Moving on, here is your monthly pick of biobanking buzz from the OpenSpecimen team. Seats are fast filling up for our Annual Community Meetings in USA and Australia. Register ASAP to book your seats.

Your monthly pick of biobanking buzz from the OpenSpecimen team. We are excited to announce our upcoming Annual Community Meetings in USA and Australia. Register ASAP to book your seats.

Fresh of the Press

• UK Biobank requires Earth’s Geneticists To Cooperate, Not Compete.
• Patient perspectives about decisions to share medical data and biospecimens for research.
• Australia’s Brain Clot Bank opens in search of answers for stroke.
• University College London Hospitals (UCLH) launches a new open platform that matches patients to clinical trials.
• One Year After Launch, NIH’s All of Us Hits Key Milestones.
• The Childhood Cancer Data Initiative (CCDI) aims to link data from all pediatric cancer patients in the U.S.

Biobank Job Alerts

• Manager, Biobank Core Facility, University of South Alabama, USA
• Head Sample Bank – Oncology, GSK, Collegeville, Pennsylvania, USA
• Biorepository Technician, Precision Medicine Group, Maryland, USA
• Biobank Technician, UCLA Health, California, USA
• Laboratory Quality and Training Officer, UK Biobank, Manchester, UK
• Health Informatician, Wellcome Sanger Institute, Cambridgeshire, UK
• Biorepository Project Coordinator, Medpace, Leuven, Belgium
• Biobank Manager, Agency for Science, Technology, and Research (A*STAR), Singapore

Upcoming Events

OpenSpecimen News

Case study: Oxford biobank replaced their legacy database with OpenSpecimen to manage their biospecimens better.

v6.2 release: OpenSpecimen v6.2 was released on Sep 15th with new features, bug fixes, and improvements. Read the announcement here.

OSCON’19

Attendees:

Krishagni: Srikanth Adiga, Poornima Govindrao

Washington University: Dave Mulvihill, Lee Myrick, Anu Vadakkumcheril

University of Utah: Scott Claerhout, Randy K. Madsen

Thomas Jefferson: John Reber

Allegheny Health Network: Michael Anderson

Jewish McGill: Kerry McKenna

University Health Network (Toronto): Dianne Chadwick

University of Maryland: Coleen Damcott

University of California Davis: Irmgard M Feldman

Johns Hopkins: Bob Lange

http://forums.openspecimen.org/t/openspecimen-v4-2-released/999/1

For more details email us at contact@krishagni.com.

~Sri

Many companies delegate customer support to a “support team” – usually a team of junior staff who have spent some time in poking around the product –  just enough to act as if they know the product. Many companies even outsource it.

Unfortunately, in India (maybe even outside), many people consider support and QA as low-class work. Many developers think it is beneath their status to do it. They don’t realize that it will, in fact, help them become a much better developer – especially if you are in a product development company.

Most times the support staff are busy “defending” the product – even when it’s a genuine shortcoming of the product. They tell the user why “what is” is good enough and how the client can “make do” with it. It can be very frustrating for the clients and a major loss of ideas to improve the product and build new features.

This is why the top leadership and product developers should be involved in support. Many times, it is amazing to see how what they built is used in the real world – both in a positive or negative ways. You will see clients using a feature in a way you didn’t imagine. Other times, you will see that even though you built it to solve a particular problem, it still does not really do that effectively. Maybe it needs a bit more fine tuning.

This is why the CEOs, CTOs, and product development team should be monitoring client support tickets and answer then personally when possible. What the heck – even Steve Jobs used to reply to customer emails (click here).

That reminds me of a personal story. I was charged 1200$ for a Budget car rental when the original booking was for $200. Unfortunately, I didn’t see the initial contract papers (usually in a very light ink printed using a dot matrix). For 3-4 months I haggled with the customer support to get it rectified with no success. Until one day I read the above article about how CEOs of big companies respond to client emails and decided to try my luck with the CEO of Budget. I emailed the President/CEO/MD etc of Budget telling them my sob story. The very next day I got an email from the assistant of one of the top guns saying the issue is resolved and the money is refunded!

OpenSpecimen can be integrated with REDCap (or other EDCs like OpenClinica) to eliminate manual data entry and query data across the two systems. The plugin is currently used by many customers including Washington University, Columbia University, Telethon Kids (Perth), and University of British Columbia (Vancouver). 

The plugin performs the one-way data synchronization from REDCap to OpenSpecimen. The data pulled includes all the instrument information (i.e. CRFs) into OpenSpecimen Forms. This data can be used to populate participants, visits, and any other clinical data.

Release highlights:

1. Bulk delete of objects
2. Export of admin objects (to move data from test to production environments)
3. Display specimen list within containers
4. Link collection protocol with distribution protocols
5. One-click specimen distribution
6. Support for multiple values of ethnicity and clinical diagnosis
7. Support for participant level custom forms (i.e. global across all CPs)
8. Better support for box scanners in rapid data entry plugin

Detailed release notes: Click here

Summary of what’s new in v4.1

Bulk edit users (e.g. select 5 pending user accounts and unlock them in one-go)

Reserve specimens from a collection protocol to one or more distribution protocols

Distribute in one-click
If collection protocol is linked to distribution protocol, users can distribute easily from collection page. This allows for immediate distribution of prospective collections.

