Studies
A Study is an analysis and publication grouping. It answers the question “which samples belong together scientifically?” — which is almost never the same as “which samples arrived in the same box?”
A sequencing order is a transaction with the facility. A study is a research
object: it has a title and description that will appear in the European
Nucleotide Archive, one MIxS checklist that all its samples share, and a single
accession (PRJEB…) once it is registered. Pipelines run against a study;
submissions are built from a study.
A sample belongs to exactly one sequencing order and to at most one
study. Sample.studyId is nullable, so a sample can sit outside any study
indefinitely, and moving it between studies means removing it from the first
one before adding it to the second.
Study or sequencing order?
| Sequencing Order | Study | |
|---|---|---|
| Purpose | Get sequencing done | Analyse and publish |
| Created by | The person requesting sequencing | The person doing the analysis |
| Owns samples | Yes — orderId is required | No — it borrows them via studyId |
| Spans | One request | Any number of orders |
| Statuses | DRAFT → SUBMITTED → COMPLETED | Boolean flags, not a status column |
| Public identifier | ORD-YYYYMMDD-XXXX, internal | PRJEB…, assigned by ENA |
| Deleting it | Destroys the samples | Leaves the samples in their orders |
The two most common shapes are: one order, one study (a self-contained project), and many orders, one study (a longitudinal survey where each sampling campaign was ordered separately but all of it publishes together).
How a study progresses
Studies have no status column. Their state is the combination of four fields,
and the interface renders a badge from them:
Draft ──mark ready──▶ Ready ──test submission──▶ Test Registered ──submit──▶ Registered| Badge | Condition |
|---|---|
| Draft | Nothing set yet |
| Ready | readyForSubmission = true |
| Test Registered / Test Expired | studyAccessionId and testRegisteredAt set; ENA test accessions expire after 24 hours |
| Partial | studyAccessionId set but no test registration — the study registered, sample registration did not finish |
| Registered | submitted = true |
The full rules are in Study Workflow.
The study workspace
Once a study exists, the sidebar gives you these surfaces:
| Surface | What it is for |
|---|---|
| Table Overview | One row per sample, every metadata column, inline editing and CSV/XLSX export |
| Overview | Study details, completion tracker, the Mark as Ready control |
| Facility Fields | Admin-only study fields (facility admins, when configured) |
| Sequencing Data | The study’s samples and their linked read files |
| Analysis | Pipeline runs launched from this study (facility admins) |
| Publishing | ENA registration and submission |
Where to start
- First study? Read Creating Studies. Have your samples’ orders submitted first — the wizard opens on sample selection.
- Choosing a checklist? Study Metadata & MIxS explains the environment packages, why the choice is effectively permanent, and how version pinning protects an old study from a catalog update.
- Getting to a publication? Study Workflow
covers
readyForSubmission, test submissions and the deletion rules.
Related sections
- Sequencing Orders & Samples — where the samples come from.
- Pipelines & Analysis — study-scoped Nextflow runs.
- Administration → Form Builders — customising the study questionnaire, including per-study questionnaires.