Metagenomics Bioinformatics

Date:

 Monday 8 - Wednesday 10 September 2014

Venue: 

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

Application opens: 

Friday 02 May 2014

Application deadline: 

Friday 11 July 2014

Participation: 

Open application with selection

Contact: 

Rebecca Greenhaff

Registration fee: 

£360

Registration closed

Overview

This course will provide biologists, who are embarking upon metagenomics research projects training to use publicly available resources to manage, share, analyse and interpret metagenomics data, including both marker gene and whole gene shotgun (WGS) approaches. Delegates will gain hands-on experience of using a range of data resources and tools, interspersed with lectures. Please note that it will not be possible to bring your own data to analyse on the course.

Audience

This course is aimed at biologists who are beginning new projects in the field metagenomics research.

Prerequisites

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:

In addition, familiarity with the R statistical package, would also be an advantage:

Syllabus, tools and resources

During this course you will learn about:

  • Data standards: Genomic Standards Consortium (GSC)
  • Data generation: Next Generation Sequencing, amplicon-based approaches (ribosomal  RNA)
  • Data submission: ENA, SRA, Webin
  • Data analysis: The Metagenomics Portal, InterPro, GO, QIIME

Outcomes

After this course you should be able to:

  • Comprehend the minimum standards required for submission to comply with the Genomic Standards Consortium (GSC)
  • Use a range of amplicon based (marker genes) and metagenomics tools including the EBI metagenomics portal
  • Submit marker genes metagenomics data to public repositories
  • Interpret results and compare them with other metagenomic datasets

Programme

Time Topic Trainer
Day 1 -8th September
09:15 Registration  
09:30 An introduction to the EBI and course expectations activity Laura Emery
10:00 Introduction to NGS  Laura Emery
10:30 Tea/coffee break  
11:00 Considerations for metagenomics data analysis and summary of workflows Alex Mitchell
12:00 Lunch  
13:00 Public Data Resources for Metagenomics Hubert Denise
14:00 Data standards and introduction to ontologies Peter Sterk
14:30 Submitting your data to public repositories Rajesh Radhakrishnan
15:30 Tea/coffee break  
16:00 Command line warm up Alex Mitchell
16:30 Participant presentations  
17:30 Poster Session  
19:00 Dinner at Hinxton Hall  
Day 2 - 9th September
09:00 Interpreting phylogenetic trees (lecture) and thinking exercises Laura Emery
10:00 Quality control (Lecture) + Quality control (trimming, primers, FASTQC) (hands-on) Hubert Denise
11:00 Tea/coffee break  
11:30 Taxonomic analysis of amplicon and shotgun data (lecture) Peter Sterk
12:30 Lunch  
13:30 Taxonomic analyses: Qiime tutorial   (Hands-on) Peter Sterk
15:30 Tea/coffee break  
16:00 Translational optimisation and codon usage in metagenomes Kristian Vlahovicek
17:30 Analysing diversity in microbial communities from metagenomics to metaproteomics Elizabeth Wellington
18:30 Close  
19:00 Coach pick-up EBI Bus turning circle  
19:30 Dinner at Trinity Hall, Cambridge  
Day 3 - 10th September
09:00 EBI Metagenomics for functional and taxonomic analysis (Lecture) and Hands-on Alex Mitchell
10:30 Tea/coffee break  
11:00 Data visualisation and comparison using R (Hands-on) Hubert Denise
12:00 Lunch  
13:00 Data management and submission with the ISA infrastructure Eamonn Maguire & Alejandra Gonzalez-Beltran
14:00 Tea/coffee break  
14:30 Implementing metagenomics workflows (Hands-on) Maxim Scheremetjew
15:30 Advice for implementing metagenomics bioinformatics and Q&A All trainers
16:30 Course feedback and wrap-up FEEDBACK Laura Emery
European Bioinformatics Institute (EMBL-EBI)
Wellcome Genome Campus Hinxton Cambridge CB10 1SD United Kingdom

At EMBL-EBI, we manage the world’s public biological data and make it freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. Set on the beautiful Wellcome Genome Campus near Cambridge in the UK, we support scientists throughout the world in seeking solutions to challenges in healthcare, agriculture and the environment.

/training/events/0000/files/content.ebi.ac.uk/venues/south_building_exterior.jpg

In association with

How to apply

Registration for this event is now closed.

 

Application deadline

11 July 2014

Number of places

30 places

Registration closed

Organisers

Laura Emery

Peter Sterk - Pfizer, UK

Alex Mitchell

Hubert Denise

Trainers

Laura Emery - EMBL-EBI, UK

Alex Mitchell - EMBL-EBI, UK

Hubert Denise - EMBL-EBI, UK

Peter Sterk - Pfizer, UK

Kristian Vlahovicek - Dept. Molecular Biology, Faculty of Science, University of Zagreb

Elizabeth Wellington - University of Warwaick, UK

Alejandra Gonzalez-Beltran - Oxford e-Research Centre, UK

Maxim Scheremetjew - EMBL-EBI, UK

Rajesh Radhakrishnan - EMBL-EBI

Alejandra Gonzalez-Beltran - Oxford e-Research Centre, UK

Eamonn Maguire

Materials & attachments

Metagenomics Bioinformatics