Slides for the EuroBioc2016 meeting in Basel
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Material for my 2016 European Bioconductor Developer Meeting talk.

MSnbase2 - disk access is the limit`

Laurent Gatto (@lgatt0) and Johannes Rainer (jotsetung)


The MSnbase package has recently been bumped to version 2.0. The major update that warranted this promotion is the development of a new back-end to access raw mass spectrometry (MS) data. Previous versions arduously loaded all the MS spectra into memory. The new back-end leverages the fast on-disk access from mzR and only accesses the raw data on-the-fly when required, guaranteeing the same but faster behaviour as the legacy infrastructure with the same API, and enabling the processing of very large datasets. This new infrastructure underpins proteomics and metabolomics data access using MSnbase2 and xcms3 respectively. In my talk, I will briefly present the new back-end and benchmark the in-memory and on-disk implementations.

Talk material

Talk script.

All the material is available under a Creative Commons Attribution-ShareAlike 4.0 International License.