Metagenomics: Managing, Analysing and Visualising Data Course

This programme is aimed at biologists who are embarking upon new research projects in the field of metagenomics. It provides training to use publically-available resources to manage, share and interpret metagenomics data. Delegates will gain hands-on practice of using the EBI metagenomics data resources, interspersed with some lectures. This includes training on data submission to the European Nucleotide Archive (ENA), the subsequent analysis pipeline, data retrieval and interpretation. We will use specially-selected data sets as illustrated examples throughout the course; mainly Amplicon-based (16S or other marker gene) approaches, whole genome shotgun metagenomic and metatranscriptomic datasets. Training will be provided by experts from the EBI and Oxford e-Research Centre (OeRC) who specialise in large-scale data management and analysis. In addition, there will be the opportunity for delegates to make suggestions to shape the provision of future EBI resources for metagenomics. The practical exercises use web-browser-based tools and assume no previous training in bioinformatics.

What will I learn?
After this course you should be able to…

Identify metagenomics data with the minimum standards required for submission to comply with the Genomic Standards Consortium (GSC)
Become familiar with the European Nucleotide Archive (ENA) database, its structure, the type of data it contains and its navigation/browsing tools
Submit metagenomics data to the Sequence Read Achieve (SRA) using both Webin and ISA interfaces
Understand in detail how metagenomics data submitted to ENA is analysed (including the use of tools such as InterPro and GO for functional characterisation)
Interpret your results and compare them with other metagenomics datasets
+ show speakers and program
Day 1 - 9 September 2013
09:30 Welcome, course introduction and expectations exercise- Laura Emery
10:00 An introduction to the minimum standards for data submission- Peter Sterk
11:00 Coffee break
11:30 Introduction to ENA and the SRA- Rajesh Radhakrishnan (tbc)
12:30 Lunch
13:30 Using Webin for online data submission hands-on practical- Rajesh Radhakrishnan (tbc)
15:00 Coffee break
15:30 Using ISA for online data submission hands-on practical- Philippe Rocca-Serra/Alejandra Gonzalez Beltran (tbc)
18:00 Drinks reception + Poster Session
19:30 Dinner at Hinxton Hall Restaurant
21:00 Shuttle bus to Holiday Inn Express - Duxford

Day 2 - 10 September 2013
08:00 Shuttle bus from Holiday Inn Express - Duxford
09:00 Taxonomic analysis of metagenomic data- Hubert Denise/Peter Sterk (tbc)
10:30 Coffee break
11:00 Taxonomic analysis of metagenomic data hands-on practical- Hubert Denise/Peter Sterk (tbc)
12:30 Lunch
13:30 Understanding metagenome function- Alex Mitchell (tbc)
15:30 Coffee break
16:00 Metagenome functional analysis hands-on practical- Alex Mitchell (tbc)
17:00 Keynote speaker speaker (tbc)
19:00 Dinner at Hinxton Hall Restaurant
21:00 Shuttle bus to Holiday Inn Express - Duxford

Day 3 - 11 September 2013
08:00 Check out of accommodatuion and shuttle bus from Holiday Inn Express - Duxford
09:00 Meta-analysis: how to query, filter and compare multiple results and get more from your data- Hubert Denise/Alex Mitchell (tbc)
10:30 Coffee break
11:00 Metagenomics meta-analysis hands-on- Hubert Denise/Alex Mitchell (tbc)
12:30 Lunch
13:30 Exploiting your data further – how to extract data for use in other tools and resources speaker (tbc)
14:00 Future resource development- Sarah Hunter
15:30 Coffee break
16:00 Informal Q&A and course evaluations- Laura Emery
16:30 Departures (delegates to organise own travel arrangements)

9 Sep - 11 Sep 2013
United Kingdom
meeting website