Experiment Management

bioAF provides structured experiment and sample management that follows community metadata standards and tracks the full lifecycle from bench to publication.

Structured metadata

Every experiment in bioAF captures MINSEQE-compliant metadata:

  • Organism, tissue type, and cell type
  • Sequencing chemistry and platform
  • Experimental conditions and treatments
  • Library preparation details

This metadata travels with your data through every step (from sample registration to pipeline execution to final results), so nothing is lost.

Sample management

Samples are organized within experiments and can be grouped into batches for processing. Each sample carries:

  • Descriptive metadata (tissue, treatment, conditions)
  • Processing status
  • Links to uploaded FASTQ files
  • Links to pipeline results

Experiment detail page with sample table, batch groupings, and status indicators

Experiment lifecycle

Every experiment moves through a defined status workflow:

Registered → Library Prep → Sequencing → FASTQ Uploaded → Processing → Pipeline Complete → Reviewed → Analysis → Complete

The current status is always visible, and every status transition is recorded in the audit log.

GEO submission export

When you’re ready to publish, bioAF can export your experiment metadata in formats compatible with GEO submission, including Excel spreadsheets with all required fields pre-populated.