Helis Academy Course: Omics data analysis through data integration - using biological pathways, networks, and linear models

Helis Academy Course: Omics data analysis through data integration - using biological pathways, networks, and linear models

Target Audience:
Darwin Incubator Niel

Galileilaan 15
2845 Niel
Belgium

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. 

Afbeelding
Interreg Vlaanderen-Nederland
Software demonstrated

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
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 head of the VIB Bioinformatics Core

Contact Alexander Botzki :

Program

Below you can find a tentative schedule which will be finetuned before the event.

Introductory lecture

Omics data repositories, and obtaining available data

Pathway analysis - Gene ontology analysis

Network analysis using Cytoscape

Multi Omics Integration (transcriptomics, proteomics, metabolomics)

Introduction Multi Omics Integration
-
Hands-on MOFA
-
Hands-on MixOmics, IntLIM, WGCNA
-

Practical info

Darwin Incubator Niel

Galileilaan 15
2845 Niel
Belgium

Parking

Parking slots are available next to the Darwin Incubator.

Public transport

- 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

Contact

VIB training
Tel: +32 9 244 66 11
Mail: training@vib.be