MongoDb is used by code from Sanofi that is integrated in the Browse tab for indexing and retrieval from large files.
Standard R server installation
TranSMART installs R. This requires site administrators to download the latest R release and install from source. Over the life of a tranSMARt release teher can be a number of changes to the behavior of R, with older versions breaking so that it becomes necessary to change tohe makefile to load a more recent version of R or of one of the packages which we depend on. These can break tranSMART.
One workaround is to provide a standard R server, perhaps with docker or some more widely supported environment so that all the required versions are available. An alternative is to provide an R mirror with only the release-time versions to support installation.
A further complication is that R depends on system libraries. New versions of packages, or of R, may include dependencies on additional library for whihc the development versions must be instaklled. These are routinely added to the env/Makefile targets for each operating system for new users.
In the pharmaceutical industry the practice has been to develop their own extensions to tranSMART. At Sanofi the Browse tab study metadata and a series of new data types were developed, but they continued to maintain their own transmart code including support for additional large files in MongoDB, an ETL package (ICE) and alternative authentication mechanisms. At Pfizer extensions to handle GWAS results were added. In both cases the native code only supported Oracle and needed to be ported to Postgres. Some ETL issues remain to be resolved. The Hyve developed new analysis methods and support for aCGH data for the TraIT projects in the Netherlands but Oracle support for these extensions has gaps (e.g. data loading).