Exploiting Metagenomics Approaches in Life Science Research

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Date:

 Tuesday 1 Thursday 3 December 2015

Venue: 

European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom

Application opens: 

Friday July 24 2015

Application deadline: 

Friday October 02 2015

Participation: 

Open application with selection

Contact: 

Frank O’Donnell

Registration fee: 

£265 (includes 2 nights accommodation & food)

Registration closed

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Overview

This course will provide a broad introduction to the field of metagenomics, including bioinformatics approaches, downstream analyses, and the use of publicly available resources and tools. The course will cover a range of metagenomics perspectives and analyses spanning from molecular ecology to medical genetics, with an emphasis on multi-metaomics. Additionally, there will be the opportunity to discuss the challenges facing researchers in the field.

Audience

This course is aimed at scientists who are embarking on metagenomics research projects.

Prerequisites

Some practical sessions in the course require a basic understanding of the Unix command line. Please ensure that you complete these free tutorials before you attend the course:

Syllabus, tools and resources

During this course you will learn about:

  • Metagenomics concepts: alternative perspectives, NGS methods, common pitfalls
  • Data standards and submission: European Nucleotide Archive (ENA), Genomic Standards Consortium (GSC)
  • Public repositories: MG Portal, MG-RAST
  • Data analyses: diversity, coverage, sample comparisons, metabolic and pathway analyses

Outcomes

After this course you should be able to:

  • Submit data to public resources for metagenomics
  • Interpret results and compare with alternative analyses
  • Use a range of tools to perform some data analyses
  • Discuss the pitfalls and challenges in the field
  • Improve experimental design
  • Transition from metagenomics to multi-metaomics

Programme

Time Topic Trainer
Day 1 - Tuesday 1 December - Metagenomics Experimental design and data submission
10:00 - 10:30 Arrival and registration  
10:30 - 11:00 Welcome and science speed dating Laura Emery
11:00 - 12:00 An introduction to sequencing technologies for metagenomics Matt Clark
12:00 - 13:00 Lunch  
13:00 - 14:00 Study design for meta-omics Emma Travis
14:00 - 14:45 Why you should submit yout data and metadata Petra ten Hoopen
14:45 - 15:15 Tea/coffee break  
15:15 - 16:15 Community metagenomics and ComMet  Liz Wellington
16:15 - 17:15 Coupling different meta-omics approaches. Discuss paper: doi:10.1038/nature14238 All, open discussion
17:15 - 18:00 Data submission hands-on Petra ten Hoopen
18:00 Poster session  
19:30 Evening Meal  
Day 2 - Wednesday 2 December - Taxonomic and functional analysis of sequence data
09:00 - 11:00 Introduction to MG-RAST and hands-on Folker Meyer
11:00 - 11:30 Tea/coffee break  
11:30 - 12:30 Introduction to MG-RAST and hands-on (cont.) Folker Meyer
12:30 - 13:30 Lunch & poster session  
13:30 - 14:30 Estimating sequence diversity and coverage Darren Wilkinson
14:30 - 15:00 EBI metagenomics portal and hands-on Rob Finn/Alex Mitchell
15:00 - 15:30 Tea/coffee break  
15:30 - 18:00 EBI metagenomics portal and hands-on (cont.) Rob Finn/Alex Mitchell 
18:00 Free time  
19:00 Evening meal  
Day 3 - Thursday 3 December - From sequence to function
09:00 - 09:45 Meta Viromes Andy Millard
09:45 - 10:30 Lecture: Human gut microbiome Sam Forster
10:30 - 11:00 Tea/coffee break  
11:00 - 12:30 AntiSMASH, biosynethic gene clusters and Secondary Metabolites (hands on) Marnix Medema
12:30 - 13:30 Lunch  
13:30 - 14:30 Introduction to ChEMBL (and hands on) Prudence Mutowo
14:30 - 15:00 Further topics

All trainers

15:00 - 15:30 Q&A and feedback survey  
15:30 End of course  
16:00 Coach to Cambridge Train Station