In an article by Alex Keown, BioSpace.com Breaking News Staff, in their May 24th issue, he reported ” Biotech researchers looking to harness the power of big data could have an easier time with the new partnership between IBM (IBM) and the tranSMART Foundation, a Massachusetts-based nonprofit organization founded in 2012 with a goal of providing a platform to share pre-competitive data for use in designing transformational medicines.” The article goes on to describe the merger with the i2b2 Foundation as well as some of the history, while focusing on the new version of the tranSMART Platform on the IBM Power8 server.
Neil Versel (GenomeWeb) wrote “As genomic tools continue to make their way from the research lab into clinical practice, the recently announced merger between the TranSmart Foundation and the Informatics for Integrating Biology and the Bedside (i2b2) aims to provide researchers and clinicians with an open-source resource that could benefit precision medicine efforts.”
Earlier this month, the two organizations announced their plans to combine into a single foundation focused on providing open-source biomedical software and databases for precision medicine. “We’re creating an entire open-source home for people who want to bring precision medicine into clinical practice,” said tranSMART Foundation CEO Keith Elliston.
Andy Oram writes in EMR & HIPPA (HealthcaseScene.com) about the potential merger of the i2b2 Foundation with the tranSMART Foundation. Andy reflects “as a harbinger of progress in medicine, the announcement is very significant”. Andy continues “Their timely merger shows that open source overcomes cultural and institutional barriers… Ultimately, they’ll contribute to the movement to target cures to patients, proceeding now under the name Precision Medicine.”
Read the full article.
Andy Oram is an editor at O’Reilly Media, a highly respected book publisher and technology information provider. An employee of the company since 1992, Andy currently specializes in open source, software engineering, and health IT,
In a Press Release released today, the i2b2 Foundation and the tranSMART Foundation announced that they have signed a Letter of Intent to merge the two foundations. While no further details were announced, both management teams are working to complete the merger in the next few months.
Together, the combined tranSMART and i2b2 foundations will enhance the synergies between their two distinct data science platforms and will further develop an integrated, open-source platform that spans the clinical and translational research domains.
See the full Press Release HERE.
In citing a recent report from KPMG and another by PwC , Taren Grom talks about the need for collaboration in today’s research and development activities for health care researchers. In PwC’s report on Pharma in 2020, they talk about collaboration as a “do or die” situation. Grom goes on to discuss how the tranSMART platform is being used for these efforts. Further, the technology is now in place to facilitate these sorts of interactions between research groups from all sectors. The transMART Foundation is cited as one of those technologies, fosters by its industry/academia Members and a broad spectrum research community of users.
The Hyve, Silver Member of the tranSMART Foundation, is offering three classes in this year’s tranSMART Training Program on programming in the tranSMART environment. The first of these classes will be presented on Monday March 27th with the others coming later in the year,
- March 27th: How to get started with tranSMART development
- June 26th: Programmatic access to data in tranSMART 17.1: The tranSMART REST API V2
- September 25th: started with modelling your data for tranSMART: Modelling and loading with the Arborist and tranSMART-batch.
See our complete training program and register for these and other classes at: 2017 Training Program
The tranSMART Foundation announced the newest release of its tranSMART platform, version 16.2. This version includes significant contributions from numerous members of the tranSMART community and provides users with more advanced functionality to enhance their translational research studies.
The newly developed features in version 16.2 include the SmartR plugin (ITTM/University of Luxembourg/eTRIKS), genomics-based cohort selection (Janssen), GWAS enhancements (Pfizer), GWAS PLINK integration (Clarivate Analytics), XNAT image database integration (Imperial College London and Erasmus Medical Center), and ETL enhancements (Imperial College London/eTRIKS).
“As an open-source platform, tranSMART wouldn’t be possible without the contributions of our community,” said Keith Elliston, Ph.D., CEO of the Foundation. “We are delighted that so many organizations have stepped up to the plate to support further development of the platform. It is a true testament to what open-source communities can offer and the value of collaboration among individuals and organizations in the scientific and technical communities.”
The expanding capabilities of the tranSMART platform provide the translational research community with an improved set of tools. For example, SmartR plugin offers the ability to tap into the richness of R to provide workflows for Boxplot, correlation, heat map line graph, and volcano plots. Others will be added in upcoming releases. In addition, there is a workflow that provides a link to the Qiagen Ingenuity Pathway Analysis. Another example is the Janssen contributed genomics cohort selection, HiDome, which supports the use of gene expression and other high dimensional data in the Comparison and Summary Statistics tabs to build cohorts.
Each of these contributions has followed tranSMART’s contributor process and guidelines, producing a product that has been subjected to automated testing all along the process. The 16.2 release exemplifies the Foundation’s ability to bring new innovations to the platform from a variety of community contributors, while maintaining the quality and reliability of the platform through its release process.
For its first training class in 2017, the tranSMART Foundation in cooperation with its Silver Member Rancho BioSciences has announced an “Introduction to the tranSMART Platform” training class.
The class will be held on Monday January 30th at 11AM Eastern on its Go To Webinar service.
Pre-registration is required and can be found HERE.
The entire monthly 2017 Training Program has also been announced and available at this LINK. In addition to Rancho BioSciences, Silver Members Clarivate Analytics and the Hyve will be contributing instructors and training materials for the classes.
The tranSMART Foundation announces that Elsevier Science has become a Silver Member of the Foundation.
Contributors to this release include: ITTM, U Luxembourg, Erasmas Medical Center, Imperial College of London, J&J, Pfizer, Clarivate Analytics (formerly Thomson Reuters), U Liverpool, eTRIKS, TraIT, and the Hyve.