Location & dates EMBL Heidelberg, Germany 20 - 27 Apr 2020
Deadlines Application closed
organiser_EMBO_Course_2017

Programme

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Please note the below programme still subject to changes

Day 1 - Monday 20 April 2020
TimeSpeakerLocation
08:45 - 09:00

Bus from ISG Hotel to EMBL ATC entrance

ISG Hotel Bus Stop

09:00 - 09:15

Welcome and EMBL Overview
Elisabeth Zielonka - EMBL Heidelberg, Germany

Coutryard Room A & B

09:15 - 09:30

Introduction to Training Lab and House notes
Yvonne Yeboah - EMBL Heidelberg, Germany

Coutryard Room A & B
09:30 - 09:45

Welcome and Introductions
José Eduardo González Pastor - Center of Astrobiology (CSIC/INTA), Spain

Coutryard Room A & B

09:45 - 10:45

Flash talks participants

Coutryard Room A & B

10:45 - 11:00

Coffee Break

Coutryard Room A & B

11:00 - 12:00

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

Coutryard Room A & B

12:00 - 13:00

Lunch break

EMBL Canteen

13:00 - 14:00

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

Coutryard Room A & B

14:00 - 15:00

Group Activity

Coutryard Room A & B

15:00 - 16:00

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

Coutryard Room A & B
16:00 - 16:30

Coffee break

Coutryard Room A & B

16:30 - 17:30

Lecture: What bring metagenomic approach in cardiometabolic and nutrition-related disorders?
Karine Clement - ICAN INSERM, France

Coutryard Room A & B

17:30 - 19:30

Poster Session

Coutryard Room A & B

19:30 - 20:30

Dinner

ATC Rooftop Lounge

20:30

Bus to ISG Hotel

ATC Bus Stop

Day 2 - Tuesday 21 April 2020
TimeSpeakerLocation
08:45 - 09:00

Bus from ISG Hotel to EMBL ATC entrance

ISG Hotel Bus Stop

09:00 - 09:15

Quick overview of the day
José Eduardo González Pastor - Center of Astrobiology (CSIC/INTA), Spain

Courtyard Room  A+B

09:15 - 10:30

Practical: Extraction of metagenomic DNA in groups from soil samples
José Eduardo González Pastor - Center of Astrobiology (CSIC/INTA), Spain   
Arantxa Lopez - FISABIO, Spain

Training Lab A+B

10:30 - 11:00

Coffee Break   
Firstname lastname - Institute, Country

Courtyard Room  A+B
11:00 - 12:30

Practical: Quality control of DNA samples and Nanopore 16s PCR set up
Rajna Hercog - EMBL Heidelberg, Germany
Ferris Jung - EMBL Heidelberg, Germany

Training Lab A+B

12:30 - 13:30

Lunch break

EMBL Canteen

13:30 - 14:30

Practical: Discussion of Extraction Results
José Eduardo González Pastor - Center of Astrobiology (CSIC/INTA), Spain   
Arantxa Lopez - FISABIO, Spain

Training Lab A+B

14:30 - 15:30

Lecture: Metagenomics and other culture-independent tools to study virus communities
Josefa Antón Botella - University of Alicante, Spain

Courtyard Room  A+B

15:30 - 16:45

Practical: Nanopore: 16S PCR cleanup, finishing library preparation and starting sequencing run, followed by Genomics Core Facility Tour
Rajna Hercog - EMBL Heidelberg, Germany    
Ferris Jung - EMBL Heidelberg, Germany

Training Lab A+B | Gene Core Facility

Flexible Coffee Break

Courtyard Room  A+B

17:00 - 19:00

Practical: Nanopore: 16S analysis/ DNA cleanup and Sequencing start
Rajna Hercog - EMBL Heidelberg, Germany   
Ferris Jung - EMBL Heidelberg, Germany

Training Lab A+B

19:00 Dinner EMBL Canteen
19:00 Bus to ISG Hotel ATC Bus Stop
Day 3 - Wednesday 22 April 2020
TimeSpeakerLocation
08:45 - 09:00

Bus from ISG Hotel to EMBL ATC entrance

ISG Hotel Bus Stop

09:00 - 09:15

Quick overview of the day
José Eduardo González Pastor - Center of Astrobiology (CSIC/INTA), Spain

Courtyard Room  A+B

09:15 - 09:45 Practical: Test digestion conditions for metagenomic DNA and preparation of agarose gels
José Eduardo González Pastor - Center of Astrobiology (CSIC/INTA), Spain
Arantxa Lopez - FISABIO, Spain

