics

Generate comprehensive reports for laboratory management, regulatory compliance, and research insights.

Available Reports:

• Inventory Status Report: Current quantities by strain, location, or status

• Usage Analytics: Consumption patterns by strain, researcher, project, or time period

• Compliance Audit Trail: Complete chain of custody from receipt to disposal

• Maintenance Schedule: Upcoming and overdue subculture tasks

• Cost Allocation: Strain usage costs distributed by project or grant

• Storage Utilization: Freezer capacity and organization metrics

Custom Dashboards:

• Real-time inventory levels with visual indicators

• Usage trends and forecasting

• QC verification status tracking

• Storage temperature monitoring integration

• Team productivity metrics

Integration Capabilities

ELN Integration

Seamlessly connect strain management with experimental documentation:

• Embed strain selection widgets directly in experiment templates

• Auto-populate materials lists from strain consumption records

• One-click navigation from experiments to complete strain provenance

• Link protocols directly from growth condition records

• Attach experimental results back to strain records for historical context

Barcode System Integration

Streamline operations with barcode scanning:

• Scan container barcodes for instant information retrieval

• Log consumption events by scanning container and experiment barcodes

• Verify correct container retrieved from storage

• Mobile app support for scanner integration at freezer locations

• Generate barcode labels in batch during aliquot preparation

Equipment Integration

Connect with laboratory instruments and monitoring systems:

• Link to freezer temperature monitoring for continuous cold chain verification

• Integrate with automated storage and retrieval systems (ASRS)

• Connect plate readers or incubators for automated growth tracking

• Import data from colony counters or imaging systems

• Sync with environmental monitoring systems for GMP compliance

External Database Connectivity

Enable data exchange with institutional and external systems:

• Import strain metadata from ATCC, DSMZ, or other culture collections

• Export strain catalog for regulatory submissions or publications

• Sync with institutional biorepository management systems

• API access for custom integrations with LIMS or research databases

• Automated backup to institutional archives

Customization Options

Custom Fields and Attributes:

• Add institution-specific fields (internal project codes, funding sources)

• Create custom dropdown vocabularies for classifications

• Implement calculated fields (days since last use, estimated passages remaining)

• Design custom layouts for different strain types (bacteria vs. yeast vs. fungi)

Custom Workflows:

• Design multi-step approval processes for strain distribution

• Implement quarantine periods for newly received strains

• Create specialized workflows for GMP-regulated production strains

• Configure automated routing for QC verification failures

Custom User Interfaces:

• Build simplified mobile interface for consumption logging only

• Create public-facing strain catalog for external collaborators (view-only)

• Develop kiosk mode for freezer room terminals

• Design role-specific dashboards for curators vs. researchers

Custom Notifications:

• Configure email alerts for specific strain events (usage, subculture, QC)

• Set up SMS notifications for critical alerts (freezer temperature, contamination)

• Create webhook integrations for Slack or Microsoft Teams notifications

• Design custom notification rules based on strain characteristics or user roles

Troubleshooting

Common Issues and Solutions

Issue: Cannot Find Strain in Search Results

Symptoms: Searching for a known strain returns no results or incomplete results

Solution:

1

Verify search terms match exactly (check spelling and capitalization if case-sensitive)

2

Try searching by alternate identifiers (catalog number, lab code, or characteristics)

3

Check if filters are applied that exclude the strain (biosafety level, source, status)

4

Verify you have appropriate permissions to view the strain record

5

Contact system administrator if strain may have been archived or deleted

Issue: Container Shows "Depleted" but Physical Container Still Has Material

Symptoms: System indicates container is empty, but physical vial has visible material

Solution:

1

Locate the container record in the core_container table

2

Review consumption history to identify when status was changed to "Depleted"

3

If status was changed in error, update container status back to "Available"

4

Update quantity field to reflect actual remaining volume

5

Add note documenting the correction and investigation findings

Regular physical inventory audits help prevent and detect discrepancies between system records and actual stock levels.

Issue: Missing Consumption Logs After Retrieval

Symptoms: Containers were retrieved from storage but no consumption records exist

Solution:

1

Immediately create consumption records for all missing entries

2

Use container barcode history or laboratory notebooks to determine usage details

3

Contact users who accessed storage during the timeframe for information

4

Update container quantities and status based on actual current state

5

Implement mandatory mobile device usage at storage locations to prevent future gaps

Issue: Unable to Create New Container - Batch Not Found Error

Symptoms: System won't allow container creation citing missing or invalid batch reference

Solution:

1

Verify the batch record exists in core_batch table for the target strain

2

If batch doesn't exist, create appropriate batch record first with lot number and date

3

Ensure batch is linked to correct strain record

4

Retry container creation selecting the newly created batch

Issue: Storage Location Hierarchy Doesn't Match Physical Layout

Symptoms: Difficult to find containers because system organization differs from physical arrangement

Solution:

1

Photograph current physical storage layout showing actual organization

2

Map the discrepancies between system and physical locations

3

Decide whether to reorganize physical storage or update system structure (updating system is usually easier)

4

Batch update storage location assignments in core_storage to match reality

5

Re-label physical locations with codes matching system

6

Communicate changes to all laboratory personnel

Performance Issues

Slow Search Response

Causes: Large dataset, complex queries, or insufficient system resources

Solutions:

• Use more specific search criteria to narrow results

• Filter by storage location, strain type, or date ranges

• Contact system administrator to optimize database indexing

• Consider archiving historical data older than specified retention period

Report Generation Timeout

Causes: Requesting large date ranges or too many records simultaneously

Solutions:

• Break large reports into smaller date ranges

• Use filters to limit scope of analysis

• Schedule resource-intensive reports for off-peak hours

• Export data for offline analysis in spreadsheet tools

Getting Additional Help

If you encounter issues not covered in this troubleshooting section:

• Consult the Labii Knowledge Base at https://docs.labii.com

• Contact your laboratory's designated system administrator

• Submit a support ticket through the Labii support portal

• Schedule a live chat or video call with Labii support team

• Join the Labii community forum for peer-to-peer assistance

Related Documentation

• Inventory Management Overview - Understanding Labii's inventory management framework

• Storage Management - Detailed guide to storage location organization

• Batch and Lot Tracking - Managing batches across applications