Location & dates EMBL Heidelberg, Germany 12 - 19 Jun 2019
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organiser_EMBO_Course_2017

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