TranSMART 17.1: time series, samples, cross-study concepts and more

The tranSMART Annual Meeting 2016 on October 25-27 in La Jolla at UCSD was a great success! We had many good community presentations and trainings in the use of tranSMART worldwide, and also some world-class keynotes by a.o. Larry Smarr and Rob Knight of UCSD about microbiome research. This blog post focuses on the most important topic presented by The Hyve: a full update on the ongoing project leading to a new and improved version of the tranSMART backend, called tranSMART 17.1.

The Hyve has been selected by the tranSMART Pro Alliance for the execution of the tranSMART 17.1 development project, a major investment in the platform that will bring crucial data modelling features and important code improvements.

The project is organized by the tranSMART Foundation (led by CEO Dr. Keith Elliston and managed by CTO Prof. Yi-Ke Guo from Imperial College) and supported by four major pharmaceutical companies: Pfizer, Roche, Sanofi and AbbVie. The project will focus on developing a stable backend exposed via a new iteration of the REST API. It will be part of the 17.1 release of the platform, scheduled for the 1st half of 2017 (explaining the version number 17.1).

On the functional side the development brings back and enhances the support for time series, samples, and cross-study concepts. This is accomplished by re-alignment with the i2b2 data model, on top of which tranSMART was built, extended with the features which make tranSMART unique: the organization in studies, the support for modelling clinical trial event grouping and high dimensional data support.

Also the data types tranSMART supports are extended with transcript-level RNA-Seq data and the support for storing large files is developed through integration with the Arvados large-scale storage and computation platform.

For a deeper look into the functional enhancements of the 17.1 development project, please have a look at the slides and presentation given by the business analyst of the project Ward Weistra at the Annual Meeting:


A functional overview of the tranSMART 17.1 development project from Ward Weistra

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On the technical side the 17.1 development project tackles many features which will make the platform more stable, future-proof and will make development much more enjoyable. This includes automated-test coverage for all Core API and REST API calls and documentation of those calls and the full database schema.

Also all 10+ core repositories needed to build tranSMART are now put in one repository, to allow for a one step build of the project. And with the upgrade to Grails 3 that is included we are moving to the much newer Java 8 and Gradle build system.

For a deeper look into the technical improvements of the 17.1 development project, please have a look at the slides and presentation given by developer on the project Piotr Zakrzewski at the Annual Meeting:


tranSMART 17.1 technical overview from The Hyve

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All in all the tranSMART 17.1 development is an important investment in the tranSMART platform and should make both scientists and developers using the platform very excited!

The requirements and the design document for the development project have been made publicly available on the tranSMART Foundation Wiki: If you have any questions, please don't hesitate to contact us for more details.