Questions about OpenSpecimen (FAQs)?

OpenSpecimen

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Is there additional detailed information about the service?

To view slides from the September 30 workshop, visit: An Introduction to OpenSpecimen

Presenters; Jim Potter, Matt Marcetich, Bob Lang, Jennifer Parks, Pam Murray and Diana Gumas; shared how OpenSpecimen can enhance the Precision Medicine Initiative.

 

 

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Does the OpenSpecimen Team offer storage for specimens?

The OpenSpecimen Team does not store specimens, but the following research cores have specimen storage facilities:

GRCF Core
Biorepository & Cell Center
https://grcf.jhmi.edu/biorepository-cell-center/
Director:  Melissa V. Olson, Ph.D.
410-955-6327, mvolson@jhu.edu

Johns Hopkins Biological Repository
Bloomberg School of Public Health
http://www.jhsph.edu/research/labs/biorepository/contact.html
Director: Dr Homayoon Farzadegan
410-955-3786, JHBRLab@jhsph.edu

Hopkins Conte Digestive Diseases Basic and Translational Research Core Center
http://jhugicc.org/GIConteCenter/pages/cores/translationalResearchEnhancementCore.html
Translational Research Enhancement Core (Biorepository)
Director: James J. Potter
410-614-0130, jpotter@jhmi.edu

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Does OpenSpecimen support barcoding?

Yes. OpenSpecimen has a data entry field for barcode values. At this time, these values can be manually entered.  Study teams have used second-party barcode software (i.e. BarTender) to print barcoded labels using data exported from OpenSpecimen.

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Is OpenSpecimen web-based or platform-dependent?

OpenSpecimen is web-based, and the JHU instance resides behind JHU’s firewall. OpenSpecimen can be accessed on nearly any platform, but is best viewed using Google Chrome or Mozilla Firefox.

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How much does OpenSpecimen cost?

OpenSpecimen is free to use for JHU SOM investigators and their teams.

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Can I use OpenSpecimen if I currently use another database to manage biospecimens?

Yes. The OpenSpecimen team can help migrate legacy biospecimen data from another database. OpenSpecimen has MS Excel-based forms used to upload legacy data, and the OpenSpecimen team can help with arranging legacy data to fit these forms.

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Is OpenSpecimen integrated with Epic?

No, not currently. The OpenSpecimen team is working on integrating surgical pathology reports with the OpenSpecimen application to better facilitate annotation of specimens with specimen pathology diagnoses.

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Who has Super Admin privileges and how secure is my data?

Only members of the OpenSpecimen Team have Super Admin privileges. Admin privileges can be granted to study PIs and other members of the study team at the discretion of the PI; additional users can be provisioned by the study team. Users can access data for their studies only.

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Could you tell what open source means? What does that mean for our study?

OpenSpecimen is an open source web application developed by Krishagni Solutions, a software vendor. The application source code is freely available to download, install and even modify under the open source BSD 3-clause license (https://github.com/krishagni/openspecimen/blob/trunk/LICENSE.md). IT@JH has installed an instance of the OpenSpecimen application and underlying database on our own secure servers behind the Hopkins firewall. In other words, your data safely reside on JHU servers.

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Is there somewhere I could test OpenSpecimen publicly?

Yes. A public demo site (non-JHU) is available for testing here: demo.openspecimen.org, and you will be prompted to sign up for an account. JHU has a Test instance available, and the OpenSpecimen Team would be glad to set up a demo with you and explain further.

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