Metagenomics: Managing, Analysing and Visualising Data Course
Course Overview
This course aims to provide biologists who are embarking upon metagenomics research projects 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. 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.
Audience
This programme is aimed at biologists who are embarking upon new research projects in the field of metagenomics. The practical excercises use web-browser-based tools and assume no previous training in bioinformatics.
Syllabus, Tools and Resources
During this course you will learn about metagenomics:
- Data standards: Genomics Standards Consortium (GSC), Amplicon-based approaches, WGS, metatranscriptomics
- Data submission: ENA, SRA, Webin, ISA
- Data analysis: The Metagenomics Portal, InterPro, GO
- Data retrieval and interpretation
| Time | Topic | Trainer |
|---|---|---|
| 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 | Sequencing platforms and file formats | Peter Sterk |
| 11:50 | Introduction to ENA and the SRA | Rajesh Radhakrishnan |
| 12:50 | Lunch | |
| 13:50 | Using Webin for online data submission (including hands-on practical) | Arnaud Oisel |
| 15:00 | Coffee break | |
| 15:30 | Using ISA for online data submission (Including hands-on practical) | Philippe Rocca-Serra/Alejandra Gonzalez Beltran |
| 17:00 | Keynote Lecture | Dusko Ehrlich |
| 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 | ||
| 09:00 | Metagenomics analysis pipeline - Introduction and overview (including hands-on practical) | Hubert Denise/Alex Mitchell |
| 10:30 | Coffee break | |
| 11:00 | Understanding metagenome function (including hands-on practical) | Alex Mitchell |
| 12:30 | Lunch | |
| 13:30 | Taxonomic analysis of metagenomes | Peter Sterk |
| 15:30 | Coffee break | |
| 16:00 | Building workflows using Taverna | Maxim Scheremetjew |
| 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 accommodation and shuttle bus from Holiday Inn Express - Duxford | |
| 09:00 | Other useful resources for studying environmental communities | Attilla Csordas, Amy Tang |
| 09:40 | ENA advanced search | Nicole Silvester |
| 10:00 | Coffee break | |
| 10:30 | Other useful resources for studying environmental communities and discussion | Reza Salek, Adam Faulconbridge |
| 11:30 | Future resource development - prioritising new tools and features for metagenomics | All (facilitated by Jenny Cham) |
| 13:00 | Lunch | |
| 14:00 | Review of prioritisation excercise including delegate presentations | All (facilitated by Jenny Cham) |
| 14:30 | Informal Q&A and course evaluations | Laura Emery |
| 15:00 | Departures (delegates to organise their own travel arrangements) | |
Course Materials - Day 1
Course Materials - Day 2
Course Materials - Day 3
Registration will be via a selection process therefore applicants should be aware that, in order to be considered for a place on this course, they MUST complete the application page as well as submit a short CV, research interests. Incomplete applications will NOT be considered. Details of how to submit these extra documents will be provided on your application confirmation email.
Application registration closes 12 July 2013 (12:00 midday GMT). There will be a maximum of 30 participants on this course. Successful applicants will be notified by 26 July 2013 and will then be asked to confirm their place on the course by re-registering and paying the course fee.
Please note that the registration fee of £350.00 includes:
- All meals (breakfast, lunch, dinner and refreshment breaks)
- Course materials
- Use of a computer in the EMBL-EBI IT Training Room throughout the course
- 2 night's Accommodation at Holiday Inn Express - Duxford (9 & 10 September 2013)
- Shuttle bus transfers to and from the accommodation as mentioned in the agenda
Application for this event is now closed.