Location & dates EMBL Heidelberg, Germany 12 - 19 Jun 2019
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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Day 1 - Wednesday 12 June 2019
TimeSpeakerLocation
09:00 - 09:15

Welcome and EMBL Overview
Elisabeth Zielonka

Courtyard Room A+B

09:15 - 09:30 Introduction to Training Lab and House notes
Yvonne Yeboah

Courtyard Room A+B

09:30 - 10:00 Welcome and Introductions
José Eduardo González Pastor - Center of Astrobiology (CSIC/INTA), Spain

Courtyard Room A+B

10:00 - 11:00 Lecture: Metagenomics: Concepts, historical milestones and next advance
José Eduardo González Pastor - Center of Astrobiology (CSIC/INTA), Spain

Courtyard Room A+B

11:00 - 12:00

Lecture: Metagenomics library preparation for NGS
Vladimir Benes

Courtyard Room A+B

12:00 - 13:00

Lunch break

EMBL Canteen

13:00 - 14:30

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

Courtyard Room A+B

14:30 - 15:15 Group activity
Elisabeth Zielonka - EMBL Heidelberg, Germany

Courtyard Room A+B

15:15 - 16:45

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

Courtyard Room A+B

16:45 - 18:00

Flash talks participants

Courtyard Room A+B

18:00 - 19:00 Dinner

ATC Foyer

19:00 - 20:30

Poster session

ATC Foyer
20:30

Bus back to Holiday Inn Hotel

Day 2 - Thursday 13 June 2019
TimeSpeakerLocation
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 B

10:30 - 11:00

Coffee Break

Courtyard Room A+B

11:00 - 12:30

Practical: Quality control of DNA samples and Nanopore 16s PCR set up
José Eduardo González Pastor - Center of Astrobiology (CSIC/INTA), Spain
Arantxa Lopez - FISABIO, Spain

Training Lab 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 B

14:30 - 16:45 Practical: Nanopore: 16S PCR cleanup, finishing library preparation and starting  sequencing run, followed by Genomics Core Facility Tour
Dinko Pavlinic - EMBL Heidelberg, Germany
Bianka Baying - EMBL Heidelberg, Germany
Laura Villacorta - EMBL Heidelberg, Germany

Training Lab B

16:45 - 17:00

Coffee Break

Courtyard Room A+B

17:00 - 18:30

Practical: Nanopore: 16S analysis/ DNA cleanup and Sequencing start
Dinko Pavlinic - EMBL Heidelberg, Germany
Bianka Baying - EMBL Heidelberg, Germany
Laura Villacorta - EMBL Heidelberg, Germany

Training Lab B

18:30 - 19:30

Dinner

EMBL Canteen

19:30

Bus back to Holiday Inn Hotel

Day 3 - Friday 14 June 2018
TimeSpeakerLocation
09:00 - 09:25 Lecture: Single cells genomics
Christoph Merten - EMBL Heidelberg, Germany

Courtyard Room A+B

09:25 - 10:30

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

Courtyard Room A+B

10:30 - 11:00

Nanopore sequencing results
Jan Provaznik - EMBL Heidelberg, Germany

Courtyard Room A+B

11:00 - 11:30 Coffee Break

Courtyard Room A+B

11:30 - 12:30

Digestion of metagenomic DNA for cloning in the libraries (once that digestion conditions are determined)

Training Lab B

12:30 - 13:30 Lunch break

EMBL Canteen

13:30 - 15:00

Purification from gel of the digested metagenomic DNA

Training Lab B

15:00 - 15:30 Coffee break

Courtyard Room A+B

15:30 - 18:00

Cloning of the metagenomic DNA + overnight ligation

Training Lab B

18:00 - 19:00

Hands-on/Introduction to Linux I
Giuseppe D'Auria - Chair FISABIO-University of València, Spain, Spain

Computer Training Lab

19:00 - 20:00

Dinner

EMBL Canteen

20:00

Bus back to Holiday Inn Hotel

Day 4 - Saturday 15 June 2019
TimeSpeakerLocation
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 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: Sequence data "Shotgun Sequencing, and Meta[gen|transcript]omics analysis
Giuseppe D'Auria - Chair FISABIO-University of València, Spain, Spain

