Location & dates EMBL Heidelberg, Germany 23 - 30 Apr 2018
Deadlines Application closed
organiser_EMBO_Course_2017

Programme

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Day 1 - Monday 23 April 2018
TimeSpeakerLocation

09:00 - 09:15

Welcome and EMBL Overview 
Elisabeth Zielonka

ATC Courtyard Room A+B

09:15 - 09:30

Introduction to Training Lab and House notes
Yvonne Yeboah

ATC Courtyard Room A+B

09:30 - 10:00

Welcome and Introductions 
José Eduardo González Pastor

ATC Courtyard Room A+B

10:00 - 11:00

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

ATC Courtyard Room A+B

11:00 - 12:00

Lecture: Metagenomics library preparation for NGS 
Vladimir Benes

ATC Courtyard Room A+B

12:00 - 13:00

Lunch

EMBL Canteen

13:00 - 14:30

Short talk by participants

ATC Courtyard Room A+B

14:30 - 15:30

Lecture: Metagenomics: Concepts, historical milestones and next advance
José Eduardo González Pastor

ATC Courtyard Room A+B

15:30- 15:45

Coffee break

ATC Courtyard Room A+B
15:45 -16:45

Group activity: Basic concepts and background quiz
Elisabeth Zielonka

ATC Courtyard Room A+B

16:45 - 18:30

Poster session

Top of Helix A

18:30 - 19:30

Dinner

EMBL Canteen

Day 2 - Tuesday 24 April 2018
TimeSpeakerLocation
09:00 - 09:15

Quick overview of the day
José Eduardo González Pastor

ATC Courtyard Room A+B

09:15 - 10:30

Practical: Extraction of metagenomic DNA in groups [from samples brought by the students (environmental)] 
José Eduardo González Pastor, Arantxa Lopez

Training Lab B 

10:30 - 11:00

Coffee Break 

ATC Courtyard Room A+B

11:00 - 12:30

Practical: Extraction Results
José Eduardo González Pastor, Arantxa Lopez 

Training Lab B 

12:30 - 13:30

Lunch

EMBL Canteen
13:30 - 14:30

Practical: Extraction Results (cont.)
José Eduardo González Pastor, Arantxa Lopez 

Training Lab B 

14:30 - 15:45

Practical: Nanopore: 16S analysis/ Sample preparation and PCR set-up
Dinko Pavlinic, Bianka Baying

Training Lab B 

15:45 - 16:00

Coffee Break

ATC Courtyard Room A+B

16:00 - 17:30

Practical: Nanopore: 16S analysis/ DNA cleanup and Sequencing start
Dinko Pavlinic, Bianka Baying

Training Lab B 

17:30 - 18:30

All/Discussion Session

ATC Courtyard Room A+B

18:30 - 19:30

Dinner

EMBL Canteen

19:30 - 21:00

Poster Session  

Top of Helix A

Day 3 - Wednesday 25 April 2018
TimeSpeakerLocation
09:00 - 09:15

Quick overview of the day
José Eduardo González Pastor

ATC Courtyard Room A+B

09:15 - 10:30

Practical: Test digestion conditions for metagenomic DNA and preparation of agarose gels
José Eduardo González Pastor, Arantxa Lopez  

Training Lab B 

10:30 - 11:00

Coffee Break

ATC Courtyard Room A+B

11:00 - 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

EMBL Canteen

13:30 - 15:00

Purification from gel of the digested metagenomic DNA

Training Lab B 
15:00 - 15:30

Coffee break

ATC Courtyard Room A+B

15:30 - 19:00

Cloning of the metagenomic DNA + overnight ligation

Training Lab B 

19:00 - 20:30

Dinner

EMBL Canteen

Day 4 - Thursday 26 April 2018
TimeSpeakerLocation
09:00 - 09:15

Quick overview of the day
José Eduardo González Pastor

ATC Courtyard Room A+B

09:15 - 11:00

Practical: Transformation in E. coli of the library
José Eduardo González Pastor, Arantxa Lopez

Training Lab B 

11:00 - 12:00

Methodological lecture and discussion session:
Metagenomics experimental design: Common shortcoming and pitfalls
José Eduardo González Pastor

ATC Courtyard Room A+B

12:00 - 13:00

Lunch

EMBL Canteen

13:00 - 14:00

Lecture: Sequence data "Shotgun Sequencing, and Meta[gen|transcript]omics analysis
Giuseppe D'Auria

ATC Courtyard Room A+B

14:00 - 15:30

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

ATC Courtyard Room A+B

15:45

Free evening with tour of Heidelberg

 

