Performance and Software Integration

Objectives

The first objective of this work package is to develop software and build a computing environment that extends the current R system to make it future-proof in terms of performance of large-scale statistical calculations. This goal has overlaps with those of WP8, however, here we are taking a more fundamental, longer-term approach, and the approaches of WP8 and WP9 will complement each other towards the overarching goal of improving performance while simplifying usage. A second, important objective enabled by this WP is to improve integrability of R/Bioconductor workflows into corporate software environments; this forms the basis of platform-as-a-service facilities described in WP10, T10.3. To achieve these innovative goals, this work package will:

  • Resolve existing performance barriers to research and exploitation of results, including the representation of ‘S4’ objects,
  • Develop out-of-memory data representations of common multi-omics software objects developed in WP8,

Evaluate, refine, and implement implicit parallelization in end-user genomics workloads.

Participating partners

  • BeDataDriven, The Hague (Lead Partner)
  • Roswell Park Cancer Institute, Buffalo