Components of the “Multi-omics Research Environment Sample Clauses

Components of the “Multi-omics Research Environment tranSMART is a knowledge management application that enables scientists to develop and refine research hypotheses by investigating correlations between genetic and phenotypic data. Within the “Multi-omics Research Environment” tranSMART is a core component for the clinical data analysis. A detailed description of tranSMART analysis options for the vertical projects is provided in deliverable D13.2. R Cloud gives the opportunity to use any of the existing R packages for the data analysis. In addition, R Cloud supports parallel R computing. For example, a researcher from a vertical project can install and use R package “RobustRankAggreg” developed by University of Tartu (Xxxxx et. al), get the list of genes/transcripts and store them back into tranSMART with the scores calculated by the Robust Rank Aggregation algorithm. Docker is an open-source project that automates the deployment of applications inside software containers, by providing ad additional layer of abstraction and automation of operating-system-level virtualization. From the end-user perspective Docker encapsulates software dependencies, for example those dependencies are especially complex in case of next generation sequencing pipelines, and provides ready to go solutions that can be used without time-consuming pipeline installation process. A Docker cluster is a cloud platform solution – a cluster of VMs under orchestration of OpenLava (LSF) with Docker installed on each VM. Docker cluster gives the possibility to run dockerized analysis pipelines in parallel. Both R Cloud and tranSMART’s analytical part are mostly supposed to be used for the down- stream analysis. Non-massive data like microarray results can also be analysed in the R Cloud; however, vast amounts of data from next generation sequencing at the pre- processing stage need a special approach and a lot of computational power. For such data we have provided a Docker cluster solution with a number of pipelines adapted for cloud computing. At the moment we have pipelines to deal with genomics, transcriptomics, small RNAs sequencing, proteomics and metabolomics data. All the mentioned components make up a very flexible system that can satisfy all possible needs of the vertical projects. The new dockerized pipelines can be added to the Docker cluster by vertical project request.
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Related to Components of the “Multi-omics Research Environment

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