Microme Workshop on Microbial Metabolism
MICROME is an EU Framework Programme 7 Collaborative Project. Grant Agreement Number 222886-2
Next generation sequencing techniques have led to the deciphering of thousands of bacterial genomes, and the accumulation of a wealth of information about the diversity of natural enzymatic functions. Yet accessing and mining this data remains a difficult problem.
In this course, partners from the Microme project, a collaborative European effort to improve resources for bacterial metabolism, will teach in a number of practical workshop sessions aimed at guiding the participants through the complexities of networks of metabolites and biochemical pathways within the current knowledge.
Audience
This course is aimed at biologists already working on bacterial genomes, annotation and metabolism who are embarking upon projects that aim to mine large datasets. This course requires no prior knowledge of metabolic reconstruction.
Syllabus, Tools and Resources
During this course you will learn about…
Bacterial Genomics: Ensembl Genomes, UniProt
Bacterial Metabolism: ChEBI, RhEA, UniPathway, BioCyc, KEGG
Learning Objectives
After this course you should be able to…
- How to access public bacterial genome data through interactive and programmatic interfaces with the Ensembl platform
- How to explore metabolic data in different contexts using UniProt and UniPathway web sites
- How to review genome annotation in a comparative framework using MicroScope
- How to use the power of comparative analysis to complete our knowledge of metabolic pathways and their evolutionary history
- How to perform automated metabolic reconstruction and pathway design
| Time | Topic | Trainer |
|---|---|---|
| Day 1 - 8 October 2013 | ||
| 12:30 | Registration and Lunch | |
| 13:30 | General introduction biochemistry reminder and metabolic data reconciliation issue. Exploring bacterial metabolism with UniProt/UniPathway resources |
Anne Morgat |
| 15:30 | Coffee break | |
| 16:00 | Exploring bacterial genomes with Ensembl | Paul Kersey/Lee Falin/Dan Staines |
| 18:00 | Close of day | |
| 19:00 | Workshop Dinner - Wellcome Trust Conference Centre | |
| Day 2 - 9 October 2013 | ||
| 09:00 | MicroScope, a collaborative platform for genome annotation, comparative genomics and microbial diversity exploration | Eugeni Belda & Claudine Medigue François Lefevre & Damien Mornico |
| 10:30 | Coffee break | |
| 10:45 | Reconstruction and expert curation of genome-scale metabolic networks with MicroScope | Eugeni Belda & Claudine Medigue François Lefevre & Damien Mornico |
| 12:15 | Lunch | |
| 13:15 | Genome Scale Metabolic Networks: reconstruction, properties and applications Stoichiometric and Constraint-based Modeling Tutorial |
Marco Pagni & Mathias Ganter |
| 15:00 | Metabolic CAD / Bioretrosynthesis | Pierre-Yves Bourguignon |
| 16:00 | Coffee break | |
| 16:30 | Predicting operons, regulons and metabolic pathways from bacterial genomes | Jacques van Helden |
| 18:00 | Close of day | |
| 19:00 | Workshop Dinner - Red Lion, Hinxton | |
| Day 3 - 10 October 2013 | ||
| 09:00 | Metagenomics | Peter Sterk/Alex Mitchell/Hubert Denise |
| 10:30 | Coffee break | |
| 11:00 | Comparative genomics of metabolic pathways and the computational inference of their ancestral states | Fotis Psomopoulos & Christos Ouzounis |
| 12:45 | Concluding remarks and feedback | Paul Kersey & Anne Morgat |
| 13:00 | Close of workshop and Lunch | |
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 23 August 2013 (12:00 midday GMT). There will be a maximum of 30 participants on this course. Successful applicants will be notified by 23 August 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 £100.00 includes:
- All meals listed in the agenda (breakfast, lunch, dinner and refreshment breaks)
- 2 night's onsite accommodation at Wellcome Trust Conference Centre (8 & 9 October 2013)
- Course materials
- Use of a computer in the EMBL-EBI IT Training Room throughout the course
Application is now closed