Location & dates EMBL Heidelberg, Germany 23 - 30 Apr 2018
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organiser_EMBO_Course_2017
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Programme

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Day 1 - Monday 23 April 2018
TimeSpeakerLocation

09:00 - 10:00

Welcome & Introductions
José Eduardo González Pastor

 

10:00 - 11:00

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

 

11:00 - 12:00

Lecture: Metagenomics library preparation for NGS 
Vladimir Benes

 

12:00 - 13:00

Lunch

EMBL Canteen

13:00 - 14:30

Short talk by participants

 

14:30 - 15:30

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

 

15:30- 15:45

Coffee break

15:45 -16:45

Group activity: Basic concepts and background quiz
Arantxa Lopez

16:45 - 18:00

Lecture & Discussion Session: Extractions in Metagenomics
José Eduardo González Pastor

18:00 - 19:15

Dinner

EMBL Canteen

19:15

Poster session

 

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

Quick overview of the day
José Eduardo González Pastor

 

09:15 - 10:30

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

 

10:30 - 11:00

Coffee Break 

 

11:00 - 12:30

Practical: Extraction Results
José Eduardo González Pastor, Arantxa Lopez 

 

12:30 - 13:30

Lunch

EMBL Canteen
13:30 - 14:30

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

14:30 - 15:45

Practical: Nanopore: 16S analysis/ Sample preparation and PCR set-up
Vladimir Benes

15:45 - 16:00

Coffee Break

 

16:00 - 17:30

Practical: Nanopore: 16S analysis/ DNA cleanup and Sequencing start
Vladimir Benes

 

17:30 - 18:30

All/Discussion Session

 

18:30 - 19:30

Dinner

EMBL Canteen

19:30

Poster Session  

 

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

Quick overview of the day
Arantxa Lopez

 

09:15 - 10:30

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

 

10:30 - 11:00

Coffee Break

 

11:00 - 12:30

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

 

12:30 - 13:30

Lunch

 EMBL Canteen

13:30 - 15:00

Purification from gel of the digested metagenomic DNA

15:00 - 15:30

Coffee break

15:30 - 19:00

Cloning of the metagenomic DNA + overnight ligation

19:00

Dinner

 EMBL Canteen

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

Quick overview of the day
José Eduardo González Pastor

 

09:15 - 11:00

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

 

11:00 - 12:00

Lecture: Some theory on taxonomy, phylogeny and diversity measures based on 16S rRNA gene amplicons and direct metagenomic
Ramon Rossello-Mora

 

12:00 - 13:00

Lunch

 EMBL Canteen

13:00 - 14:00

Methodological lecture and discussion session:
Metagenomics experimental design: Common shortcoming and pitfalls

José Eduardo González Pastor

 

14:00 - 15:00

Lecture: Metagenomics in silico: what can I do
Giuseppe D'Auria

15:00 - 16:30

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

16:30

Free dinner with tour of Heidelberg

 

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

Quick overview of the day

 

09:15 - 10:00

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

 

10:00 - 10:30

Coffee break  

 

10:30 - 12:30

Lecture and Hands-on/Introduction to Linux
David Pérez-Villarroya

 

12:30 - 13:30

Lunch 

 EMBL Canteen

13:30 - 15:30

Lecture and Hands-on/Introduction to Linux
David Pérez-Villarroya

15:30 - 16:00

Coffee break

16:00 - 18:30

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

18:30 - 20:00

Dinner

 EMBL Canteen

20:00

Panel discussion & drinks at the ISG hotel

 

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

Quick overview of the day
Kostas Konstantinidis

 

09:15 - 11:00

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

 

11:00 - 11:15

Coffee break

 

11:15 - 12:15

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

 

12:15 - 13:15

Lunch 

 EMBL Canteen

13:15 - 14:15

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

14:15 - 16:15

Free Slot MiniIon

16:15 - 16:45

Coffee break

 

16:45 - 18:00

Lecture: Diversity matters, a place for a classification of uncultured microorganisms in Taxonomy
Ramon Rossello-Mora

18:00 - 19:00

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

19:00

Dinner

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

Quick overview of the day
Kristian Vlahovicek

 

09:15 - 11:15

Lecture and Hands-on: Functional analysis,InterProScan
Lorna Richardson

 

11:15 - 11:30

Coffee break

 

11:30 - 13:00

Lunch break

 EMBL Canteen

13:00 - 14:00

Lecture and Hands-on: Databases
Hurbert Denise

 

14:00 - 16:00

Group activity with presentations and coffee:
Design of Metagenomics experiments and workflow
Jose Eduardo Pastor

16:00 - 17:00

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

17:00 - 18:00

Hands-on: INCA
Kristian Vlahovicek

 

18:00 - 18:30

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

18:30

Dinner

EMBL Canteen
Day 8 - Monday 30 April 2018
TimeSpeakerLocation
09:00 - 09:15

Quick overview of the day
Giuseppe D'Auria

 

09:15 - 10:30

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

 

10:00 - 10:45

Coffee Break  

 

10:45 - 12:15

Lecture and Hands-on: Binning in Metagenomics
Kostas Konstantinidis 

 

12:15 - 13:15

Lunch

EMBL Canteen
13:15 - 14:00

Hands -on: Introduction to R for Bioinformatics (cont.)
Giuseppe D'Auria


 

14:00 - 15:00

Hands-on/MEGAN
Daniel Huson

15:00 - 15:30

Coffee break

 

15:30 - 17:30

Hands-on/Time to practice and for questions

17:30 - 18:30

Wrap-up and conclusions

18:30

Drinks and Course Dinner