Computer Training Lab

14:00 -14:30

Coffee break

Computer Training Lab

14:30 - 16:30

Hands-on/Introduction to Linux II
Giuseppe D'Auria - Chair FISABIO-University of València, Spain, Spain

Computer Training Lab

16:30 Bus to Neckarmünzplatz

16:50

Free evening with tour of Heidelberg

Day 5 - Sunday 16 June 2019
TimeSpeakerLocation
09:00 - 09:15 Quick overview of the day
Giuseppe D'Auria - FISABIO, 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 B

10:00 - 10:30

Coffee break

Computer Training Lab

10:30 - 11:30

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

Computer Training Lab

11:30 - 12:30

Lecture: Theory on taxonomy, phylogeny and diversity measures based on 16S rRNA gene amplicons and metagenomes
Kostas Konstantinidis - Georgia Institute of Technology, USA

Computer Training Lab

12:30 - 13:30

Lunch

EMBL Canteen

13:30 – 15:30

Lecture: 16S rRNA gene analysis from amplicons and metagenomes
Kostas Konstantinidis - Georgia Institute of Technology, USA

Computer Training Lab
15:30 - 16:00

Coffee break

Computer Training Lab

16:00 – 18:30

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

Computer Training Lab
18:30 - 20:30 Dinner & drinks/ BBQ

20:30 Bus back to Holiday Inn Hotel
Day 6 - Monday 17 June 2019
TimeSpeakerLocation
09:00 - 09:15 Quick overview of the day
Kostas Konstantinidis - Georgia Institute of Technology, USA

Computer Training Lab

09:15 - 11:00

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

Computer Training Lab

11:00 - 11:15

Coffee break

Computer Training Lab

11:15 – 12:15

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

12:15 - 13:15

Lunch break

EMBL Canteen

13:15 – 14:15 Lecture and Hands-on: Tools for specialized analyses of metagenomes
Kostas Konstantinidis - Georgia Institute of Technology, USA

Computer Training Lab

14:15 – 16:15

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

Computer Training Lab

16:15 - 16:45 Coffee break

Computer Training Lab

16:45 - 18:00

MiniIon data anaysis: QC and Taxonomy profiling
Jan Provaznik - EMBL Heidelberg, Germany

Computer Training Lab and Gene Core Facility

18:00 - 19:00

Dinner

ATC Foyer

19:00 - 20:30

Poster Session

ATC Foyer

20:30

Bus back to Holiday Inn Hotel

Day 7 - Tuesday 18 June 2019
TimeSpeakerLocation
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: Metagenomic assembly, ORF finding, functional annotation
Giuseppe D'Auria - Chair FISABIO-University of València, Spain, Spain

Computer Training Lab

11:15 - 11:30 Coffee break

Computer Training Lab

11:30 - 13:00

Lecture and Hands-on: Lecture and Hands-on: Functional and taxonomic analysis with MGnify
Alex Mitchell - EMBL-EBI, UK

Computer Training Lab

13:00 - 14:00 Lunch break

EMBL Canteen

14:00 - 17:00

Lecture and Hands-on: Lecture and Hands-on: Functional and taxonomic analysis with MGnify
Alex Mitchell - EMBL-EBI, UK

Computer Training Lab

17:00 - 18:00

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

Computer Training Lab

18:00 - 18:30

Group activity/ Wrap-up of the day + Q&A

Computer Training Lab

18:30 Bus to Flammkuchenhof
19:00

Dinner at Flammkuchenhof

Day 8 - Wednesday 19 June 2019
TimeSpeakerLocation
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

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

Computer Training Lab

10:30- 10:45

Coffee Break  

Computer Training Lab

10:45 - 12:00

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

Computer Training Lab

12:00 - 13:00 Lunch break

EMBL Canteen

13:00 - 14:00 Hands-on/MEGAN
Daniel Huson - University of Tübingen, Germany
Computer Training Lab
14:00 - 15:00

Lecture: MiniIon 16S analysis
Jan Provaznik - EMBL Heidelberg, Germany

Computer Training Lab

15:00 - 16:30 Group activity

Computer Training Lab

16:30 - 16:45 Coffee break

Computer Training Lab

16:45 - 17:45

Hands-on/Time to practice and Q&A

Computer Training Lab

17:45 - 18:45

Wrap-up and conclusions

Computer Training Lab

18:45

Bus to Neckarmünzplatz

19:00

Dinner Downtown