Helis Academy Course: Omics data analysis through data integration - using biological pathways, networks, and linear models
General context
The first Helis Academy Omics Data Analysis course is a collaborative effort between Maastricht University and VIB in which you will learn about transcriptomics data analysis and multi-omics data integration. We will begin the course addressing how you obtain published data from data repositories and then cover basic pre-processing steps. We will continue by introducing you to molecular pathways, from what they are, to how to make your own, to how to use them in advanced omics data analysis (transcriptomics, proteomics, metabolomics) and how this compares Gene Ontology analysis. The course will continue by zooming out to utilize your pathway analysis in a broader network analysis so you can see the bigger picture. Finally, we will finish with a day to show you how to integrate Omics data sets in an unsupervised statistical way using linear models.
It is possible to register for separate workshops on different days, a detailed program can be found below.
WikiPathways, ELIXIR Core data repositories for omics data and the Gene Ontology
PathVisio https://www.pathvisio.org/
Cytoscape: https://cytoscape.org/
Expander: http://acgt.cs.tau.ac.il/expander/
MOFA (Multi‐Omics Factor Analysis—a framework for unsupervised integration of multi‐omics data sets) - http://msb.embopress.org/content/14/6/e8124
Page for installing PathVisio: https://www.pathvisio.org/downloads/installation/
Page where you can download Cytoscape: https://cytoscape.org/download.html
Docker image comprising popular Omics data integration tools: https://github.com/vibbits/rocker_conda_data_integration
Trainers
Lauren Dupuis
Post doctoral researcher at Maastricht University in the Department of Bioinformatics BiGCaT
Martina Summer-Kutmon
Assistant professor at Maastricht University in the Department of Bioinformatics BiGCaT and the Maastricht Center for Systems Biology
Susan Steinbusch
Assistant professor at Maastricht University in the Department of Bioinformatics BiGCaT
Friederike Ehrhart
Assistant professor at Maastricht University in the Department of Bioinformatics BiGCaT
Alexander Botzki
Alexander Botzki is heading the Technology training unit at VIB, the Flemish Institute of Biotechnology, Belgium. The main mission of this unit is providing technology training in domains of VIB Technologies, Bioinformatics & AI, Software Development, and Research Data Management. Between 2014 and 2022, he was head of the VIB Bioinformatics Core. From September 2009 to July 2014, he was responsible for the roll-out of E-Notebook (electronic lab notebook) to VIB's researchers within 75 research groups.
Before joining VIB, Alexander worked on various computational biology projects for Algonomics (bought by Lonza, 2008-2009) and DevGen (now Syngenta, from 2006-2008). During Alexander's PostDoc at Sanofi Aventis in Strasbourg, he executed various virtual screening campaigns on the compound selection of the merged enterprise. He received his doctoral degree with the group of Prof. Dr. Armin Buschauer (University of Regensburg, Germany) on 'Structure-based design of hyaluronidase inhibitors'.
Program
Below you can find a tentative schedule which will be finetuned before the event.
Lecture: Introduction to pathways
Lunch
Lecture: Introduction to PathVisio and WikiPathways
Practical: WikiPathways academy
Break
Practical: Draw your own pathway in PathVisio
Wrap up (Quiz and Q&A)
Lecture: Data repositories and data-preprocessing
Practical: Pre-processing hands-on with ArrayAnalysis
Lunch
Lecture: Pathway analysis
Practical: Pathway analysis
Break
Lecture: Gene Ontology Analysis
Practical: Gene Ontology Analysis
Wrap up (Quiz and Q&A)
Lecture: Network Biology
Practical: Pathways as a source for network biology
Gene Ontology-analysis in Cytoscape
Lunch
Lecture and practical: Protein-Protein Interactions
Break
Practical: Automation demo or work on your own dataset
Wrap up (Quiz and Q&A)
Multi Omics Integration (transcriptomics, proteomics, metabolomics)
Introduction Multi Omics Integration
Hands-on MOFA
Lunch
Hands-on MixOmics
Practical info
Niel - Darwin Incubator
Galileilaan 15
2845 Niel
Belgium
Niel - Darwin Incubator
- Bus 500 from Mechelen or Antwerp Central Station - stop Stop Reet Az Rivierenland and a 15 min walk
- a 15 min walk from Niel train station: direction from google
Niel - Darwin Incubator
Parking slots are available next to the Darwin Incubator.