Benjamin Schubert's Workflows

Epitope-based Vaccine Design Workflow usin... (3)

• Download

Population-based vaccine design workflow in KNIME. AlleleFrequency is used to specify the geographical region or population of interest and returns a tab-separated list of HLA alleles with their corresponding occurrence probability within the selected population. This file, together with a FASTA file containing protein sequences, or a file containing peptides is used as input to EpitopePrediction, which generates a file containing the predicted binding affinities of the (generated) peptides a...

Created: 2016-11-30 | Last updated: 2017-04-11

Credits: Benjamin Schubert

HLA ligandomics workflow using OpenMS and ... (2)

• Download

HLA ligandomics workflow combining native KNIME, OpenMS, and ImmunoNodes nodes. The workflow extracts MS data from PRIDE and performs mass spectra identification with X!Tandem, annotates the results with details of the given target/decoy database, calculates false discovery rates and filters for 5% FDR using OpenMS’ nodes. The identified peptides are annotated with their respective binding affinity predicted by NetMHC using the EpitopePrediction node. Finally, simple summary statistics ...

Created: 2016-11-30 | Last updated: 2017-04-11

Credits: Mathias Walzer