Training Lab A+B

09:45 - 11:00

Practical introduction: Single cells genomics   
Tobias Wenzel - EMBL Heidelberg, Germany

Courtyard Room  A+B

11:00 - 11:15

Coffee Break

Courtyard Room  A+B

11:15 - 12:30

Practical: Digestion of metagenomic DNA for cloning in the libraries
José Eduardo González Pastor - Center of Astrobiology (CSIC/INTA), Spain    
Arantxa Lopez - FISABIO, Spain   

Training Lab A+B

12:30 - 13:30 Lunch break

EMBL Canteen

13:30 - 14:30

Practical: Purification from gel of the digested metagenomic DNA
José Eduardo González Pastor - Center of Astrobiology (CSIC/INTA), Spain    
Arantxa Lopez - FISABIO, Spain  

Training Lab A+B

Flexible Coffee break

Courtyard Room  A+B

15:00 - 17:00

Practical: Cloning of the metagenomic DNA + overnight ligatio
José Eduardo González Pastor - Center of Astrobiology (CSIC/INTA), Spain    
Arantxa Lopez - FISABIO, Spain

Training Lab A+B

17:00 - 19:30

Practical (single cell microbial genomics): Droplet generation for single cell genomics and PCR set-up
Tobias Wenzel - EMBL Heidelberg, Germany

Computer Training Lab

19:30 - 20:30

Dinner

 ISG Hotel

20:30

Bus to ISG Hotel

ATC Bus Stop

Day 4 - Thursday 23 April 2020
TimeSpeakerLocation
08:45 - 09:00

Bus from ISG Hotel to EMBL ATC entrance

ISG Hotel Bus Stop

09:00 - 09:15

Quick overview of the day
José Eduardo González Pastor - Center of Astrobiology (CSIC/INTA), Spain

Courtyard Room  A+B

09:15 - 11:00

Practical: Transformation in E. coli of the library
José Eduardo González Pastor - Center of Astrobiology (CSIC/INTA), Spain
Arantxa Lopez - FISABIO, Spain

Training Lab A+B

11:00 - 12:00

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

Courtyard Room  A+B

12:00 - 13:00

Lunch break

EMBL Canteen

13:00 - 14:00

Lecture: Hands-on/Introduction to Linux I
Giuseppe D'Auria - FISABIO Sequencing and Bioinformatics Service, Spain

Courtyard Room  A+B

14:00 -14:30 Coffee break

Courtyard Room  A+B

14:30 - 17:00

Hands-on/Introduction to Linux II
Giuseppe D'Auria - FISABIO Sequencing and Bioinformatics Service, Spain

Computer Training Lab

17:00

Free evening with tour of Heidelberg

17:00 - 17:30

Bus to ISG Hotel

ATC Bus Stop
17:30 - 18:00

Bus to Bismarkplatz

ISG Hotel bus stop

Day 5 - Friday 24 April 2020
TimeSpeakerLocation
08:45 - 09:00

Bus from ISG Hotel to EMBL ATC entrance

ISG Hotel Bus Stop

09:00 - 09:15 Quick overview of the day
Giuseppe D'Auria - FISABIO Sequencing and Bioinformatics Service, Spain

Computer Training Lab

09:15 - 10:00

Practical: Analysis of some colonies from the metagenomic libraries -Interpretation of results
José Eduardo González Pastor - Center of Astrobiology (CSIC/INTA), Spain
Arantxa Lopez - FISABIO, Spain

Training Lab A+B

10:00 - 10:30

Coffee break

Computer Training Lab

10:30 - 12:30 Lecture: Diversity matters, a place for a classification of uncultured microorganisms in Taxonomy
Kostas Konstantinidis - Georgia Institute of Technology, USA

Computer Training Lab

12:30 - 13:30

Lunch

EMBL Canteen

13:30 - 15:30

Lecture and Hands-on: the MiGA web-server: the genome-equivalent of RDP/Silva SSU web-servers
Kostas Konstantinidis - Georgia Institute of Technology, USA

Computer Training Lab

15:30 - 18:30

Practical (single cell microbial genomics): Visualization of droplets and single cell analysis
Tobias Wenzel (EMBL Heidelberg)

Flexible Coffee break

Computer Training Lab

18:30 - 19:30

Lecture and Hands-on: Tools for specialized analyses of metagenomes
Kostas Konstantinidis - Georgia Institute of Technology, USA

