Computational Workflows for Molecular Analytics: Integrating and Contextualizing Omics Data
Reproducible and high-throughput data analyses in the omics domains require combination of software tools in automated workflows. A complete workflow captures the experimental design and guides the analysis from raw data all the way to final statistical analysis and visualization. In mass spectrometry based proteomics, a typical workflow may contain steps such as format conversion, retention time alignment, calibration, feature extraction, peptide identification, validation, protein inference, peptide and protein quantitation, enrichment analysis and projecting the results on biological networks. The data can be integrated with existing datasets in public repositories and contextualized by mining the biomedical literature. This talk will focus on the software tools performing these operations, how to find those fit-for-purpose, assemble them into workflows, and benchmark the individual tools and workflows. Applications include integration of genome-wide SNP, RNA-Seq and proteomics data, optimizing targeted mass spectrometry assays, identification of biological species and tissues, and visualizations based on machine learning that provide novel insights into proteomics or metabolomics data.
Date:
15 February 2019, 9:00 (Friday, 5th week, Hilary 2019)
Venue:
Big Data Institute (NDM), Old Road Campus OX3 7LF
Venue Details:
LG0 seminar room
Speaker:
Dr. Magnus Palmblad (Leiden University Medical Centre)
Organising department:
Target Discovery Institute
Organisers:
Professor Benedikt Kessler (University of Oxford),
Professor Gil McVean (Oxford Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford)
Organiser contact email address:
benedikt.kessler@ndm.ox.ac.uk
Hosts:
Professor Benedikt Kessler (University of Oxford),
Professor Gil McVean (Oxford Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford)
Part of:
TDI Seminar Series
Booking required?:
Not required
Audience:
Members of the University only
Editor:
Kate Humphrey
