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NORBIS Summer School 2019


Multivariate analysis of omics data with special emphasis on metabolomics

Time: June 17-21 2019
Location: Pharmacy building at University of Tromsø The Arctic University of Norway
Lecturers: Ines Heiland, Terkel Hansen, Hans Stenlund, Virginie Brun, Joseph Diab
Schedule: We start at 11 Monday morning and wrap up by 15 Friday afternoon.

Registration deadline: closed

Social: Reserve Tuesday night for a medium difficulty hike to enjoy the midnight sun in Tromsø, and Thursday evening for a BBQ dinner!
Software preparations: Download a free version of SIMCA-P software, more information will come soon.

Picture made using Vos Viewer

Program

Can be found here

Description

Multivariate data analysis is applied to complex data sets involved in Omics (transcriptomics, proteomics and metabolomics). In this practical and hands-on summer school, we will work with methods for the analysis, visualisation, and interpretation of ‘omics’ data with a special focus on metabolomics.
The course will cover the following topics.

  • Metabolism: Introduction to the biochemistry of metabolic pathways
  • Metabolomics: experimental methods (including an introduction into metabolite mass spectrometry), targeted and untargeted metabolomics, stable isotope labelling
  • Introduction to Proteomics.
  • Study design: Confirmatory vs exploratory experiments. Profiling vs finger printing.
  • Multivariate analysis: Principals of (principle component analysis) PCA and (partial least square) PLS.
  • Data pre-treatment techniques: scaling, transformation, missing values, etc.
  • Application of PCA to detect outliers, trends and patterns in Omics data.
  • Multivariate Models fitting, interpretation and visualization.
  • Orthogonal Projections to Latent Structures Discriminant Analysis (OPLS-DA) for identification of potential biomarkers.
  • S-plot (one model) and SUS-plot (two models) for biomarker identification.
  • Basic pathway analysis and pathway modelling.

The school is largely based on practical sessions where the students will apply multivariate analysis on their own data using R packages and/or Simca (available for 30 days free trial). In addition, students will be introduced to metaboanalyst (open access online tool for statistical, functional and integrative analysis of metabolomics data. We will furthermore give a short introduction in how to integrate omics data into pathway modelling approaches.

Target audience

PhD students (and post docs) who:

  • Works with multivariate data, especially in the omics field.
  • Wish to optimize their data analysis workflow.
  • Wish to learn about metabolomics methodology and application is system biology.

Learning outcomes

After completion of this summer school, participants will be able to

  1. Understand fundamental principles of multivariate data analysis and interpretation.
  2. Perform statistical integration and feature selection using multivariate methodologies.
  3. Apply those methods to high throughput omics studies, including their own studies.
  4. Have a basic knowledge about methods and approaches used in metabolomics.

Prerequisites
Previous knowledge of statistical inference, probability distributions, and regression models.

NORBIS members will have priority, and will have their travel expenses covered, as usual. NORBIS post docs may apply for travel support to contact-norbis@uib.no.

 

Tentative program for 2019 NORBIS summer school

Monday 17th of June

11:30-12:00 Welcome

Introduction to NORBIS

Introduction to the summer school

Joseph
12:00-12:30 Lunch  
12:30-14:00 What is metabolites, metabolism and metabolomics Hans
14:00-14:15 Coffee break  
14:15-16:00 Metabolomics study design

Targeted vs untargeted metabolomics

Hans
16:00-17:00 Poster session  

Dinner: Pizza?

 

Tuesday 18th of June

9:00-10:00 Introduction to Mass spectrometry and signal processing Hans
10:00-11:30 Data pre-treatment normalization, transformation

Principle component analysis PCA

Hans
11:30-12:30 Lunch  
12:30-14:00 Detecting outliers/batch effect.

Dimension reduction

Hans
14:00-14:15 Coffee break  
14:15-17:00 Practical session Hans & Joseph

Social activity: Evening hike kl. 19:30 (weather dependent)

 

Wednesday 19th of June

9:30-10:30 Introduction to Proteomics     Jack Bruun
10:30-11:30 The application of proteomics in biomarker discovery   Virginie Brun
11:30-12:30 Lunch  
12:30-14:00 Multivariate Regression models

PLS-OPLS

Hans
14:00-14:15 Coffee break  
14:15-17:00 Practical session Hans & Joseph

Visit to the proteomic and metabolomic platforms at IFA

 

Thursday 20th of June

 9:00-10:00 Introduction to system biology Ines
10:00-11:30 Pathway analysis Joseph
11:30-12:30 Lunch  
12:30-14:00 Pathway modelling Ines
14:00-14:15 Coffee break  
14:15-17:00 Practical session Hans & Joseph

Social activity: BBQ (weather dependent)

 

Friday 21th of June

9:00-11:30 Participants presentation  
11:30-12:30 Lunch  
12:30-14:00 Participants presentation  
14:00-15:00 QA and discussion session  
15:00 Good bye    

P.S: The program is subject to small changes.

 

 

Previous summer schools:

NORBIS summer school 2018: “Robust and reproducible practices in bioinformatics programming“, Oslo, August 6-10 2018

NORBIS summer school 2017: “Communicating research by visualisation, illustration and storytelling”, Bergen, 28 Aug – 1 Sept 2017. 

NORBIS summer school 2016: “An introduction to molecular biology, bioinformatics and biostatistics, Bergen, 13-17 June 2016.