If you’ve ever lost sleep wondering how you can share medical record data, clinical trial data and ‘omics data, boy do I have some good news for you…
The tranSMART Project has released the first open source version of the award winning tranSMART software to the translational research community. tranSMART General Public License (GPL) 1.0 RC1 is now broadly available to institutions seeking an open framework for integrating and sharing data across medical records, clinical trials, reference content, and ‘omics data. The software is a product of multiple collaborations among non-profits, academic medical centers, pharmaceutical companies, and commercial groups. In addition to the release, the tranSMART Project team has established an online framework for open source developers and scientists actively contributing from multiple sites through a central GitHub repository, wiki, and organizational governance board. Visit www.transmartproject.org for more information.
The tranSMART Project is led by a board of informatics leaders from non-profit organizations focusing on pre-competitive strategies for drug discovery. This includes Sage Bionetworks (Mike Kellen), CHDI Foundation (Keith Elliston) and three major pharmaceutical organizations including Janssen Research & Development, LLC. Each group has contributed software extensions and expertise towards achieving the GPL release. In addition to the leadership team, more than eight sites have installed and are piloting pre-release versions of the software with their own data sets.
Stephen Friend, President of Sage Bionetworks, said: “We are very excited to see tranSMART enter the open source community and support pre-competitive sharing of software and scientific data in a model that will lead to the type of breakthroughs that Sage was founded to facilitate.”
Key academic medical centers leading the project include University of Michigan and Imperial College London. Imperial College London, led by Yike Guo, professor in computing science in the Department of Computing, has been applying tranSMART software to deliver knowledge management and data sharing systems for IMI research projects such as UBIOPRED. The University of Michigan NCIBI is working to provide a US academic home for the tranSMART software including multiple internal deployments and leading a work stream for API development and integration of NCIBI tools.
“The tranSMART biomedical knowledge management platform has a model that scales across groups to facilitate productive public/private partnerships,” said Brian Athey, PhD, Professor and Chair, Department of Computational Medicine and Bioinformatics, Michigan Institute for Clinical Health Research. “We are working with the tranSMART Project to take it to the next level to achieve the full potential of the vision.”
The tranSMART software was internally developed as a translational research data repository for Janssen R&D. The primary features for data analysis were produced as an extension of the open source i2b2 software (informatics from the bench to the bedside) with specific adaptations and extensions to provide researchers with workflows in drug discovery and pharmaceutical R&D. In December 2011, Janssen R&D decided to transition the software into open source under GNU General Public License v3.0. The first full release of tranSMART 1.0 is planned for July 2012 with the current GPL release providing a full beta preview of features and tools to be delivered in the final release. The tranSMART 1.0 release includes a major update to the framework, including an upgrade to leverage i2b2 1.6, a plug-in environment for R based analytics, new correlation analysis algorithms, and new multi-modal data export utilities.
Recombinant Data Corp., an original developer of the software, worked closely with early adopters to integrate the software from multiple partnering sites and has supported most deployments to date. Recombinant Data continues to offer commercial support to sites seeking integrated delivery of the software. “We believe that open source is an ideal way to produce and share scientific software tools and we are excited to see work that we have done become rapidly adopted by the scientific community,” said Dan Housman, CTO Recombinant Data.