Guided tour

How SampleTown works

SampleTown follows an environmental-DNA sample from the moment it is a bottle of lake water to the moment it is a published, standards-compliant dataset. This tour walks the whole path — the eight stages of the lab workflow, and the tools that work across all of them.

New here? Everything below is read-only reading. When you want to try it, sign in with the demo account (guest / guest) — a lab pre-loaded with example data.

The big picture

Almost everything in SampleTown is one long chain. Each record is created from the one before it and carries its context forward, so from any sequencing read you can trace back to the exact litre of water and the site it came from. That chain is the backbone of the app:

1 Projects The umbrella for a field campaign
2 Sites Where a sample was collected
3 Samples The physical thing you collected
4 Extracts DNA (or RNA) pulled from a sample
5 PCR Plates Amplifying a target gene
6 Library Plates Barcoding for the sequencer
7 Sequencing Runs Turning libraries into reads
8 Analyses Making sense of the reads

One lab, one workspace

Everything you create lives inside a lab. You can belong to several and switch between them from the name in the top-left.

Every record is linkable

Each entity has a permanent QR code and /id/… link — print it on a tube, scan it to jump back.

Standards-first

Samples are MIxS-compliant and exports are submission-ready, so your data travels cleanly to public archives.

Getting started

1 · Sign in

Sign in with GitHub or a local username and password. The public demo is guest / guest — read/write access to a lab loaded with example data, a good place to click around.

2 · Land in a lab

The first time you sign in you either start your own lab (you become its admin) or accept an invite to join one. A lab is your team's private workspace — no data is ever shared across labs.

3 · Know your role

Roles are set per-lab:

🐙Admin — manages people, invites, lab settings and backups, on top of everything a user can do.
🐟User — reads and writes all the science: projects, samples, plates, runs and the lab's vocabularies.
🐚Viewer — read-only. Every edit button is hidden and every write is refused.

The sample lifecycle

The eight stages, in order. Each has a list view (sortable, filterable, selectable) and a detail page with a breadcrumb tracing it all the way back up the chain.

Projects

— The umbrella for a field campaign Open /projects →

A project groups everything in one research initiative — its sites, its samples, and all the downstream lab work — under a single name.

What you record: Project name · principal investigator & institution · contact email · funding sources · free-text description.
How it connects: The top of the tree. A project contains sites, and through them every sample, extract, plate, run and analysis beneath.
What you can do: Create, edit or duplicate a whole project; bulk-delete; see a roster of everyone who contributed to any record inside it; attach permits and check their coverage.

Sites

— Where a sample was collected Open /sites →

A site is a geographic sampling location — a lake shore, a transect point, a borehole — with coordinates and a habitat description.

What you record: Site name & short code · latitude / longitude · geographic name (country:region) · ENVO biome & local feature · access notes.
How it connects: Belongs to a project. Samples are collected at a site.
What you can do: Drop a pin on an interactive map to set coordinates; the list view plots every site as a colour-ranked pin; keep a photo gallery per site.

Samples

— The physical thing you collected Open /samples →

A sample is one physical specimen taken at a site on a date — a litre of filtered water, a sediment core, a swab. This is the MIxS-compliant heart of the record.

What you record: Sample name · collection date · environmental medium · depth / elevation · the readings (temperature, salinity, pH, oxygen…) · collection gear & method · storage / preservation — plus hundreds of optional MIxS slots.
How it connects: Belongs to a project and a site. DNA extracts are made from a sample.
What you can do: Add one at a time, through a fast quick-capture form, or by batch-importing a spreadsheet; add extra MIxS columns to the table on the fly; attach photos; read permit coverage (✓ / ✗) right in the list.

Extracts

— DNA (or RNA) pulled from a sample Open /extracts →

An extract is nucleic acid isolated from a sample — the input to PCR and sequencing.

What you record: Extract name & date · extraction method / kit · nucleic-acid type · concentration & volume · 260/280 & 260/230 quality ratios · storage room / freezer box.
How it connects: Belongs to a sample. Feeds PCR reactions and library preps.
What you can do: Create, edit or duplicate; record quantification numbers (NanoDrop, Qubit) and yield.

