Location & dates EMBL Heidelberg, Germany 26 Oct - 2 Nov 2020
Deadlines Application closed
organiser_EMBO_Course_2017

EMBL Courses and Conferences during the Coronavirus pandemic

With the onsite programme paused, many of our events are now being offered in virtual formats.


Registration is open as usual for many events, with back-up plans in place to move further courses and conferences online as necessary. Registration fees for any events affected by the COVID-19 disruption are fully refundable.


More information for participants of events at EMBL Heidelberg can be found here.

Programme

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Please note the below programme still subject to changes

Day 1 - Monday 26 October 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

Courtyard Room A & B

09:15 - 09:30

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

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

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

Courtyard Room A & B

09:45 - 10:45

Flash talks participants

Courtyard Room A & B

10:45 - 11:00

Coffee Break

Courtyard 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

Courtyard 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

Courtyard Room A & B

14:00 - 15:00

Group Activity

Courtyard Room A & B

15:00 - 16:00

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

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

Coffee break

Courtyard Room A & B

16:30 - 17:30

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

Courtyard Room A & B

17:30 - 19:30

Poster Session

Courtyard Room A & B

19:30 - 20:30

Dinner

ATC Rooftop Lounge

20:30

Bus to ISG Hotel

ATC Bus Stop

Day 2 - Tuesday 27 October 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 28 October 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 29 October 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 30 October 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 31 October 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 1 November 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 2 November 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