(from Sept 29, 2015 – originally posted on LinkedIn)
We released OpenSpecimen v2.0 in June 2015 and since then made a couple of minor releases (v2.1 and v2.2). This post is about this incredible journey from caTissue to OpenSpecimen.
For the uninitiated…
OpenSpecimen is a free and open source biobanking informatics platform being used in 35+ biobanks across 13 countries.
Some of the top academic research centers who use OpenSpecimen are:
- Stanford University
- Johns Hopkins University
- Univ of Leicester
- Univ of Melbourne
- Univ of New South Wales
- Victorian Cancer Biobank
- National Center for Biological Sciences (Bengaluru)
- Singapore General Hospital
End users at OSCON15 – Community Meet at Thomas Jefferson Philadelphia
A bit of history… 2004-2011
caTissue project started in 2004, funded by NCI under the caBIG program and developed by Washington University (WU). I was one of the first developers on this project via Persistent Systems to whom WU used to outsource its software development efforts. In 2011, NCI decided to stop the funding of the caBIG program including the caTissue project.
This meant a lot of adopters who were using caTissue had nowhere to go for bug fixes, improvements, and new features.
This coincided with the period when I left Persistent to start my entrepreneurial journey. Initially, after trying my hand at developing a software solution to doctors in Pune and failing, I saw an opportunity with caTissue. Being open source, it was convenient for us to continue the development without any licensing or legal issues.
Starting caTissue Plus…2011-2014
This is when we started the caTissue Plus project. “Plus” meant NCI’s original caTissue with bug fixes and improvements. Very soon adopters of NCI caTissue started seeing value in our Plus version and started upgrading. In the next two years, we made 3 major releases and accumulated 20+ customers across the globe.
Challenges…
The biggest challenge we faced was the poor code quality of caTissue and outdated technology-stack. This meant maintaining the software and adding new features was a nightmare. It was not flexible to cater to the wide-range of workflows of the biobanking world and was also very slow when dealing with large data.
The second problem was the name “caTissue”. Whats in the name they say! However, it does matter. “caTissue” seemed like cancer or tissue specific product and therefore others stayed away from it.
Birth of OpenSpecimen..2014
This is when we rebranded to “OpenSpecimen” and also started rewriting caTissue from scratch. Across two major releases, OS v1.0 and v2.0, over nearly 15 months, we rewrote the complete product.
Today OS v2.x does not have a single line of code from caTissue.
OpenSpecimen is also a “rethink” of how biobanking informatics should be designed. It adopts latest web technologies, API first approach, 100% REST API based, and very easy to develop new plugins/extensions.
API-first / platform approach…
With OpenSpecimen we focused heavily on being fully REST API based platform. It is easy to integrate, write new apps, plugins, etc without modifying OpenSpecimen source code. This means you can customize to meet very specific local workflows and still be upgrade-proof.
Current status
Being free and open source, OpenSpecimen is the most cost effective biobanking informatics solution yet very powerful to meet highly complex needs.
We are seeing much greater interest in the global biobanking community in OpenSpecimen. Centers like Stanford University are adopting OpenSpecimen. Most of the current adopters have already upgraded to v2.x or are planning their upgrade.