OpenSpecimen

OpenSpecimen is the university's central system for managing and tracking research specimens and collections. It's designed to help labs, research groups, and collections of all sizes securely store, organise, and share specimen data in a consistent, easy-to-use platform.

OpenSpecimen Toolkit

Frequently Asked Questions

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Who is OpenSpecimen for?

Research Labs collecting biological samples (like blood, tissue, DNA)
Archaeology, Anthropology & Palaeontology managing artefacts and fossils
Environmental Scientists handling soil, water, or plant specimens
Biobanks and Core Facilities that store and distribute samples
Anyone involved in specimen collection, storage, analysis, or sharing

Why use OpenSpecimen?

Provides a unified platform for researchers to maintain a comprehensive and consistent audit trail of all specimen-related activities.
Enhances data security by consolidating specimen information currently scattered across multiple systems (e.g. Excel, OneNote, paper records) into a secure, centralised environment.
Improves incident response by enabling quick identification of specimens stored in specific containers (e.g. freezers) and highlighting available alternative storage locations in the event of an outage or technical issue.
Supports granular access control through user roles and permissions, ensuring appropriate data access based on user responsibilities.
Facilitates advanced specimen discovery with powerful querying capabilities, allowing researchers to locate specimens based on type, condition, donor characteristics, and other key attributes.
Reduces institutional risk by ensuring that specimen data is captured in a standardised and verifiable format, helping to meet potential insurance requirements in the event of specimen loss or damage.
Aligns with industry best practices, as many leading universities and research institutions globally are adopting OpenSpecimen to modernise and streamline their biobanking operations.

Specimen Centric Vs Participant Centric

OpenSpecimen also makes it easy for researchers to manage and register specimens in participant-centric studies, where the focus is on tracking samples linked to individual participants over time.

With OpenSpecimen, researchers can:

Register specimens directly to participants using unique identifiers, ensuring accurate linkage between biospecimens and participant data.
Track longitudinal collections, such as multiple timepoints or follow-up visits, which is essential for clinical trials and cohort studies.

OpenSpecimen Toolkit

Find below our list of resources and guided modules:

Frequently asked questions

What is a Site in OpenSpecimen?

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.

What is a Collection Protocol (CP)?

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.

Is OpenSpecimen just for biological samples?

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.

Do I need ethics approval to use OpenSpecimen?

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.

Can I use OpenSpecimen just for tracking storage?

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.

What if multiple people in my lab need access?

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.

What if my data is messy and incomplete?

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.

What if my specimens don’t have a consistent storage layout?

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.

Do I need to upload all my data right away?

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.

What if I don’t use barcodes on my specimens?

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.