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Administration

Platform administration, user management, and instrument configuration.

Admin role

Platform administrators have elevated permissions that extend beyond group membership:

  • View all content across all groups (regardless of visibility settings)
  • Manage instruments and QC platform configuration
  • Import Fragment Analyzer data
  • Link samples to QC runs across all groups
  • Manage news posts
  • Access system-wide statistics

Admin status is assigned at the database level and is separate from group roles.

Instrument management

The instrument overview page (Docs → Instruments & QC) shows all sequencing platforms with:

  • Instrument inventory (model, serial number, status)
  • Run counts and sample totals per platform
  • Recent run activity
  • Project folder summary

Sample-run linking

Administrators can link ISA samples to QC runs to establish provenance between the LIMS and sequencing dashboards:

  1. Navigate to the Sample-Run Links admin page
  2. Select a platform (Illumina, Nanopore, PacBio)
  3. Browse runs and select one
  4. Map QC samples to ISA samples
  5. Confirm the linkage

Fragment Analyzer import

The Fragment Analyzer import tool parses PDF reports from Agilent Fragment Analyzer instruments and creates measurement records linked to ISA samples:

  1. Navigate to FA Import
  2. Upload a Fragment Analyzer PDF report
  3. Review the parsed data and map samples to ISA entities
  4. Confirm the import

Supported methods: DNF-471 (RNA + RQN), DNF-464 (large DNA), DNF-473 (NGS fragment analysis).

API key management

Users can create API keys for programmatic access to the platform:

  1. Navigate to API Keys in the user menu
  2. Click Create Key
  3. Give it a descriptive name
  4. Copy the key immediately — it is shown only once

Keys can be revoked or deleted at any time. Each key tracks its last-used time and request count.

Notification preferences

Users configure their notification preferences from the user menu. Available notification types:

  • Review requests and decisions
  • Comment and @mention notifications
  • Task assignments
  • Group invitations

Email notifications (when configured) are sent via PHPMailer over SMTP.

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