BCC2020 has ended
➞ Set your timezone before doing anything else on this site (home page, on the right)
Limit what is shown by Type, Category, or Hemisphere
Registration closed July 15.

BCC2020 is online, global, and affordable. The meeting and training are now done, and the CoFest is under way.

The 2020 Bioinformatics Community Conference brings together the Bioinformatics Open Source Conference (BOSC) and the Galaxy Community Conference into a single event featuring training, a meeting, and a CollaborationFest. Events run from July 17 through July 25, and is held in both the eastern and western hemispheres.

Back To Schedule
Tuesday, July 21 • 12:50 - 12:55
Development of TranSMART and Applications in Biomedical Research 🍐

Sign up or log in to save this to your schedule, view media, leave feedback and see who's attending!


The presenter(s) will be available for live Q&A in this session (BCC West).

Peter Rice 1, Kendra Elliston 2, Keith Elliston 2, Rudy Potenzone 3

1 Oryza Bioinformatics Ltd, Royston, UK. Email: ricepeterm@yahoo.co.uk
2 Axiomedix Inc., Bedford, MA, USA.
3 I2b2 tranSMART Foundation, Wakefield MA, USA.

Project Website: https://wiki.transmartfoundation.org/
Source Code: https://github.com/transmart-foundation/transmart/
License: GPLv3 Language: Grails, R, SQL, Groovy, Kettle

TranSMART is a suite of data exploration, visualization, and ETL tools, which were developed by
pharma for translational research studies based on the i2b2 project www.i2b2.org. Clinical and
omics data from clinical trials can be analyzed through a web client or exported for local analysis.
Over 200 curated studies from GEO, TCGA and other sources are available for public download

When an open source version was made available in 2012 several major projects (especially
eTRIKS https://www.etriks.org/ and TraIT https://trait.health-ri.nl/ in Europe) added support for
PostgreSQL in addition to the original Oracle database, increased the available datatypes, and added
many new plugin features. The latest version 19.0 includes a full code review, upgrades the grails
and Postgres versions and other internal libraries, accelerates data loading, and supports the
standard i2b2 data model.

The i2b2 code from which tranSMART arose is now also fully open source. We have new funding to
support development in both tranSMART (clinical and `omics data) and i2b2 (clinical data for all
patients) to share common database platform.

TranSMART continues to be developed and maintained by a community effort, coordinated by the
i2b2 tranSMART Foundation and is supported by Axiomedix Inc with a publicly available
knowledgebase built in Zendesk https://transmart.support.axiomedix.com/.

We have several current projects applying tranSMART in biomedical research:

In a project with Dell Technologies funding we are curating 80+ Coronavirus studies (SAR-
CoV-2, SARS-CoV and MERS-CoV) from the Gene Expression Omnibus and other sources for
a public tranSMART 19 server to be available from June 2020. The datasets will also be
available for download into any tranSMART instance. We expect to expand the analysis
repertoire of tranSMART to meet the urgent needs of CoVid19 research.

We have a public TB Data Commons site https://transmart-ospf.axiomedix.net/transmart/
with the Open Source Pharma Foundation http://www.ospfound.org/ loaded with data for
Tuberculosis and emerging tropical viruses plus Metformin studies relevant to TB research.


Peter Rice

Oryza Bioinformatics Ltd.

Tuesday July 21, 2020 12:50 - 12:55 EDT