Day 5 - Friday 27 April 2018
TimeSpeakerLocation
09:00 - 09:15

Quick overview of the day
Giuseppe D'Auria

Computer Training Lab

09:15 - 10:00

Practical: Analysis of some colonies from the metagenomic libraries -Interpretation of results 
José Eduardo González Pastor, Arantxa Lopez 

Training Lab B

10:00 - 10:30

Coffee break  

Computer Training Lab

10:30 - 12:30

Lecture and Hands-on/Introduction to Linux
Giuseppe D'Auria

Computer Training Lab 

12:30 - 13:30

Lunch

EMBL Canteen

13:30 - 14:30

Lecture: Some theory on taxonomy, phylogeny and diversity measures based on 16S rRNA gene amplicons and direct metagenomic
Kostas Konstantinidis

Computer Training Lab 

14:30 - 15:30

Lecture and Hands-on: Binning in Metagenomics
Kostas Konstantinidis 

Computer Training Lab

15:30 - 16:00

Coffee break

Computer Training Lab

16:00 - 17:00

Lecture and Hands-on: Binning in Metagenomics (cont.)
Kostas Konstantinidis

Computer Training Lab

16:00 - 18:30

Hands-on: Metagenomics in silico: what can I do
Giuseppe D'Auria

Computer Training Lab

18:30

Bus to ISG Hotel

19:00 - 20:00

Dinner & drinks/ BBQ (weather permitting)

ISG Restaurant

Day 6 - Saturday 28 April 2018
TimeSpeakerLocation
09:00 - 09:15

Quick overview of the day
Kostas Konstantinidis

Computer Training Lab

09:15 - 11:00

Lecture: Diversity matters, a place for a classification of uncultured microorganisms in Taxonomy
Kostas Konstantinidis

Computer Training Lab

11:00 - 11:15

Coffee break

Computer Training Lab

11:15 - 12:15

Hands-on: Introduction into the processing of raw data
Giuseppe D'Auria

Computer Training Lab

12:15 - 13:15

Lunch 

EMBL Canteen

13:15 - 14:15

Lecture and Hands-on: Upstream analysis: data organisation and standards in metagenomics
Giuseppe D'Auria

Computer Training Lab
14:15 - 16:15

Lecture and Hands-on: Metagenomic assembly,ORF finding, functional annotation
Giuseppe D'Auria

Computer Training Lab

16:15 - 16:45

Coffee break

Computer Training Lab 

16:45 - 18:00

MiniIon

Computer Training Lab 
18:00 - 19:00

Group activity/ Wrap up of the day- quiz activity covering the topics taught during the previous two days (Bioinformatics)

Computer Training Lab
19:00 - 20:30

Dinner

EMBL Canteen
Day 7 - Sunday 29 April 2018
TimeSpeakerLocation
09:00 - 09:15

Quick overview of the day
Kristian Vlahovicek

Computer Training Lab

09:15 - 11:15

Hands-on: Introduction to R for Bioinformatics
Giuseppe D'Auria

Computer Training Lab

11:15 - 11:30

Coffee break

Computer Training Lab

11:30 - 13:00

Lecture and Hands-on: Functional and taxonomic analysis with EBI Metagenomics
Alex Mitchell

Computer Training Lab 

13:00 - 14:00

Lunch

EMBL Canteen

14:00 - 17:00

Lecture and Hands-on: Functional and taxonomic analysis with EBI Metagenomics
Alex Mitchell

Computer Training Lab  

17:00 - 18:00

Lecture: Analysis Tools Overview: INCA, MILC and MELP
Kristian Vlahovicek

Computer Training Lab 

18:00 - 18:30

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

Computer Training Lab
19:00 

Course Dinner

Downtown Restaurant
Day 8 - Monday 30 April 2018
TimeSpeakerLocation
09:00 - 09:15

Quick overview of the day
José Eduardo González Pastor

Computer Training Lab

09:15 - 10:30

Hands-on: INCA
Kristian Vlahovicek

Computer Training Lab

10:00 - 10:45

Coffee Break  

Computer Training Lab

10:45 - 12:15

Hands-on/MEGAN
Daniel Huson

Computer Training Lab

12:15 - 13:15

Lunch

EMBL Canteen
13:15 - 14:00

Hands-on/MEGAN
Daniel Huson

Computer Training Lab

14:00 - 15:00

GeneCore Tour
Jan Provaznik

GeneCore

15:00 - 15:30

Coffee break

Computer Training Lab

15:30 - 17:30

Hands-on/Time to practice and Q&A

Computer Training Lab
17:30 - 18:30

Wrap-up and conclusions

Computer Training Lab
18:30 - 20:30

Course Dinner

EMBL Canteen