Guide for Bench Scientists

This guide covers the day-to-day workflow for bench scientists using bioAF. Everything here happens in your web browser, no command line or coding required.

Registering an experiment

  1. Click New Experiment from the Experiments page
  2. Fill in the experiment metadata:
    • Name and description
    • Organism and tissue type
    • Chemistry (e.g., 10x Chromium 3’ v3)
    • Any relevant experimental conditions
  3. Click Create

New Experiment form with metadata fields

bioAF uses MINSEQE-compliant metadata standards so your experiments are publication-ready from the start.

i What is MINSEQE?
MINSEQE (Minimum Information about a high-throughput Nucleotide SeQuencing Experiment) is a community standard for the metadata you should record about a sequencing experiment. bioAF's experiment form is built around this standard so you capture everything you'll need for publications, GEO submissions, or regulatory review.

Adding samples

  1. Open your experiment and click Add Samples
  2. For each sample, enter:
    • Sample name and description
    • Tissue type and cell type
    • Treatment conditions
    • Any custom metadata fields
  3. You can add samples one at a time or batch upload from a spreadsheet

Sample table showing batch of samples with metadata columns

Uploading FASTQ files

  1. Navigate to your experiment’s Data tab
  2. Drag and drop your FASTQ files, or click Upload
  3. bioAF automatically associates files with the correct samples based on naming conventions

File upload dialog with drag-and-drop area

i Can the sequencer upload automatically?
Yes. If your admin has configured auto-ingest, bioAF watches for new files from your sequencer and imports them automatically. Ask your admin if this is set up.

Viewing results

Once a pipeline has run on your experiment:

QC dashboards

Navigate to Results > QC on your experiment page. The QC dashboard shows quality metrics for your sequencing run, cell counts, read depth, mapping rates, and more.

QC dashboard showing cell counts, read depth, and quality metrics

Interactive single-cell visualization

Click View in cellxgene to open an interactive explorer for your single-cell data. You can:

  • View UMAP/t-SNE embeddings
  • Color cells by gene expression, cluster, or metadata
  • Select cell populations for comparison
  • Export plots

CellxGene Discover showing UMAP embedding colored by cell type clusters

Downloading results

From the Data tab, you can browse and download any output files, count matrices, processed h5ad files, plots, and reports.

Getting notifications

bioAF can notify you when:

  • A pipeline finishes running on your experiment
  • QC results are available
  • Someone comments on your experiment
  • Your experiment’s status changes

Check your notification preferences under your Profile settings.