Location & dates EMBL Heidelberg, Germany 7 - 14 May 2017
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Programme

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Day 1 - Sunday 7 May 2017
TimeSpeaker

Metagenomics Background and State of the art + Getting to know each other
Chair: Jacqueline Dreyer-Lamm

10.00 - 11.00

Welcome and Introduction, Groups Expectactions Activity
Jacqueline Dreyer-Lamm - EMBL Heidelberg, Germany

11.00 - 12.00

Lecture:
The impact of Metagenomics, on genes and genomes discovery
Gabrielle Potocki-Veronese -INRA-LISBP, France

12.00 - 13.00

Lunch

13.00 - 14.30 Short talks by participants
14.30 - 15.30

Lecture:
Metagenomics: Concepts, historical milestones and next advances
José Eduardo Gonzalez Pastor - Center of Astrobiology (CSIC/INTA), Spain

15.30 - 15.45 Coffee break
15.45 - 16.45

Lecture:
Basic Concepts and Background Quiz 
Jacqueline Dreyer-Lamm - EMBL Heidelberg, Germany

16.45 - 18.00

Lecture and Discussion session:
Extractions in Metagenomics
Emelia De Force - QIAGEN, Germany
José Eduardo Gonzalez Pastor - Center of Astrobiology (CSIC/INTA), Spain

18.00 - 19.15

Dinner

19.15

Poster Session - Even Numbers

Bus to hotel

Day 2 - Monday 8 May 2017
TimeSpeaker

Metagenomics Bench Challenge: DNA extraction!
Chair: José Eduardo González Pastor

09.00 - 09.15

Quick overview of the day structure

09.15 - 10.30

Practical:
Extraction of metagenomic DNA from samples brought by the students (environmental) in groups

10.30 - 11.00 Coffee break
11.00 - 12.30 Practical:
DNA isolation continues
12.30 - 13.30

Lunch

13.30 - 15.00

Extraction Results:
Preparing and running the gels

15.00 - 15.30 Coffee break
15.30 - 16.30

Lecture:
Metagenomics library preparation for NGS
Vladimir Benes - EMBL Heidelberg, Germany

16.30 - 18.30

Discussion Session

18.30 - 19.30

Dinner

19.30

Poster Session - Odd Numbers

Bus to hotel

Day 3 - Tuesday 9 May 2017
TimeSpeaker
Construction of metagenomic library
Chair: Arantxa Lopez
09.00 - 09.15

Quick overview of the day structure 
Arantxa Lopez

09.15 - 10.30

Practical:
Test digestin conditions for metagenomic DNA and preparation of agarose gels

10.30 - 11.00

Coffee break

11.00 - 12.30 Practical:
Digestion of metagenomic DNA for cloning in the libraries (once that digestion conditions are determined)
12.30 - 13.30

Lunch

13.30 - 15.00 Practical:
Purification from gel of the digested metagenomic DNA
15.00 - 15.30

Coffee break

15.30 - 17.30

Practical:
Cloning of the metagenomic DNA in pBluescript SKII + Overnight ligation

19.00

Dinner

Bus to hotel

Day 4 - Wednesday 10 May 2017
TimeSpeaker

Transformation of the library and HTS-Tour of Core Genome Seq Facilities and Experimental Design
Chair: José Eduardo González Pastor

09.00 - 09.15

Quick overview of the day
José Eduardo González Pastor

09.15 - 11.00

Practical:
Transformation in E. coli of the library

11.00 - 12.00 Lecture:
Some theory on taxonomy, phylogeny and diversity measures based on 16S rRNA gene amplicons and direct metagenomics
Ramón Rosselló-Móra - Marine Microbiology Group at the IMEDEA, SpainSpain
12.00 - 13.00 Lunch
13.00 - 14.00

Methodological lecture and discussion session:
Metagenomics experimental design: Common shortcoming and pitfalls
José Eduardo Gonzalez Pastor - Center of Astrobiology (CSIC/INTA), Spain

14.00 - 15.00

Metagenomics in silico: what can I do with my data?
Giuseppe D'Auria - Foundation for the Promotion of Health and Biomedical Research of Valencia Region - FISABIO, Spain

15.00 - 16.00 Coffee and Q&A
16.00

Free Evening

** Optional - Guided tour @ 16:30 (bus will drop off at the meeting point)

Day 5 - Thursday 11 May 2017
TimeSpeaker
From raw to clean data - Horizontal Gene Transfer
Chair: Ramón Rosselló-Mora
09.00 - 09.15

Quick overview of the day
Ramón Rosselló-Mora

09.15 - 10.00

Practical:
Analysis of some colonies from the metagenomic libraries.
Interpretation of results

10.00 - 10.30 Coffee break
10.30 - 12.30

Lecture and Hands-on:
Introduction to Linux
David Pérez-Villarroya - University of Valencia, Spain