Computer Training Lab

18:15 - 18:30

Bus to ISG Hotel

ATC Bus Stop

18:45

Dinner & drinks/ BBQ

ISG Hotel
Day 6 - Saturday 25 April 2020
TimeSpeakerLocation
08:45 - 09:00

Bus from ISG Hotel to EMBL ATC entrance

ISG Hotel Bus Stop

09:00 - 09:15

Quick overview of the day
Giuseppe D'Auria - FISABIO, Spain

Computer Training Lab

09:15 - 11:00

Lecture: Some theory on taxonomy, phylogeny and diversity measures based on 16S rRNA gene amplicons and direct metagenomic
Bartoemu Viver Pizà  - IMEDEA, Spain

Computer Training Lab

11:00 - 11:15 Coffee break

Computer Training Lab

11:15 – 12:15

Lecture: Practical session 16S rRNA gene amplicons and direct metagenomic
Bartoemu Viver Pizà - IMEDEA, Spain

Computer Training Lab

12:15 - 13:15

Lunch break

EMBL Canteen

13:15 – 14:15

Hands-on: Practical session 16S rRNA gene amplicons and direct metagenomic
Bartoemu Viver Pizà - IMEDEA, Spain

Computer Training Lab
14:15 – 15:00

Hands-on: Introduction to 16S rDNA profiling using QIIME2
Giuseppe D'Auria - FISABIO, Spain

Computer Training Lab

15:00 - 15:30

Coffee break

Computer Training Lab

15:30 - 18:15

Hands-on: Introduction to 16S rDNA profiling using QIIME2
Giuseppe D'Auria - FISABIO, Spain

Computer Training Lab

18:15 - 19:15

Dinner

Computer Training Lab

19:15 - 21:15

Poster Session

21:15

Bus to ISG Hotel

ATC Bus Stop
Day 7 - Sunday 26 April 2020
TimeSpeakerLocation
08:45 - 09:00

Bus from ISG Hotel to EMBL ATC entrance

ISG Hotel Bus Stop

09:00 - 09:15

Quick overview of the day
Kristian Vlahovicek - University of Zagreb, Croatia

Computer Training Lab

09:15 – 11:15

Lecture and Hands-on: Upstream analysis: data organisation and standards in metagenomics and Metagenomic assembly, ORF finding, functional annotation
Giuseppe D'Auria - FISABIO Sequencing and Bioinformatics Service, Spain

Computer Training Lab

11:15 - 11:30

Coffee break

Computer Training Lab

11:30 - 13:00 Practical: MiniIon data anaysis: QC and Taxonomy profiling   
Jan Provaznik - EMBL Heidelberg, Germany

Computer Training Lab

13:00 - 14:00

Lunch break

Computer Training Lab

14:00 – 15:00

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

Computer Training Lab
15:00 - 15:30

Coffee break

Computer Training Lab

15:30 - 17:30

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

Microscopy room and Computer Training Lab

17:30 -18:30

Presentation preparation

Computer Training Lab

19:00 - 20:00 Dinner

20:00

Bus to ISG Hotel

ATC Bus Stop

Day 8 - Monday 27 April 2020
TimeSpeakerLocation
08:45 - 09:00

Bus from ISG Hotel to EMBL ATC entrance

ISG Hotel Bus Stop

09:00 - 09:15

Quick overview of the day
José Eduardo González Pastor - Center of Astrobiology (CSIC/INTA), Spain

Computer Training Lab

09:15 - 10:30

Lecture and Hands-on: Functional and taxonomic analysis
Georg Zeller - EMBL Heidelberg Germany

Computer Training Lab

10:30- 10:45 Coffee break

Computer Training Lab

10:45 - 12:00 Practical: Hands-on/MEGAN
Daniel Huson - University of Tübingen, Germany

Computer Training Lab

12:00 - 13:00

Lunch break

EMBL Canteen

13:00 - 14:00

Practical: Hands-on/MEGAN
Daniel Huson - University of Tübingen, Germany

Computer Training Lab
14:00 - 16:30

Group activity and Presentations

Computer Training Lab

16:30 - 16:45

Coffee break

Computer Training Lab

16:45 - 17:45

Wrap-up and conclusions

Computer Training Lab

17:45 - 18:15

Bus to ISG Hotel

ATC Bus Stop

18:15 - 18:45

Bus to Neckarmünzplatz

ISG Hotel Bus Stop

19:00

Dinner Downtown