Documentation

Getting started

What the workbench is, your account, and finding your way around.

• What the workbench is and how work is organised Reference, Workflow animation Available
• Your account How-to, Screenshots Available
• Finding your way around Reference, Screenshots Available
• Searching records How-to, Video walkthrough Available

Projects, datasets and access

The containers that hold records and decide who can see them.

• Projects and datasets explained Reference Available
• Sharing a project or dataset How-to, Screenshots Available
• The recordset console Reference, Video walkthrough Available
• Moving records between projects and datasets How-to Available

Records and evidence review

What a record holds and the views for checking it against its evidence.

• What a record holds Reference, Screenshots Available
• Maps, images, alignments and traces Reference, Screenshots Available
• Downloading records, sequences and files How-to Available

Adding specimens and sequences

Getting records into the platform, in bulk or one at a time.

• How data gets in Reference, Workflow animation Available
• Batch specimen upload How-to, Video walkthrough Available
• Adding or editing one specimen How-to, Screenshots Available
• Uploading sequences How-to, Screenshots Available
• Tracking your uploads Reference, Screenshots Available

Attaching evidence files

Photographs, documents, chromatograms, fingerprints and notebooks, stored with the record.

• Evidence files Reference Available
• Uploading an evidence package How-to, Video walkthrough Available
• Attaching a file to one record How-to, Screenshots Available

Running analyses

Choosing records, configuring a method, and reading the report.

• Running an analysis How-to, Video walkthrough Available
• Tracking jobs and reading reports Reference, Screenshots Available
• Which method answers which question Reference Available

Expert statements

Statements prepared from a record for use as evidence.

• Statements and deponents Reference Available
• Generating a statement How-to, Screenshots Available
• Review, signing and retention Reference, How-to Available

How the platform handles your data

Access, logging and retention as they are implemented.

• Access, logging and retention Reference Available

How the platform fits together

The services, how data moves between them, and how they trust each other.

• Platform architecture and data flow Reference, Workflow animation Available
• How services authenticate to each other Reference Available

Record store and search

Where records live and how they are searched and summarised.

• Records, sets, search and summaries Reference Available
• From upload to loaded record Reference, Workflow animation Available

BioStor file storage

How evidence files are typed, processed and kept.

• BioStor: what it stores and how files flow Reference, Workflow animation Available
• File types, pipelines and size limits Reference Available
• Evidence profiles Reference Available
• Object lifecycle and statuses Reference Available
• Accounts and the access model Reference Available

Analysis service

How jobs are queued, run and returned.

• Broker, scheduler, worker and storage Reference, Workflow animation Available
• Job lifecycle Reference Available
• Anatomy of a result package Reference Available

Analytical methods

One page per method: purpose, inputs, the parameters actually applied, outputs and limitations.

• The methods and their shared pipeline Reference Available
• Identification Reference Available
• Distance summary Reference Available
• Barcode gap Reference Available
• Diagnostic characters Reference Available
• Tree construction Reference Available
• Sequence composition Reference Available
• Specimen and sequence exports Reference Available
• Specimen and sequence ingest Reference Available

Identification engine

The public identification service and its reference libraries.

• How the public identification service decides Reference Available
• Reference libraries and builds Reference Available

Method validation and quality

What is known about each method's performance and limits.

• Software, versions and citations Reference Available
• Known limitations of the methods Reference Available
• Validation studies Reference Planned

Building new analyses

Creating a method from the template module and running it within the platform.

• Building a method from the template How-to Available
• Registering a method in the workbench How-to Available
• Testing a method How-to Available

Getting started

Which API to use, how to authenticate, and the conventions they share.

• Which API to use Reference Planned
• Authentication Reference Planned
• Conventions and errors Reference Planned

Endpoint references

Generated from each service.

• Workbench API Reference Elsewhere
• Data API Reference Planned
• Analysis API Reference Planned
• BioStor API Reference Planned

Webhooks

Notifications BioStor sends when processing finishes.

• BioStor webhooks Reference Planned

Recipes

Worked examples for common integrations.

• Submit an analysis and collect the result How-to Planned
• Upload a file and attach it to a record How-to Planned
• Load specimen records in bulk How-to Planned
• Search and export records How-to Planned

Accounts

Who administers the platform and how accounts are created and managed.

• The administrator role Reference Available
• Inviting a new user How-to, Screenshots Available
• Managing accounts How-to Available

People and institutions

The registries that statements and records draw on.

• The people registry and deponents How-to Available
• Institutions How-to Available

Reference lists

Markers, primers, geography and taxonomy.

• Markers and primers How-to Available
• Geography How-to Available
• Taxonomy How-to Available

Projects and datasets

Administering recordsets across the platform.

• Overseeing projects and datasets How-to Available

Oversight

Watching the work that flows through the platform.

• The submission queue Reference, Screenshots Available
• Analysis jobs Reference Available
• Statements Reference Available
• Publication requests How-to Available
• Activity reports Reference Available

Data standards

The Barcode Core Data Model and the forensic extension.

• Barcode Core Data Model (BCDM) Reference Elsewhere
• BCDM forensic extension Reference Elsewhere
• Field dictionary Reference Planned
• Controlled vocabularies and validation rules Reference Planned
• Darwin Core crosswalk Reference Planned
• Upload templates Reference Planned

Quick reference

Tables to look things up in.

• Access levels at a glance Reference Planned
• File types and limits Reference Planned
• Upload and job statuses Reference Planned
• Glossary Reference Planned

Help and updates

• Release notes Reference Planned
• Frequently asked questions Reference Elsewhere
• Support How-to Elsewhere
• System status Reference Elsewhere