Metagenomics: From the Bench to Data Analysis

he research area of Metagenomics is positioned at the intersection of many disciplines. Thus, the aim of this course is to provide an overview of the main aspects involved in metagenomics - from the bench to data analysis. By a balanced approach of lectures and practical session, not only a general background will be provided but also the tools employed in metagenomics as well as its relationship with other disciplines will be elucidated.

The methodological, technical and theoretical wealth arising from such complex and dynamic field as the metagenomic research define its biggest challenges, which are plenty and at many different levels in the work-flow. This course will expose the participants to these challenges at all levels.
+ show speakers and program

Day 1 - 14 April 2013 Time Speaker Title



DAY 1: Metagenomics Background and State of the art + Getting to know each other

Chair: Jacqueline Dreyer
09.00 Jacqueline Dreyer, EMBL Heidelberg, Germany “Welcome and Introduction”, Groups Expectations Activity
Edward DeLong, Massachusetts Institute of Technology, USA "The impact of Metagenomics, on genes and genomes discovery”


Coffee break
Peer Bork, EMBL Heidelberg, Germany "Metagenomics in silico: Concepts, historical milestones and next advances"
Lunch
Short talks by participants
Coffee break
José Eduardo Gonzalez Pastor, CSIC/INTA, Spain "Metagenomics Bench: Concepts, historical milestones and next advances"
Manuel Ferrer, CSIC, Institute of Catalysis, Spain "Metagenomics: general conceptual background, tools and relationships with other disciplines"
José Eduardo Gonzalez Pastor, CSIC/INTA, Spain

Jacqueline Dreyer, EMBL Heidelberg, Germany
Basic Concepts and Background Quiz
18:15 Dinner
19:15-onwards Poster Session
21:00 Bus to hotel



Day 2 - 15 April 2013 Time Speaker Title



DAY 2: Metagenomics Bench Challenge: DNA extraction!

Chair: Manuel Ferrer
09.00 Manuel Ferrer, CSIC, Institute of Catalysis, Spain Quick overview of the day structure
José Eduardo Gonzalez Pastor, CSIC/INTA, Spain

Manuel Ferrer, CSIC, Institute of Catalysis, Spain
Arantxa Penya, Universitat de les Illes Balears, Spain
Jacqueline Dreyer, EMBL Heidelberg, Germany
Practical session:

Extraction of metagenomic DNA from samples brought by the students (environmental) in groups of 4 (so total 5 groups)
Coffee break with quiz activity covering background processes underlying the steps taken in the lab during the

morning: aim is to open questions that will be addressed during the second part of the morning
José Eduardo Gonzalez Pastor, CSIC/INTA, Spain

Manuel Ferrer, CSIC, Institute of Catalysis, Spain
"DNA isolation continues"
Lunch
Extraction Results: preparing and running the gels
Coffee break
José Eduardo Gonzalez Pastor, CSIC/INTA, Spain "Extractions in Metagenomics"
(recapitulation of the main points and learning objectives of the day, comparative perspectives

of the differences in methodologies, techniques and awareness elements depending on the types of samples (e.g. environmental, soil, water, human biome)
18:30 Dinner
19:30 Bus to hotel


Day 3 - 16 April 2013 Time Speaker Title



DAY 3: Construction of metagenomic library

Chair: José Eduardo González Pastor
09.00 José Eduardo Gonzalez Pastor, CSIC/INTA, Spain Quick overview of the day structure
Practical Session:

Test digestion
Coffee break
Practical Session continues:

Digestion of metagenomic DNA
Lunch
Practical Session:

Purification from gel of the digested metagenomic DNA
Coffee break
Practical Session continues:

Cloning of the metagenomic DNA

Lectures when waiting time:
Manuel Ferrer: Plasmids to use for metagenomic library construction
Ramón Rosselló-Mora: primer selection, size of amplification.
20:00 Dinner
21:00 Bus to hotel


Day 4 - 17 April 2013 Time Speaker Title



DAY 4: Transformation of the library and HTS-Tour of Core Genome Seq Facilities and Experimental Design

Chair: Arantxa Penya
09:00 Manuel Ferrer, CSIC, Institute of Catalysis, Spain Quick overview of the day
Practical session: Transformation of the library
Ramón Rosselló-Móra, Marine Microbiology Group at the IMEDEA, Spain "Differences between evolution and phylogeny"
Coffee and Tour Vladimir Benes - Genome Core facilities
Lunch
Methodological lecture and discussion session:

Metagenomics experimental design: Common shortcoming and pitfalls
17:00 Free evening in Heidelberg

Day 5 - 18 April 2013 Time Speaker Title





DAY 5: From raw to clean data - Horizontal Gene Transfer
Chair: Vladimir Benes
09:00 José Eduardo Gonzalez Pastor, CSIC/INTA, Spain Quick overview of the day
Practical session: Analysis of some colonies from the metagenomic libraries
Giuseppe D'Auria, CSISP, Spain "Pyrosequencing, Shotgun Sequencing, and Metatranscriptomics analysis”
Coffee break
Vladimir Benes, EMBL Heidelberg, Germany “Next Generation Sequencing Data Analysis”
Lunch
Group activity and Coffee break “Design of Metagenomics experiments and workflow”
Giuseppe D'Auria, CSISP, Spain "Introduction into the processing of raw data"
Panel discussion
19:00 Dinner
20:00 Bus to hotel

Day 6 - 19 April 2013 Time Speaker Title





DAY 6: Metagenomics data analysis and Diversity*
Chair: Daniel Huson
09:00 Ramón Rosselló-Móra, Marine Microbiology Group at the IMEDEA, Spain “Diversity matters”
Coffee break with quiz activity covering the topics taught during the previous two days
Giuseppe D'Auria, CSISP, Spain "Pyrosequencing for metagenomics: accessing and organizing raw data"
Lunch
Kristian Vlahovicek, University of Oslo, Norway Methodological lecture: “Analysis Tools Overview: INCA, MILC and MELP”
Kristian Vlahovicek, University of Oslo, Norway Hands on Session: “INCA”
Coffee break
Sarah Hunter, EMBL-EBI Hinxton, United Kingdom “Public data resources”
Daniel Huson, Tübingen University, Germany “Phylogenetics Trees and Networks”
19:00 Dinner
20:00 Bus to hotel


Day 7 - 20 April 2013 Time Speaker Title





DAY 7: Metagenomics Data analysis *
Chair: Kristian Vlahovicek
09:30 Daniel Huson, Tübingen University, Germany “New methods and algorithms for analysing metagenomic datasets”
Coffee break
Daniel Huson, Tübingen University, Germany “MEGAN”
Lunch
Daniel Huson, Tübingen University, Germany continues- “MEGAN”
Coffee break
Hands on Session:
Time to practice and for questions
Feedback- and wrap up! online EMBO feedback questionaires
“Best Poster Prize” & “Best Scoring Group”
18:30 Drinks and Course dinner
20:00 Bus to hotel

10 Apr - 20 Apr 2013
Heidelberg
Germany
meeting website