Automated workflow composition in mass spectrometry-based proteomics.

ABSTRACT:

Motivation

Numerous software utilities operating on mass spectrometry (MS) data are described in the literature and provide specific operations as building blocks for the assembly of on-purpose workflows. Working out which tools and combinations are applicable or optimal in practice is often hard. Thus researchers face difficulties in selecting practical and effective data analysis pipelines for a specific experimental design.

Results

We provide a toolkit to support researchers in identifying, comparing and benchmarking multiple workflows from individual bioinformatics tools. Automated workflow composition is enabled by the tools' semantic annotation in terms of the EDAM ontology. To demonstrate the practical use of our framework, we created and evaluated a number of logical

SUBMITTER: Palmblad M 

PROVIDER: S-EPMC6378944 | biostudies-literature | 2019 Feb

REPOSITORIES: biostudies-literature