Containers Features
View and export specimens from container view at any level like freezer, rack, box etc. Users can also select specimens from this view and perform bulk operations like aliquot, derivative, event etc.

To download

Enterprise version: http://www.openspecimen.org/marketplace/v4-1/
Community version: https://github.com/krishagni/openspecimen/tree/v4.1

Please let us know in case of any questions or feedback.

Biobanking is a very dynamic and diverse field where a “one size fits all” approach does not work. 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 making the whole process much more complicated.

Therefore the biobanking informatics platform has to be very flexible to support these different types of workflows and data collection needs.

Disease based (ad-hoc) collections

These are left over biospecimens after patient care collected for prospective use. Typically there are no “planned events” for participant visits here, e.g. pre-operation, operation, post-operation, etc.

OpenSpecimen lets you create “highly customised” data entry screens for such ad-hoc collections. The screens can be customised to support:

1. Single specimen data entry screen
2. Deposit specimens in a batch (i.e. create multiple specimens in one go)

Specimen centric vs Participant centric collections

OpenSpecimen by default expects participant details (e.g., identifiers, demographics, etc). However, often biobanks only collect a deidentified participant ID or sometimes does not collect any information of the participant.

OpenSpecimen allows you to configure each study based on these requirements. Within a single instance of OpenSpecimen, every collection protocols can be configured differently, i.e. one protocol can be specimen centric whereas another protocol can be participant centric.

Longitudinal collections (multi-site clinical study or trial)

Longitudinal studies have a collection calendar i.e. day 0, day 30, day 45, etc. Each day has specific primary samples collected from the participant and sent to the biobank. The biobank staff process the samples and create aliquots etc and store them in the freezers. This process can get complicated if it involves multiple sites, pre-printing of labels and managing collection kits.

OpenSpecimen provides the following features:

1. Complete calendar of collection
2. Label and barcode pre-printing
3. Bulk pre-registration of participants
4. Dispatching collection kits to receiving centers
5. Integration with box scanner

Rapid data entry (barcode based)

In high throughput collections, based on barcoded tubes, OpenSpecimen allows you to configure “box layouts” and box scanner integration. This allows you to collect specimens for one or more patients at once by scanning a box of samples at one go.

Summary

New workflows are identified as OpenSpecimen is adopted in more and more biobanks. Instead of “customizing” OpenSpecimen for each biobank, Krishagni has been enhancing the “configurability” of OpenSpecimen to support these new use cases. This development approach has resulted in OpenSpecimen becoming a highly powerful and flexible informatics platform capable of satisfying any kind of biospecimen collection needs. This can evidenced by widespread adoption of OpenSpecimen; today 60+ biobanks across 15 countries use OpenSpecimen.

For more details or demo, email contact@openspecimen.org.

•  v3.4 release
•  New adopters
•  Case studies
•  4.0 release plan

•  Durrer Center for Cardiovascular (Amsterdam / BBMRI-NL)
•  University of Maryland (Baltimore)
•  University of Pennsylvania
•  University of Michigan (MTPI)
•  FIND Diagnostics (Geneva)

•  Why and how Durrer center selected OpenSpecimen?
•  Johns Hopkins – Adoption over the years

•  Integration with automated freezers (Hamilton BIOS)
•  Consent coding and consent validation during distribution
•  Bulk registration and collection kit preparation
•  Enhancements to rapid and simple data entry plugins
•  OpenClinica integration

Software development stack

1. User interface: Angular 1 and Angular 2
2. Backend: Java Spring

Prerequisite software

1. Browsers: Latest versions of Chrome, Firefox, Internet Explorer, Safari on Mac
2. Databases: Oracle 11g & 12g OR MySQL 5.x
3. Web server: Apache Tomcat 7.x and 8.x
4. App server: Apache Front-ending (for high availability)

REST APIs

OpenSpecimen is a 100% REST API enabled application. The user interface uses the REST APIs, i.e. all the functionality exposed via the user interface is also available via REST APIs.

To read more, visit the REST API documentation page.

Identity Provider Integration

OpenSpecimen can be integrated with institution’s identity provider (like Active Directory) using LDAP or SAML. This will ensure that end users do not have to remember multiple username and passwords to access their OpenSpecimen account.

To read more, visit the Identity Provider documentation page.

Barcode printer integration

OpenSpecimen can be integrated with any type of barcode printer (Zebra, Brady, etc) with the help of an intermediate software like Bartender, NiceLabel, CodeSoft, etc.

To read more, visit the printer configuration page.

Integration with external databases or instruments

OpenSpecimen can be easily integrated with any external databases (e.g. RedCAP, OpenClinica, Epic, CoPath, Aperio, etc) or instruments (e.g. automated freezers, testing instruments, etc).

To read more, visit integration home page.