Connecting tranSMART with the power of R

One of the keys to successful translational medical research is getting the right data to the right people in the right format. Achieving this requires supporting the many relevant data types, ensuring curated data is stored in an easily accessible location, and allowing secure access for tools and end-users. The number of solutions for this roughly equals the number of institutions active within the field. Unfortunately, their combined efforts are anything but greater than the sum of their parts.

This is where tranSMART does things differently. It too provides a solution for the above challenges, but instead of being developed behind closed doors, it is an open source effort that is growing organically to suit the needs of its community. This is reflected in the way tranSMART is structured and developed. Functionalities are modularised as much as possible, allowing them to be changed without affecting the other parts. Communication between the modules is handled by well defined APIs that guarantee certain standards and simplify the implementation of brand new parts. This ensures that tranSMART has all of the core capabilities that you expect from a data warehouse, while allowing anyone to extend these capabilities and contribute to the project as whole.

The new features of tranSMART since its release into the wild are legion, ranging from the support of new datatypes such as RNAseq, miRNA and proteomics data to an integrated genome browser. One of the most recent feature add-ons tries to leverage the power of another open source community: R. The R Project has been a staple of bioinformaticians for many years and has recently grown to become the most popular and widely used tool. Thanks to tranSMART’s RESTful API (another new feature), it was relatively simple to develop an R package which can be used to connect to a tranSMART server and retrieve all the data you wish as native R objects, ready for your favourite analysis or visualization.

Instead of re-inventing the wheel, tranSMART fits many wheels already in existence by keeping its architecture flexibel yet robust, and it just got a powerful new R wheel to show for it.

If you want to find out what tranSMART can do for you or your organisation, please contact us.