Utah CTSI OpenSpecimen User Guide

 

 

Clinical and Translational Sciences Institute - Biomedical Informatics Core

 

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Welcome to the user documentation for the OpenSpecimen Biorepository.  The University of Utah has chosen OpenSpecimen supported by Krishagni Systems as the biospecimen respository. It is subsidized by the Clinical and Translational Science Institute. Implementations are supported by the Biomedical Informatic Core of the CTSI. Much of the documentation from Krishagni is applicable and available on the web. BMIC has created this knowledge base of articles and videos to support the University’s researchers and staff.

Overview statement for inclusion in IRB applications:

"OpenSpecimen (http://openspecimen.org) is a modular, open-source specimen inventory and tracking system which simplifies for researchers the process of locating and analyzing tissue specimens for use in clinical/translational research based on tissue, clinical, and genomic characteristics. This tool permits users to track the collection, storage, quality assurance, and distribution of biospecimens as well as data related to the participant and study protocol from which biospecimens are collected; regardless of the nature of biospecimen transactions that occur or the type of biospecimens (tissue, biofluids, nucleic acid) involved in the transaction. OpenSpecimen uses a Common Security Model to support authentication, authorization, roles and privileges.

OpenSpecimen is supported and maintained by the Clinical and Translational Sciences Institute (CTSI ctsi.utah.edu) in the Center for High Performance Computing Protected Environment (CHPC chpc.utah.edu). The system is HIPAA compliant following standard best practices and deployed in the University of Utah Downtown Data Center where physical and network access is tightly controlled and monitored 24/7/365. Specimen and system data are backed up nightly."

External OpenSpecimen Resources:

OpenSpecimen Environments:

Training Environment (Non-HIPAA):

The training system in used for getting up to speed on how to use the system and configuring a lab or biobank here at the U. It is NOT intended for any protected data.

Protected Environments (HIPAA):

TEST:  The Test environment is intended for testing of import and production deployment of new protected data for labs and biobanks. Collection protocols can be built, tested and copied to the production environment.

PRODUCTION:  Once a user is satisfied with the collection protocol or data imported, it can be implemented in Production.  Deletion of data is not possible once entered in to OpenSpecimen. This is done for strict auditing purposes.


FAQs

  • How do I get started implementing OpenSpecimen in my lab?

    • Implementing OpenSpecimen for your lab requires assistance from the BMIC OpenSpecimen team. Requests to use the system will be evaluated and prioritized in the implementation queue. You can request access to the OpenSpecimen training platform and follow our Knowledge Articles to become familiar with the system and how it can support your lab by registering your interest in ProTracks and indicating you would like to use the CTSI OpenSpecimen biorepository management system.

  • How much time would it take to get OpenSpecimen up and running in my lab?

    • The time estimate for a basic OpenSpecimen implementation is generally 4-6 months. The length of time varies depending upon lab specific parameters such as

      • legacy data migration vs. current study enrollment

      • conformity and standardization of existing sample data and metadata

      • commitment & availability of lab staff to support required lab effort during the install

      • complexity of workflow process

  • What is the cost to use OpenSpecimen?

    • OpenSpecimen is a biobanking informatics platform partially subsidized for University of Utah research needs by the Clinical Translational Science Institute. Basic functionality for specimen storage & tracking is provided. However additional application external modules, plug-ins and custom form development is not part of the basic installation and would require funding.

  • How does OpenSpecimen support different types of workflows and data collection needs?

    • Biobanking is a very dynamic and diverse field where a “one size fits all” approach is not applicable. Biospecimens could be collected for disease based biobanks (e.g. cancer biobank, orthopedic biobank, etc) or for a longitudinal clinical study or trial. Each study or disease has its own data collection needs. Thus OpenSpecimen can be configured for the various types of workflows and data collection needs:

      • Disease based ad-hoc collections

      • Specimen Centric collections

      • Participant Centric collections

      • Longitudinal collections

      • Bar code based Rapid data entry

  • Can specific or sensitive data be hidden from users?

    • OpenSpecimen allows controlling of data access by assigning roles to users. The privileges can be controlled at a very granular level for each resource in the system. This provides the lab to grant varying levels of viewing / editing data and performs specific functions

Search for an article

OpenSpecimen Canvas 101 course:

 

Knowledge Articles

Video Overviews of OpenSpecimen

 

 

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