PCR Plates

— Amplifying a target gene Open /pcr →

A PCR plate holds a set of reactions that share the same primers and cycling conditions — one reaction per well, each amplifying one extract.

What you record: Plate name & date · target gene / subfragment · forward & reverse primers (or pick a saved primer set) · annealing temperature & cycles · per reaction: well, band observed, post-PCR concentration.
How it connects: Reactions draw from extracts and feed library preps.
What you can do: Lay reactions out on a 96-well grid; export the plate as TSV; print a plate map for the bench notebook. Reactions can also live "orphan", off any plate.

Library Plates

— Barcoding for the sequencer Open /libraries →

A library prep turns a PCR product (or an extract directly) into a sequencer-ready, indexed library. Library plates group preps the way PCR plates group reactions.

What you record: Plate name · library type / source / selection · platform & instrument · i7 / i5 index sequences · prep kit · fragment size · final concentration.
How it connects: Sourced from a PCR reaction or an extract. Loaded onto sequencing runs.
What you can do: Assign indices per well; export or print the plate; SRA-aligned vocabulary keeps everything submission-ready.

Sequencing Runs

— Turning libraries into reads Open /runs →

A run is one sequencing job — a flowcell load — that produces FASTQ files. Many libraries ride on a single run.

What you record: Run name & date · platform & instrument · flow-cell ID · run & FASTQ directories · total reads & bases.
How it connects: Holds many libraries. Analyses are run on it.
What you can do: List every library multiplexed onto the run; point at where the raw data lives on disk.

Analyses

— Making sense of the reads Open /analysis →

An analysis records a bioinformatics pipeline run against a sequencing run’s data — the taxonomy tables, reports and results.

What you record: Pipeline name / version / profile · status (pending → running → complete / failed) · input & output directories · reference database · results summary · report link.
How it connects: Belongs to a sequencing run. The end of the chain.
What you can do: Track pipeline status; link out to the HTML report or dashboard.

Tools that work everywhere

A handful of features sit above the workflow and apply to every stage.

🛒 The cart

Tick boxes on any list to drop records into the cart. It follows you across pages and survives a reload. Use it to print a batch of labels, or to spin up the next stage in bulk — selected samples become new extracts, extracts become a PCR plate, and so on. Carts can be saved and shared with the lab.

⊞ Scan & QR codes

Every record carries a QR code. Open the scanner (top bar) and read it with a phone camera or a handheld barcode scanner to jump straight to the record. Scan a blank, pre-printed label in the field to claim it as a fresh sample on the spot.

🏷️ Labels

Generate Avery-sheet PDFs or print to a Zebra label printer. Pre-print blank ID labels before a field trip, or print labels for exactly the items in your cart — each with its QR code and name.

🔍 Dashboard, search & calendar

The home page counts every entity at a glance and shows a colour-coded activity calendar following the ROYGBIV path of a sample's life. The magnifier jumps to a search that matches any name, ID, person or date. Every table sorts, filters, colour-codes (shift-click a header) and multi-selects.

Import & export

Import a spreadsheet

Upload a TSV or Excel file of samples. SampleTown maps your columns, matches or creates sites by coordinates, and shows a full dry-run preview before anything is written — the import is all-or-nothing. Start from a downloadable template for any checklist and extension.

Export MIxS

Pull your samples out as a MIxS-compliant TSV — the whole lab or a single project, for any checklist and extension. Because it is standards-aligned, it drops straight into downstream sequence archives.

Go to Import / Export →

Standards & governance

SampleTown is opinionated about doing eDNA data well — both technically and ethically.

MIxS, end to end

Samples speak MIxS (Minimum Information about any Sequence). The Glossary is a searchable reference for every field, checklist and extension — the same definitions the sample forms link to inline.

Permits & sensitive locations

Permits are first-class records with GGBN-aligned types (collecting, export, PIC, MAT, ethics…). Every sample should be traceable to one, and the samples list shows coverage at a glance. Flag a sample's location as sensitive to coarsen its coordinates on export, protecting sites where precise locations could enable harm.

FAIR, CARE and the rest

The Principles page lays out the governance story in full — FAIR as the technical floor, CARE and OCAP® for Indigenous data sovereignty, and the Nagoya Protocol backdrop for genetic-resource consent.