Understanding Workspaces

Workspaces in VariantMiner are data containers that organize and isolate genomic data within organizations. They provide a secure, structured environment for managing files, samples, subjects, and analysis results.

What is a Workspace?

A workspace is a logical container within an organization that holds:

• Files: VCF, BAM, and other genomic files

• Samples: Biological specimens from patients

• Subjects: Patient/individual records

• Orders: Analysis requests and workflows

• Reports: Clinical reports and interpretations

• Variant Data: Processed variant information

Workspace Benefits

Data Isolation

• Complete separation between different projects or studies

• Prevents accidental data mixing

• Maintains patient privacy and compliance

• Independent access controls

Project Organization

• Group related samples and analyses

• Maintain consistent naming conventions

• Track project progress and milestones

• Archive completed projects

Collaboration

• Share data with specific team members

• Control access levels by workspace

• Collaborative analysis and reporting

• Activity tracking and audit trails

Workspace Hierarchy

Organization
├── Workspace A (e.g., "Cancer Panel Study")
│   ├── Files (VCF, BAM files)
│   ├── Samples (Patient specimens)
│   ├── Subjects (Patient records)
│   ├── Orders (Analysis requests)
│   └── Reports (Clinical reports)
├── Workspace B (e.g., "Rare Disease Cohort")
│   ├── Files
│   ├── Samples
│   └── ...
└── Workspace C (e.g., "Quality Control")
    ├── Files
    └── ...

Workspace Types

Clinical Workspaces

• Purpose: Clinical testing and reporting

• Data: Patient samples for diagnostic testing

• Access: Restricted to clinical staff

• Compliance: HIPAA and other regulatory requirements

Research Workspaces

• Purpose: Research studies and investigations

• Data: De-identified or consented research samples

• Access: Research team members

• Compliance: IRB and research protocols

Quality Control Workspaces

• Purpose: Laboratory quality assurance

• Data: QC samples and control materials

• Access: Laboratory staff and supervisors

• Compliance: Laboratory accreditation standards

Training Workspaces

• Purpose: User training and education

• Data: Synthetic or anonymized training data

• Access: Trainees and instructors

• Compliance: Educational use policies

Accessing Workspaces

Workspace Selector

• Located in the top navigation bar

• Shows your available workspaces

• Click to switch between workspaces

• Current workspace is highlighted

Workspace Dashboard

Each workspace has its own dashboard showing:

Workspace dashboard displaying files, members, and workspace statistics

• File processing status

• Recent activity

• Sample counts

• Order progress

• Storage usage

Permissions Required

To access a workspace, you need:

• Organization membership

• Workspace-specific role assignment

• Appropriate permission level for your tasks

Default Workspace

Setting Your Default

• Choose the workspace you use most frequently

• System opens to default workspace on login

• Can be changed in user profile settings

• Saves time and improves workflow efficiency

Organization Default

• New users may be assigned to organization default workspace

• Typically a general-purpose or training workspace

• Administrators can configure organization defaults

• Users can request access to additional workspaces

Workspace Context

Data Scoping

When working in VariantMiner:

• All data views are scoped to current workspace

• Searches only return results from current workspace

• Reports only include data from current workspace

• Activity tracking is workspace-specific

Switching Context

To work with data in different workspaces:

• Use workspace selector to switch

• Interface updates to show new workspace data

• Bookmarks and saved searches are workspace-specific

• Recent activity resets to new workspace

Best Practices

Workspace Organization

• Descriptive Names: Use clear, meaningful workspace names

• Consistent Structure: Follow organization naming conventions

• Purpose Alignment: Create workspaces based on projects or studies

• Size Management: Keep workspaces focused and manageable

Data Management

• Regular Cleanup: Remove obsolete files and data

• Archive Completed: Archive finished projects appropriately

• Monitor Usage: Track storage and processing usage

• Backup Important: Ensure critical data is backed up

Access Control

• Principle of Least Privilege: Grant minimum necessary access

• Regular Review: Periodically review workspace access

• Role Clarity: Ensure users have appropriate roles

• Documentation: Document workspace purpose and access policies

Common Workspace Scenarios

Multi-Project Laboratory

├── Workspace: "Oncology Panel 2024"
├── Workspace: "Cardio Panel 2024" 
├── Workspace: "Exome Analysis"
├── Workspace: "Quality Control"
└── Workspace: "Training Environment"

Research Institution

├── Workspace: "Autism Study Cohort"
├── Workspace: "Cancer Genomics Project"
├── Workspace: "Population Genetics"
└── Workspace: "Method Development"

Clinical Laboratory Network

├── Workspace: "Site A - Clinical Testing"
├── Workspace: "Site B - Clinical Testing"
├── Workspace: "Central QC"
└── Workspace: "R&D Projects"

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Ready to create and manage workspaces? Continue to Creating & Managing Workspaces for detailed instructions.