Figure 1: A screenshot from http://transmartproject.org/wiki/display/TSMTGPL/Transmart+Developer+Workshop+Summary website showing a growing number of tranSMART adopters in non-profit, pharma and government sectors. Non-profit organizations were the largest growing users of tranSMART. The platform was released into public domain in mid-2012.
tranSMART, an open source platform for translational medicine, is emerging as a preferred solution for many academic, non-profit, and commercial organizations (Figure 1). The open source platform provides value in that it allows for an enhanced collaboration between various groups within an organization, through sharing of early stage results, as well as increased transparency. Ideally, implementation of a common translational medicine platform will result in additional value, such as early adoption of best practices, cost effectiveness due to the elimination of redundant experiments, and faster drug and biomarker discoveries – all of which will speed up the research.
In essence, tranSMART is a data warehouse where curated content and data can be stored. The underlying database (based on I2B2 schema) is adapted to house phenotypical, genomic, proteomic, metabolomics, and other data types.
tranSMART’s public version is equipped with many analytical tools that will be useful to researchers. In addition to simple t-test and chi-squared tests that can be performed to compare data for cohorts of patients, tranSMART allows researchers to generate heatmaps and perform clustering algorithms on high-throughput data. A PLINK workflow allows SNP data visualization and analysis. Many other add-on statistical packages are currently available (box plot with ANOVA, Fischer test, k-means clustering and others) and new ones can be added easily as needed.
A crucial component of any translational medicine platform is the data that populates the underlying database. If data sharing within an organization, and, ideally, within the broader community is desired then a full semantic alignment and ontological consistency is required. Members of our team have previous experience with several tranSMART projects including the one described in the original publication with Johnson & Johnson, performed as the legacy GeneGo organization , and thus have built up a considerable amount of expertise in clinical, preclinical and OMICs data curation and preparation for this platform. Together with its domain expertise in pathways and systems biology, Rancho Biosciences is uniquely positioned to deliver fast and accurate data curation services.
In general, implementation of the tranSMART platform can involve server configuration, platform optimization, secure access setup, data ETL (Extract, Transform & Load), bug tracking and fixes, platform updates, and many other tasks. The Rancho Biosciences team includes software engineers, IT personnel, biologists, and data curators to assist with any issues related to tranSMART implementation.
Rancho BioSciences tranSMART hosted service
Rancho BioSciences has tranSMART hosted on a server accessible for our customers to use. They can use it for testing, as a collaborative environment or to run analysis. Rancho BioSciences will maintain and update the platform, working on integrations and workflows. We can also customize it to meet your needs such as creating dashboards, adding your R scripts and adapting export capabilities.
For a FREE trial or pricing please email services @RanchoBioSciences.com or call 1-866-260-2198/ 1-760-717-7881
Rancho BioSciences tranSMART installation service
Rancho BioSciences can send IT personnel to your site to install tranSMART, integrate it with third party tools, add R scripts and develop workflows. This usually takes a week and includes testing.
For questions and pricing please email services @RanchoBioSciences.com or call 1-866-260-2198/ 1-760-717-7881
- Yike Guo CTO of the tranSMART foundation