Micro B3 OSD Analysis Workshop 2015
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Date:
Monday 9 - Friday 13 March 2015Venue:
European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United KingdomApplication opens:
Friday 09 January 2015Application deadline:
Sunday 01 February 2015Participation:
Open application with selectionContact:
Johanna LangrishRegistration fee:
€100Registration closed
Overview
The OSD Analysis Workshop / Jamboree will bring together OSD participants and members of the OSD Analysis Core Team, with the aim of transforming the OSD primary analysis results into biological and ecological meaning.
Participants will gain hands-on experience of using several approaches for the analysis of marine metagenomics data obtained as part of the MicroB3 project. Additionally there will be the opportunity for knowledge exchange and the exploration of current challenges and developments in the field.
Audience
This course is aimed at partners of the Micro B3 project with metagenomics sequence data obtained from OSD in June 2014. The course assumes basic experience in sequence data analysis. Some of the tools to be introduced on the course will require the use of Linux/Unix commands and the R statistics package. We strongly recommend that you familiarise yourself with these. Free tutorials are available from:
Syllabus, tools and resources
During this course you will learn about:
- Data standards
- Data submission
- Data analysis
- Data integration
Outcomes
After this course you should be able to:
- Identify data with the minimum standards required for submission to comply with the Genomic Standards Consortium (GSC)
- Submit metagenomics data to public repositories (both amplicons & metagenomes)
- Apply bioinformatics techniques to integrate ecological and contextual data
- Use bioinformatics tools to analyse OSD data
- Interpret results to uncover new biological meaning
Programme
| Time | Topic | Trainer |
|---|---|---|
| Monday 09 March 2015 |
||
| 12:00 - 12:30 | Arrival & Lunch | |
| 12:30 - 13:00 | Introduction to the EBI | Laura Emery |
| 13:00 - 15:00 | Introduction and Practical session | Pascal Hingamp/Chris Bowler |
| 15:00 - 15:30 | Tea/coffee break | |
| 15:30 - 17:00 | Sequence and submission - Accessing the OSD data (ENA + MB3-IS) | Ivaylo Kostadinov |
| 18:00 | Shuttle Bus | |
| 19:00 | Dinner at The Red Lion, Holiday Inn Express, Duxford | |
| Tuesday 10 March 2015 |
||
| 08:45 | Shuttle Bus | |
| 09:00 - 10:00 | First steps before analysis: Quality control of the OSD sequence data | Antonio Fernandez |
| 10:00-11:00 | Keynote Lecture (Kendrew Lecture theatre) | |
| 11:00-11:30 | Tea/coffee break | |
| 11:30 - 13:00 | The M2B3 Standards | Petra ten Hoopen |
| 13:00 - 14:00 | Lunch | |
| 14:00 - 15:00 | Propose your own 'hands-on themes' | OSD Analysis team |
| 15:00 - 15:30 | Tea/coffee break | |
| 15:30 - 17:00 | Propose your own 'hands-on themes' | OSD Analysis team |
| 18:00 | Shuttle Bus | |
| 19:00 | Dinner at The Red Lion, Holiday Inn Express, Duxford | |
| Wednesday 11 March 2015 |
||
| 08:45 | Shuttle Bus | |
| 09:00 - 10:00 | Numerical ecology approaches to analysing high-dimensional data & sharing analytical knowledge (GUSTA ME) | Pier Luigi Buttigieg |
| 10:00 - 10:30 | Tea/coffee break | |
| 10:30 - 12:00 | MG-Portal | Alex Mitchell |
| 12:00 - 13:00 | Lunch | |
| 13:00 - 15:00 | Propose your own 'hands-on themes' | OSD Analysis team |
| 15:00 - 15:30 | Tea/coffee break | |
| 15:30 - 17:00 | Propose your own 'hands-on themes' | OSD Analysis team |
| 18:00 | Shuttle Bus | |
| 19:00 | Dinner at The Red Lion, Holiday Inn Express, Duxford | |
| Thursday 12 March 2015 |
||
| 08:45 | Shuttle bus | |
| 09:00 - 10:00 | Oceanographic data | Stephane Pesant |
| 10:00 - 10:30 | Tea/coffee break | |
| 10:30 - 12:00 | Biogeography: Concepts and modelling | Daniele Ludicone |
| 12:00 - 13:00 | Lunch | |
| 13:00 - 15:00 | Propose your own 'hands-on themes' | OSD Analysis team |
| 15:00 - 15:30 | Tea/coffee break | |
| 15:30 - 16:45 | Propose your own 'hands-on themes' | OSD Analysis team |
| 16:45 | Shuttle Bus to Cambridge for 'free time' in Cambridge | |
| 19:00 | Cambridge College Dinner, Downing College | |
| Friday 13 March 2015 |
||
| 08:45 | Shuttle Bus | |
| 09:00 - 10:00 | The OSD Paper | Mesude Bicak |
| 10:00 - 10:30 | Tea/coffee break | |
| 10:30 - 12:00 | Summary of OSD 2015 | |
| 12:00 - 13:00 | Lunch & Feedback | |
| 13:00 | Departures - A coach is booked to take participants to Cambridge Train Station (from Cambridge, participants will be able to take the train to all main line train stations). | |
In association with
How to apply
Application deadline
01 February 2015
Number of places
30 places
Organisers
Laura Emery
Frank Oliver Glöckner - Jacobs University, Germany
Trainers
Laura Emery - EMBL-EBI, UK
Pascal Hingamp - CNRS, France
Chris Bowler - CNRS, France
Antonio Fernandez - MPI Bremen, Germany
Petra Ten Hoopen - EMBL-EBI, UK
Pier Luigi Buttigieg - Max Planck Institute for Marine Microbiology, Germany
Alex Mitchell - EMBL-EBI, UK
Stephane Pesant - Center for Marine Environmental Sciences, Germany
Daniele Ludicone - Stazione Zoologica Anton Dohrn Naples (SZN), Italy
Mesude Bicak - Oxford e-Research Centre, UK