EMBO Practical Course on Metabolomics Bioinformatics for Life Scientists

Date:

  Monday 25 February 2013

Application opens: 

Sunday July 15 2012

Application deadline: 

Wednesday January 02 2013

Contact: 

Alison Barker

Registration closed

Overview

Is it right for me?

This course is aimed at advanced PhD students and post-doctoral researchers who are planning to improve their ability or learn new techniques in metabolomics and applying optimal data analysis methods using various bioinformatics tools in their research. The aim of this course is to familiarize the participants with advanced data analysis and data fusion methodologies and provide hands-on training on the latest analytical approaches and abilities to visualized and map metabolic changes on the relevant pathways.

What will I learn?

Lectures will give insight into how biological knowledge can be generated from metabolomics experiments and illustrate different ways of analyzing such data using variety of open source and freely available tools. Practicals will consist of computer exercises that will enable the participants to apply statistical methods and different analytical and data processing software to the analysis of metabolomics data under the guidance of the lecturers and teaching assistants.  Familiarity with the technology such as data acquisition with NMR and MS is required. Ideally also some experience with R/Bioconductor (basic understanding of the syntax and ability to manipulate R objects) and the Unix/Linux operating system.

What will it cover?

The course covers optimal study design for metabolomics experiments, various data analysis methods, usage of online databases and resource as well theoretical a practical approaches on data fusion. Other topics will include: visualization of metabolomics data on metabolic pathways, methods of identification of unknown compounds, differential expression, data quality and reproducibility assessment using statistical analysis and optimal experimental study design.

You will be able to:

  • Understand the fundamental principles of metabolomics experimental design and to learn the best practice for conducting metabolomics experiments  

  • Understand the fundamental principles of the data analysis of MS-based metabolomics including: feature detection; grouping; quality control; and annotation

  • Analyse an untargeted metabolomic workflow, and learn best practice and how to avoid potential pitfalls

  • Learn about current methods in metabolomic network data analysis and how to map the identified metabolites onto a metabolic pathway

  • Develop an awareness of current trends in metabolomics and its applications to disease

  • Develop your own metabolomics experimental designs

  • Learn some methods for the advanced analysis of metabolomics data, with a particular emphasis upon data fusion methods that incorporate prior knowledge

  • Develop an awareness of strategies for dealing with sparse matrices in high-dimensional metabolomic biomarker applications

  • Learn about genome-scale metabolic networks and the regulation of metabolite pools

  • Know current conventions in metabolomics standards and why it is important for us to use them

  • Browse, search and retrieve metabolomics data from widely used public repositories, tools and resources, including how to submit metabolomics results to the MetaboLights database

Participant Survey>>>>>>>

Programme

Time Topic
Day 1 - Mon 25 February - Chair of the day - Laura Emery - Materials
13:00 - 13:30 Registration and welcoming - Metabolomics and this course (Laura Emery)
13:30 - 14:30 Group Activity - your expectations about this course (Laura Emery)
14:30 - 15:00 Tea/coffee break
15:00 - 16:30 Participants' Flash presentations (Laura Emery & Reza Salek)
16:30 - 17:30 Metabolomics: from experimental design to data analysis (Gwenaelle Le Gall)
17:30 - 19:00 Poster Session with refreshments
19:30 Evening meal at Wellcome Trust Conference Centre
Day 2 - Tue 26 February - Chair of the day - Reza Salek - Materials
09:30 - 09:45 Overview of the day's structure (Reza Salek)
09:45 - 11:00 Dissecting an untargeted metabolomic workflow (Oscar Yanes)
11:00 - 11:30 Tea/coffee break
11:30 - 13:00 Dissecting an untargeted metabolomic workflow (Oscar Yanes)
13:00 – 14:00 Lunch
14:00 – 15:30 Analysis of LCMS-based metabolomics data:feature detection, grouping, quality control, high-throughput analysis, annotation,.Cont (Ron Wehrens & Pietro Franceschi)
15:30 - 16:00 Tea/coffee break
16:00 - 17:30 Analysis of LCMS-based metabolomics data:feature detection, grouping, quality control, high-throughput analysis, annotation,.Cont (Ron Wehrens & Pietro Franceschi)
17:30 - 18:30 Group activity and Discussion (Speakers of the day)
19:30 Evening meal at Wellcome Trust Conference Centre
Day 3 - Wed 27 February - Chair of the day - Kenneth Haug - Materials
09:30 - 09:45 Overview of the day's structure (Kenneth Haug)
09:45 - 11:00 Metabolomics data analysis in the context of metabolic networks  (Fabien Jourdan)
11:00 - 11:30 Tea/coffee break
11:30 - 13:00 Metabolomics data analysis in the context of metabolic networks, continues (Fabien Jourdan)
13:00 - 14:00 Lunch
14:00 - 14:15 Group activity - Energizer
14:15 - 15:30 Applications of Metabolomics to Disease and Regulation of Metabolism (Jules Griffin)
15:30 - 16:00 Tea/coffee break
16:00 - 16:45 Applications of Metabolomics to Disease and Regulation of Metabolism cont... (Jules Griffin)
16:45 - 18:30 Group activity discussion: Working on your experimental design (Gwenaelle Le Gall)
19:30 Evening meal at Wellcome Trust Conference Centre
Day 4 - Thu 28 February - Chair of the day - Reza Salek - Materials
09:30 - 09:45 Overview of the day's structure  (Reza Salek)
09:45 - 11:00 Fusing different sets of metabolomics data (Age Smilde)
11:00 - 11:30 Tea/coffee break
11:30 - 13:00 Fusing metabolomics data with prior knowledge (Age Smilde)
13:00 - 14:00 Lunch
14:00 - 15:30 Dealing with sparse matrices in high dimensional metabolomic biomarker applications (Michael Eiden)
15:30 - 16:00 Tea/coffee break
16:00 - 18:00 Genome-scale metabolic networks and regulation of metabolite pools (Kiran Raosaheb Patil)
19:30 College Dinner at Downing College Cambridge  (coach will depart at 18:45 from the Conference Centre)
Day 5 - Fri 1 March - Chair of the day - Christoph Steinbeck - Materials
09:30 - 09:45 Overview of the day's structure (Reza Salek)
09:45- 10:15 The m/z cloud (Robert Mistrik)
10:15 - 10:45 Metabolomics Standards: where are we now?  (Christoph Steinbeck)
10:45 - 11:00 Tea/coffee break
11:00 - 11:45 Metabolomics Databases and online tools (Reza Salek)
11:45 - 13:00 EBI - MetaboLights (Kenneth Haug)
13:00 - 13:30 Course feedback and informal Q&A (all speakers)
13:30 - 14:30 Lunch
14:30 Departures home