EMBO Practical Course
Metagenomics: From the Bench to Data Analysis
EMBL Heidelberg, Germany Sunday 14 April - Saturday 20 April 2013 Application closed
Course Programme
| Time | Speaker | Title |
|---|---|---|
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DAY 1: Metagenomics Background and State of the art + Getting to know each other
Chair: Jacqueline Dreyer |
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| 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” | |
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Coffee break |
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| 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 | |
| Time | Speaker | Title |
|---|---|---|
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DAY 2: Metagenomics Bench Challenge: DNA extraction!
Chair: José Eduardo González Pastor |
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| 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 |
|
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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" |
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(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) |
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| 18:30 | Dinner | |
| 19:30 | Bus to hotel | |
| Time | Speaker | Title |
|---|---|---|
|
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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 |
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| Coffee break | ||
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Practical Session continues:
Digestion of metagenomic DNA |
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| Lunch | ||
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Practical Session:
Purification from gel of the digested metagenomic DNA |
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| Coffee break | ||
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Practical Session continues:
Cloning of the metagenomic DNA Lectures when waiting time: |
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| 20:00 | Dinner | |
| 21:00 | Bus to hotel | |
| Time | Speaker | Title |
|---|---|---|
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DAY 4: Transformation of the library and HTS-Tour of Core Genome Seq Facilities and Experimental Design
Chair: María Eugenia Guazzaroni |
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| 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 |
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| Time | Speaker | Title |
|---|---|---|
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DAY 5: From raw to clean data - Horizontal Gene Transfer |
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| 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 | |
| Time | Speaker | Title |
|---|---|---|
|
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DAY 6: Metagenomics data analysis and Diversity* |
|
| 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 | |
| Time | Speaker | Title |
|---|---|---|
|
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DAY 7: Metagenomics Data analysis * |
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| 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 |
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| 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 |
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