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.
The OpenSpecimen Team does not store specimens, but the following research cores have specimen storage facilities:
Johns Hopkins Biological Repository
Bloomberg School of Public Health
Director: Dr Homayoon Farzadegan
Hopkins Conte Digestive Diseases Basic and Translational Research Core Center
Translational Research Enhancement Core (Biorepository)
Director: James J. Potter
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.
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.
OpenSpecimen is free to use for JHU SOM investigators and their teams.
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.
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.
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.
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.
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.