tranSMART 16.2
The tranSMART 16.2 was released in February 2017 for the postgres database. The Oracle version is expected in a few weeks.
Access to an demo installation or the 16.2 release can be found HERE.
Installation instructions can be found HERE.
The release can be found as signed artifacts (recommended) for download HERE and on the tranSMART-Foundation Github HERE in each repository as the branch 'release-16.2'.
Presentations at the tranSMART Foundation Annual Meeting Session A2 explored the release and details on the new capabilities that can be seen HERE.
- Overview of the Release SLIDES - RECORDING
- SmartR (SLIDES coming soon) - RECORDING
- GWAS PLINK SLIDES - RECORDING
- GWAS Extensions (SLIDES coming soon) - RECORDING
- HiDome genomics extensions - See below
- XNAT plugins - See below
- ETL Enhancements - See below
- Bugfixes (plus HiDome, XNAT, ETL) - SLIDES - RECORDING
The goals of this release are:
Continuous process improvements
Code management and bug tracking
Automated regression testing
Improved beta testing and bug fixing
PMC processes
Technical improvements
Outstanding JIRAs from 16.1
GWAS enhancements from Pfizer
ETL improvements
- Installation framework, improved modularity
- Cohort selection on -omics data from J&J
External interfaces & plugins from the Community
SmartR (eTRIKS, ITTM)
- HiDome Subsetting on -omics data (J & J, eTRIKS, TraIT)
- GWAS Results Enhancements from Pfizer
- GWAS PLINK integration from Clarivate Analytics/U Liverpool (Formerly Thomson Reuters)
XNAT imaging platform interfaces:
- TraIT/Erasmus MC (video presentation here)
- eTRIKS/Imperial College
- Ingenuity IPA pathway analysis (ITTM)
- Return of Genome Browser and Metacore plugins
- ETL Improvements (tranSMART Foundation)
New and updated features
| Link | Description |
|---|---|
| New features in 16.2 | New features not described under the plugins below |
| Issues fixed in 16.2 | This is the current list of JIRA issues being worked on for 16.2 (including those that have been completed). This includes JIRAs from 16.1 as well as new entries. |
| SmartR | Interactive analysis workflows to supersede selected advanced workflows |
| HiDome | Support for high-dimensional data in Comparison and Summary Statistics |
| Ingenuity IPA Connector | Ingenuity pathway analysis workflow under SmartR |
| XNAT import (TraIT/Erasmus) | Import of clinical variables from XNAT image systems |
| XNAT viewer (Imperial) | Links from grid view to images in XNAT systems. |
| GWAS enhancements (Pfizer) | Updates to GWAS analysis tab from Pfizer |
| GWAS PLINK (Clarivate) | Launch of PLINK to run new analyses |
| Dalliance genome browser | Genome browser fully supported from release 16.2 |
| Metacore Plugin | Metacore plugin fully supported from release 16.2 |
| ETL improvements | Improved scalability, updates to ICE tool, closer integration with tMDataLoader |
