OpenSpecimen | Biospecimen Management

What is OpenSpecimen?

OpenSpecimen is a highly configurable web-based Biobanking Laboratory Management Information System (LIMS) that helps you 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, replacing the university’s previous biobanking management application (TissueMetrix), which was adopted in late 2009 and was being used by UArizona Health Sciences, UArizona Cancer Center, and UArizona College of Medicine – Phoenix.

To see if OpenSpecimen is right for you and can accommodate your biobanking needs, please email Manuel Snyder, the OpenSpecimen Administrator, for access to the OpenSpecimen Test Environment.

ONLY IRB-approved studies and protocols will be allowed to store information in OpenSpecimen. UAHS 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 70+ 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

CUSTOM FORMS & FIELDS

  • 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

TISSUE MICROARRAYS & DNA GELS

  • Track, process, and create tissue microarrays that are made with specimens that have been entered into the biobank
  • Track DNA gel loading with the image and its associated specimens

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

OpenSpecimen Video Tutorials & Training Resources

Video Tutorials

Training Resources (Krishagni Solutions)