OpenSpecimen

OpenSpecimen is a highly-configurable, web-based biobanking laboratory management information system (LIMS) that helps users collect high-quality biospecimen data and track biospecimens from collection to utilization. OpenSpecimen is being used by many of the world’s leading research centers and is now being used by The University of Arizona. In early 2023, OpenSpecimen replaced TissueMetrix, which was adopted in late 2009 and was being used by U of A Health Sciences, U of A Cancer Center, and U of ACollege of Medicine – Phoenix.

To see if OpenSpecimen can accommodate your biobanking needs, please contact us, for more information.

ONLY IRB-approved studies and protocols will be allowed to store information in OpenSpecimen. CB2 staff is ONLY responsible for managing the OpenSpecimen application and supporting its users from a technical standpoint. It is up to each investigator to manage user access to their collection(s), maintain their IRB approvals, and protect their data in compliance with Federal Privacy Regulations (HIPAA) and with agreements with their approving IRB.

Why use OpenSpecimen?

GLOBAL ADOPTION

Used in 90+ clinical research centers across 20+ countries (including Johns Hopkins, Pittsburgh, Emory, Oxford, Cambridge, Melbourne, University of New South Wales)
Click HERE for a complete list of institutions using OpenSpecimen

UNLIMITED COLLECTION PROTOCOLS AND USER ACCOUNTS

NO LIMIT to the number of collection protocols (i.e., biobanks) that we can have in OpenSpecimen. Users can create as many collection protocols as they need to track all of their individual studies or biospecimen collections
NO LIMIT to the number of users, and we are not limited to a specific number of user licenses, so sites can create user accounts for all of their members that need access to their biobank information
Users and collection protocols will be vetted prior to access and creation, details will be made available once the vetting process has been created

NO COST TO USERS

There is no user license fee to use OpenSpecimen and no fees for creating collection protocols or general support
There may be fees for more complex collection protocol configurations or additional one-on-one support

HIGH CONFIGURABILITY

Configure screens, data entry workflows, forms, fields, and field values based on your needs

DATA COLLECTING AND REPORTING

Collect disease/study-specific data at Participant, Visit, or Specimen level, and use the Reporting module to look for specimens of interest

COMMUNITY DRIVEN

The OpenSpecimen Community meets regularly in web-meetings and online forums, and provides feedback on features, pain-points, and improvements

FOCUSED DEVELOPMENT AND RAPID IMPROVEMENT

OpenSpecimen is Krishagni Solution’s only product, so they are able to focus on improving the product and providing timely support to our users
New versions are released every 3-4 months and include application upgrades, new features, and bug fixes based on the community’s needs

OpenSpecimen Features

USER MANAGEMENT

Control user privileges at a granular level – per study or group/site
Create custom user roles and customize data privileges and access for each data level
Restrict protected health information (PHI) access
Users can have multiple roles for each collection protocol that they are assigned to

COLLECTION PROTOCOLS

Longitudinal, single-site or multi-site protocols
Define collection events, primary specimens, and processing details
Design a study calendar and track specimen collection and lineage

CONSENTS

Collect and track patient consent and validate during specimen distribution
Configure consent questions within a collection protocol and collection responses for each participant

FREEZER/STORAGE CONTAINER MANAGEMENT

Create and track any type of freezer or storage container
Restrict containers by specimen type or study
Predefine “container types” to create a complete container hierarchy with a single click
Create containers in bulk
Transfer boxes or racks from one freezer to another
Create “dimensionless” containers, or containers without predefined dimensions, for temporary storage
Automatically allocate boxes to specimens during collection

DISTRIBUTION

Track specimen distribution to researchers
Manage distribution invoicing

SHIPMENTS

Ship specimens among collaborating sites
Track the shipment, receiving, and storage of samples to both internal and external entities

CUSTOM FORMS & FIELDS

Create custom fields and forms based on your study needs using a robust UI form builder
Custom fields can be of various field types (e.g., dropdown list, checkbox, multi-select checkbox, radio button, date picker, file upload, etc.)
Custom fields can be added to default data entry pages (e.g., Participant, Visit, Specimen) and can be used in reporting
All custom fields can be queried

SPECIMEN CARTS

Create, save, and share specimen lists or mark specimens of interest for further use
Perform bulk operations like shipping, distributing, annotating, deleting, or transferring specimens

SPECIMEN CATALOGS & REQUESTS

Display specimens and collection protocol information to improve the utilization of specimen resources within your biobank
Create configurable displays and request forms for researchers to filer and request specimens of interest
Easily share data with researchers in one or more online catalogs and manage specimen requests

REPORTING

The reporting module allows users to query any data related to a specimen, participant, or user
Some reporting examples are count-based reports, inventory reports, distribution reports, consent reports, specimen processing reports
Save queries for future user, organize them in folders, and share them with other users
Export and import query definitions
Export data into CSV files

DASHBOARDS

Dashboards are a graphical representation of the current status of each collection protocol
Create and configure visually appealing dashboards per study, catalog, or system level with an easy-to-use interface
Embed dashboard graphs in external websites to display live data

BULK IMPORT

Import CSVs for almost every object to add, edit, or delete data
Includes custom forms and fields
Useful for legacy data migration and high-throughput workflows, where the manual entry of each specimen is time-consuming

REST APIs

OpenSpecimen is 100% REST API-enabled
APIs can be consumed to develop custom user-interfaces for integration with other databases
A majority of the REST APIs can be invoked only by authenticated users, which requires valid credentials and an API token

AUDIT & SECURITY

Every operation is audited for regulatory compliance
HTTPs for SSL-based encryption for data to and from the server
LDAP/SAML integration so users can log in using UArizona’s WebAuth page for authentication
Configurable password complexity for non-LDAP/SAML accounts as well as password expiration rules and other password-related security measures
Prolonged inactivity or repeated incorrect password attempts locks the user account

OpenSpecimen Modules & Plugins

REDCAP INTEGRATION MODULE

OpenSpecimen can be integrated with REDCap to enable users to query data across the two systems. For instance, biospecimen data can be stored in OpenSpecimen and clinical data can be stored in REDCap
This plugin pulls the complete dataset of the REDCap project into OpenSpecimen, which eliminates duplicate data entry and allows for integrated reports and catalogs across clinical and biospecimen data
REDCap instruments get duplicated in OpenSpecimen such that they are available via the OpenSpecimen reporting module, thus allowing users to execute highly powerful queries for specimens of interest

SPECIMEN PROCESSING WORKFLOWS PLUGIN

This plugin allows users to design highly customized specimen processing workflows, which are a series of tasks that are configured based on the specimen processing SOP of a lab or study, and multiple workflows can be designed to fit the collection and processing of each SOP
Created for high-throughput labs that process a high volume of specimens in a day and/or have many staff members
SOP-driven approach ensures that lab users can easily follow a predefined series of tasks
Each workflow consists of multiple tasks in a wizard-like user interface
Each task can be an action (e.g., create visit, receive specimen, spin blood, create aliquot, get cell count, etc.)
Each task can have data collection based on standard or custom forms and can have branching logic based on a previous task
Workflows can be assigned to one or more collection protocols and can be assigned to one or more users (e.g., blood processing is done by one user while tissue processing is being done by another)
Data validations and workflow deviations can be defined and tracked
Users can see which specimens are being processed, where they are in the processing workflow, and how many are waiting to be processed