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EMBO Practical Course

Metagenomics: From the Bench to Data Analysis

EMBL Heidelberg, Germany Sunday 14 April - Saturday 20 April 2013 Application closed
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Course Programme

 
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
  CANCELLED- Edward DeLong, Massachusetts Institute of Technology, USA "The impact of Metagenomics, on genes and genomes discovery”
 

Coffee break

  Shinichi Sunagawa, EMBL Heidelberg "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"
  José Eduardo Gonzalez Pastor, CSIC/INTA, Spain

Jacqueline Dreyer, EMBL Heidelberg, Germany

Basic Concepts and Background Quiz
  Dinner
18:15 Poster Session
19:15 Bus to hotel
 
 
Day 2 - 15 April 2013
Time Speaker Title
 

 

DAY 2: Metagenomics Bench Challenge: DNA extraction!

Chair: José Eduardo González Pastor

09.00   Quick overview of the day structure
  José Eduardo Gonzalez Pastor, CSIC/INTA, Spain

 

María Eugenia Guazzaroni, Universidade de São Paulo, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Departamento de Química, Brazil

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

 

María Eugenia Guazzaroni, Universidade de São Paulo, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Departamento de Química, Brazil

"DNA isolation continues"
  Lunch
    Extraction Results: preparing and running the gels
  Coffee break
  José Eduardo Gonzalez Pastor, CSIC/INTA, Spain

 

María Eugenia Guazzaroni, Universidade de São Paulo, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Departamento de Química, Brazil

Lectures when waiting time:

"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
  María Eugenia Guazzaroni, Universidade de São Paulo, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Departamento de Química, Brazil

 

Arantxa López López, IMEDEA, Spain

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:
María Eugenia Guazzaroni: 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: María Eugenia Guazzaroni

09:00 María Eugenia Guazzaroni, Universidade de São Paulo, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Departamento de Química, Brazil 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

Bus to Heidelberg Old Town (with an initial stop at ISG Hotel)

17:30- 1,5h Heidelberg Old Town guided tour

Free evening in Heidelberg- with individual return to hotel

 
 
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
  Ramón Rosselló-Móra, Marine Microbiology Group at the IMEDEA, Spain  “Diversity matters”
  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 Tobias Rausch, EMBL Heidelberg “Next Generation Sequencing Data Analysis”
  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 Zagreb, Croatia Methodological lecture: “Analysis Tools Overview: INCA, MILC and MELP”
  Kristian Vlahovicek, University of Zagreb, Croatia Hands on Session: “INCA”
  Coffee break
  Hubert Denise, 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”
19:00 Bus to downtown Heidelberg with a quick stop at the hotel (5 min)
19:30 Course dinner - Restaurant Bier & Brezel, Hauptstrasse 184 Heidelberg

Individual return to ISG hotel