OpenSpecimen

1.1 Getting started checklist
1.2 OpenSpecimen at a glance
1.3 Glossary of key terms

2.1 What information do I need
2.2 Request Setup of a New Site and User Accounts

3.1 Using the AI Helpdesk Tool in OpenSpecimen
3.1(b) Using the AI Helpdesk Tool in OpenSpecimen [VIDEO]
3.2 Create a Collection Protocol in OpenSpecimen
3.2(b) Create a Collection Protocol in OpenSpecimen [VIDEO]
3.3 Define Participant Requirements In OpenSpecimen
3.3(b) Define Participant Requirements in OpenSpecimen [VIDEO]
3.4 Assign User Roles in Open Specimen
3.5 Enable Auto Generated Labels in OpenSpecimen
3.5(b) Enable Auto Generated Labels in OpenSpecimen [VIDEO]
3.6 Configure Storage Containers in OpenSpecimen
3.6(b) Configure Storage Containers in OpenSpecimen [VIDEO]

Please note: Videos are available via Youtube and are not included in the module download.

4.1 Manually Enter Specimen Data into OpenSpecimen
4.1(b) Manually Enter Specimen Data into OpenSpecimen [VIDEO]
4.2 Manually Enter Participant Data into OpenSpecimen
4.2(b) Manually Enter Participant Data into OpenSpecimen [VIDEO]
4.3 Bulk Uploading Data into OpenSpecimen

Please note: Videos are available via Youtube and are not included in the module download.

5.1 Frequently asked questions
5.2 Tips from other labs

6.1 Customising your home screen

A Site typically refers to your lab, research group, or designated collection area at Flinders - such as a clinical lab at Tonsley or a field station. It defines your space within the system and determines who can access, view, or manage your specimens.

A Collection Protocol is like a digital folder that organises all specimens for a specific Flinders research project or ethics-approved study. It includes key details like the project name, lead researcher, ethics approval reference, and specimen types.

There are two types of Collection Protocols:

Participant Centric CPs follow individuals through their clinical journey, collecting specimens at defined events (e.g., Recruitment, Diagnosis, Birth).

Specimen Centric CPs manage specimens without linking to participant data.

No. OpenSpecimen supports a wide range of specimen types used at Flinders, including fossils, artefacts, soil samples, plant materials, textiles, and pigments. It’s flexible enough for diverse disciplines.

Only if your specimens require it, such as samples from human participants. For artefacts or environmental samples, ethics may not be required, but your Collection Protocol should reflect any approvals or permits relevant to your project.

Yes! Come Flinders groups use OpenSpecimen solely to record where samples are stored, such as freezers, cupboards, or field kits. You don’t need to use every feature.

You can assign access to as many users as needed. Each person can be given a role, such as Researcher, Technician, or Administrator to control what they can see or do in the system.

That’s okay, start with whatever records you have. The OpenSpecimen team can help you clean and organise your data over time. Many Flinders labs begin with partial records and build up gradually.

No problem. OpenSpecimen supports dimensionless containers, like archive boxes, field crates, or compactus drawers where items are stored loosely without specific rows or columns. You don’t need to change how you store things.

Not at all. You can start small and add more data over time. If you already have spreadsheets, the OpenSpecimen team can help you import them. Otherwise, you can manually enter new specimens as needed.

That’s absolutely fine! OpenSpecimen supports handwritten labels, printed labels, and barcoded labels. You can continue using your current method and transition to auto-generated barcoded labels later if you’d like to improve tracking across your Flinders lab or field site.