12.30 - 13.30

Lunch

13.30 - 14.30

Hands-on:
Introduction to Linux -cont
David Pérez-Villarroya - University of Valencia, Spain

14.30 - 15.30

Hands-on:
Sequence data "Shotgun Sequencing, and Meta[gen|transcript]omics analysis
Giuseppe D'Auria - Foundation for the Promotion of Health and Biomedical Research of Valencia Region - FISABIO, Spain

15.30 - 16.00

Coffee break

16.00 - 18.30

Lecture and Hands-on:
Introduction into the processing of raw data
Giuseppe D'Auria - Foundation for the Promotion of Health and Biomedical Research of Valencia Region - FISABIO, Spain

18.30

Free Evening

Day 6 - Friday 12 May 2017
TimeSpeaker

Metagenomics work-flow
Chair: Kostas Konstantinidis

09.00 - 09.15

Quick overview of the day
Kostas Konstantinidis - Georgia Institute of Technology, USA

09.15 - 11.00

Lecture and Hands-on:
Upstream analysis: data organisation and standards in metagenomics
Giuseppe D'Auria - Foundation for the Promotion of Health and Biomedical Research of Valencia Region - FISABIO, Spain

11.00 - 11.15 Coffee Break
11.15 - 12.15 Lecture and Hands-on:
Upstream analysis: data organisation and standards in metagenomics, cont.
Giuseppe D'Auria - Foundation for the Promotion of Health and Biomedical Research of Valencia Region - FISABIO, Spain
12.15 - 13.15

Lunch break

13.15 - 14.15

Lecture and Hands-on continues:
Upstream analysis: Metagenomic assembly, ORF finding, functional annotation.
Giuseppe D'Auria - Foundation for the Promotion of Health and Biomedical Research of Valencia Region - FISABIO, Spain

14.15 - 16.15

Hands-on:
Introduction to R for bioinformatics
Giuseppe D'Auria - Foundation for the Promotion of Health and Biomedical Research of Valencia Region - FISABIO, Spain

16.15 - 16.30

Coffee Break

16.30 - 18.00

Lecture and Hands On Session:
Tools for metagenomic comparative analysis and the Microbial Genome Atlas (MiGA) project
Kostas Konstantinidis - Georgia Institute of Technology, USA

18.00 - 18.30

Group Activity:
Wrap up of the day- quiz activity covering the topics taught during the previous two days

18.30

Dinner

Bus to hotel

Day 7 - Saturday 13 May 2017
TimeSpeaker
Metagenomics Data analysis
Chair: Kristian Vlahovicek
09.00 - 09.15

Quick overview of the day
Kristian Vlahovicek

09.00 - 11.15

Lecture and Hands-on:
Functional analysis, InterProScan
Lorna Richardson, EMBL-EBI, UK

11.15 - 11.30 Coffee break
11.30 - 13.00

Lecture and Hands-on:
Databases
Hubert Denise, EMBL-EBI, UK

13.00 - 14.00 Lunch
14.00 - 16.00

Group activity with presentations “Design of Metagenomics experiments and workflow”

16.00 - 17.00

Lecture:
Analysis Tools Overview: INCA, MILC and MELP
Kristian Vlahovicek - University of Zagreb, Croatia

17.00 - 18.00

Hands-on:
INCA
Kristian Vlahovicek - University of Zagreb, Croatia

18.00 - 18.30

Group activity:
Wrap up of the day- Q&A

18.30

Course Dinner Downtown

Day 8 - Sunday 14 May 2017
TimeSpeaker
Metagenomics Sample Characterization
Chair: Giuseppe D'Auria
09.00 - 09.15

Quick overview of the day
Giuseppe D'Auria

09.15 - 10.00

Lecture:
Pan-genomics, from multiple strain comparisons to phylogenomics
David Sassera - UNIPV, Italy

10.00 - 10.30

Lecture:
Resolving and quantifying taxonomic and functional entities at different scales
Kristoffer Forslund - EMBL Heidelberg, Germany

10.30 - 10.45 Coffee break
10.45 - 12.15

Lecture and Hands-on:
Downstream analysis:“Diversity matters, a place for a classification of uncultured microorganisms in Taxonomy"
Ramón Rosselló-Móra - IMEDEA, Spain

12.15 - 13.15

Lunch  

13.15 - 14.00

Lecture:
New methods and algorithms for analysing metagenomic datasets
Daniel Huson - Tübingen University, Germany

14.00 - 15.00

Hands-on:
MEGAN
Daniel Huson - Tübingen University, Germany

15.00 - 15.30

Coffee break

15.30 - 17.30

Hands-on:
Time to practice and for questions 

17.30 - 18.30

Wrap up and Conclusion

18.30

Dinner