Metagenomics Bioinformatics, Brazil 2014
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Date:
Monday 3 - Wednesday 5 November 2014Venue:
Universidade Católica de Brasília - Universidade Católica de Brasília, , Campus Avançado Asa Norte, Brasília, - DF, 71966-700, BrazilApplication opens:
Wednesday 01 October 2014Application deadline:
Thursday 16 October 2014Participation:
Open application with selectionContact:
Frank O’DonnellRegistration fee:
R$100,00Registration closed
Course Overview
This course will provide an introdution to the use of publicly available resources for the management, sharing, analysis and interpretation of metagenomics data, including both marker gene and whole gene shotgun (WGS) approaches. Delegates will gain hands-on experience of a range of data resources and tools, interspersed with lectures. Please note that it will not be possible to bring your own data for analysis during the course.
Audience
This course is aimed at wet-lab biologists who are starting out in the field of 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:
- Basic introduction to the Unix environment: www.ee.surrey.ac.uk/Teaching/Unix
In addition, familiarity with the R statistical package, would be an advantage.
- Basic R concept tutorials: www.r-tutor.com/r-introduction
Learning outcomes
After this course you should be able to:
- Comprehend the minimum standards required for data submission to comply with the Genomic Standards Consortium (GSC)
- Understand the principals behind amplicon-based (marker gene) and functional analysis of metagenomic sequence data
- Use a range of analysis tools, including the EBI metagenomics portal
- Interpret results and compare them with other metagenomic datasets
Programme
| Time | Topic | Trainer |
|---|---|---|
| Day 1 - 3rd November 2014 | ||
| 09:15 - 09:30 | Registration | |
| 09:30 - 10:00 | Introduction and course expectations | Gabriel Fernandes |
| 10:00 - 10:30 | Introduction to NGS | Gabriel Fernandes |
| 10:30 - 11:00 | Tea/coffee break | |
| 11:00 - 12:00 | Considerations for metagenomics data analysis and summmary of workflows | Alex Mitchell |
| 12:00 - 13:00 | Lunch | |
| 13:00 - 14:00 | Public data resources for metagenomics | Hubert Denise |
| 14:00 - 15:30 | Describing your data using standards. | Peter Sterk |
| 15:30 - 16:00 | Tea/coffee break | |
| 16:00 - 16:30 | Command line warm up | Alex Mitchell |
| 16:30 - 17:30 | Participant presentations | All |
| Day 2 - 4th November 2014 | ||
| 09:00 - 10:30 | Quality control | Hubert Denise |
| 10:30 - 11:00 | Tea/coffee break | |
| 11:00 - 12:30 | Taxonomic analysis of amplicon and shotgun data | Peter Sterk |
| 12:30 - 13:30 | Lunch | |
| 13:30 - 15:30 | Taxonomic analyses: Qiime tutorial | Peter Sterk |
| 15:30 - 16:00 | Tea/coffee break | |
| 16:00 - 17:00 | Taxonomic analyses: Qiime tutorial (Continued) and data visualisation using Emperor and Cytoscape | Peter Sterk |
| 17:00 - 18:00 | Keynote | TBC |
| Day 3 - 5th November 2014 | ||
| 09:00 - 09:30 | InterPro and GO for functional analysis of metagenomic data | Alex Mitchell |
| 09:30 - 11:00 | Functional analysis using EMG | Alex Mitchell |
| 11:00 - 11:30 | Tea/coffee break | |
| 11:30 - 13:00 | Analysis of metagenomics data using R | Hubert Denise |
| 13:00 - 14:00 | Lunch | |
| 14:00 - 15:00 | Implementing Metagenomics workflows with Taverna / Galaxy | Gabriel Fernandes |
| 15:00 - 15:30 | Suggestions for implementing metagenomics bioinformatics and Q&A | All |
| 15:30 - 16:00 | Course feedback and wrap-up | Gabriel Fernandes |
| 16:00 | Course close | |