Exploiting Metagenomics Approaches in Life Science Research
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Date:
Tuesday 1 - Thursday 3 December 2015Venue:
European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United KingdomApplication opens:
Friday July 24 2015Application deadline:
Friday October 02 2015Participation:
Open application with selectionContact:
Frank O’DonnellRegistration fee:
£265 (includes 2 nights accommodation & food)Registration closed
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:
- Basic introduction to the Unix environment: www.ee.surrey.ac.uk/Teaching/Unix
- Introduction and exercises for Bio-Linux 7, the Linux environment we will be using during the course: http://nebc.nerc.ac.uk/support/training/course-notes/past-notes/intro-bl7
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 | |
In association with
How to apply
In order to be considered for a place on this course applicants must do the following:
- Complete the online application form.
- Submit a PDF document to frank@ebi.ac.uk containing a short biography including your work history, a description of your current research interests and a short biography. Each document should be no longer than 100 words.
- Provide a letter of support from a supervisor or a senior co-worker explaining why you should be selected for this course.
Further details will be provided on your confirmation email after completing the online form.
Incomplete applications will NOT be considered. Please read through the following guidance document for more information on how to complete your application.
Application deadline
02 October 2015
Number of places
30 places
Organisers
Rob Finn
Elizabeth Wellington - University of Warwaick, UK
Laura Emery
Trainers
Elizabeth Wellington - University of Warwaick, UK
Folker Meyer - Argonne National Laboratory, USA
Darren Wilkinson - University of Newcastle, UK
Tom Curtis - University of Newcastle, UK
Laura Emery - EMBL-EBI, UK
Petra Ten Hoopen - EMBL-EBI, UK
Rob Finn - EMBL-EBI, UK
Sam Forster - Wellcome Trust Sanger Institute, UK
Matthew Clark - The Genome Analysis Centre (TGAC)
Prudence Mutowo - EMBL-EBI, UK
Alex Mitchell - EMBL-EBI, UK
Emma Travis - University of Wawrick, UK
Marnix Medema - Wageningen University, The Netherlands