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Microbial Metagenomics: A 360º Approach – Course and Conference Office

EMBO PRACTICAL COURSE

Microbial Metagenomics: A 360º Approach

Overview

EMBL is committed to sharing research advances and sustaining scientific interaction throughout the coronavirus pandemic. We are delighted to announce that the course is going virtual and invite you to join us online.

Course Overview

The course focuses on the highly interdisciplinary topic of metagenomics. During the course, participants will receive an overview of state-of-the-art genomic technologies and bioinformatic tools. A balanced approach of lectures and practical sessions will provide a general background and the latest advancements in the field as well as its relationship with other disciplines.

The course will start with training the participants about experimental design and the preparation of their own metagenomic libraries with soil or their (environmental) samples. The metagenomic DNA will be sequenced onsite using third generation sequencing technologies and subsequent data analysis. Thus, the students have a unique opportunity to work on the complete workflow from sample preparation to data analysis. This updated course version will also address cutting-edge single-cell microbial genomics during practical. Bioinformatics analysis is a key part of the course, where students will learn how to process data from raw sequences to the application of algorithms for analysing metagenomic datasets. Trainers will provide short lectures with follow-up hands-on exercises in order to have the participants learning and assessing their knowledge.

Audience

This course is aimed at advanced PhD students and post-doctoral researchers who are doing or planning to start research in the field of metagenomics.

Modules/Resources

  • Experimental design
  • Extraction of metagenomic DNA
  • Construction of metagenomic libraries
  • Single cell microbial genomics
  • 3rd generation sequencing (Nanopore)
  • Bioinformatic analysis of metagenomic data: data standards and submission, processing of raw data, assembly, functional annotation, overview of databases, retrieval and analysis tools.

Learning Outcomes

  • Construct your own metagenomic library
  • Analyse and organise your data
  • Interpret results, explore different databases, use different retrieval and analysis tools
  • Sequence analysis

Speakers and Trainers

Daniel Huson

Tübingen University,

Germany

Tobias Wenzel

Institute for Biological and Medical Engineering

Chile

Scientific Organisers

Course Organiser

Maria Mercedes Bacadare Goitia

EMBL Heidelberg

Germany

Nathalie Sneider

EMBL Heidelberg

Germany

Programme

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The course will start on Monday 29 March, with an onboarding session and access to the pre-recorded lectures. It will continue on Monday 12 April with the regular programme.

The course will include interactive discussion sessions, online practicals, hands on exercises and networking.

Information on the live stream and access to the course platform will be provided shortly before the start of the event.

Access to the recorded talks will be available for 1 week after the start of the event.

Participants will be required to view the pre-recorded talks prior to the main start of the course on Monday 12 April. Full-time attendance is required for the course duration.

All times in the programme below are shown as the time in Europe (Berlin, Amsterdam Paris).

To find out the equivalent time zone in your location, enter Berlin, the programme date and time along with your city into the Time Zone Converter.

Day 0 – Monday 29 March 2021
Time (Europe/Berlin)Session
14:00 – 16:30 Onboarding
Day 1 – Monday 12 April 2021
Time (Europe/Berlin)Speaker
12:45 – 13:00Overview of the day
13:00 – 13:15Welcome and house notes and course overview
13:15 – 14:30Icebreaker activity
14:30 – 14:45Break
14:45 – 15:30Discussion Session based on pre-recorded talks
Moderator: José Eduardo González Pastor – Center of Astrobiology (CSIC/INTA), Spain
Karine Clement – Sorbonne University /INSERM, France
José Eduardo González Pastor – Center of Astrobiology (CSIC/INTA), Spain
Gabrielle Potocki-Veronese – INRA-LISBP, France
15:30 – 16:00Break
16:00 – 17:00Students Presentations 
17:00 – 18:00Optional social networking session
18:00End of Day 1 – Continued access to networking and discussion platform, pre-recorded lectures and course materials on eCampus
Day 2 – Tuesday 13 April 2021
Time (Europe/Berlin)Speaker
12:45 – 13:00 Quick overview of the day
13:00 – 13:45Practical session: Sample collection and metagenomic DNA isolation
José Eduardo González Pastor – Center of Astrobiology (CSIC/INTA), Spain   
Arantxa Lopez – FISABIO, Spain
13:45 – 14:00Break
14:00 – 14:45 Practical session: How to construct and perform functional screening of metagenomic libraries
– potential pitfalls and critical steps (I)

José Eduardo González Pastor – Center of Astrobiology (CSIC/INTA), Spain   
Arantxa Lopez – FISABIO, Spain
14:45 – 15:15Networking break 
15:15 – 16:00 Practical session: How to construct and perform functional screening of metagenomic libraries
– potential pitfalls and critical steps (II)

José Eduardo González Pastor – Center of Astrobiology (CSIC/INTA), Spain   
Arantxa Lopez – FISABIO, Spain
16:00 – 16:15 Break
16:15 – 17:15 Students Presentations
17:20End of Day 2 – Continued access to networking and discussion platform, pre-recorded lectures and course materials on eCampus

Day 3 – Wednesday 14 April 2021
Time (Europe/Berlin)Speaker
12:45 – 13:00 Quick overview of the day
13:00 – 13:30Tips and Tricks Metagenomics library preparation with Nanopore 
Jan Provaznik – EBML Heidelberg, Germany
Nayara Trevisan Doimo de Azevedo – EBML Heidelberg, Germany
Laura Villacorta, – EBML Heidelberg, Germany
13:30 – 14:15Live Lab Practical: Loading of Flowcell and start of sequencing run
José Eduardo González Pastor – Center of Astrobiology (CSIC/INTA), Spain 
Jan Provaznik – EBML Heidelberg, Germany
14:15 – 14:45Break
14:45 – 15:15Computational Practical session: 16S analysis of environmental  samples using Nanopore sequencing technology
José Eduardo González Pastor – Center of Astrobiology (CSIC/INTA), Spain  
Jan Provaznik – EBML Heidelberg, Germnay
15:15 – 16:00Practical Session
Kostas Konstantinidis – Georgia Institute of Technology, USA   
16:00 – 16:15Break
16:15 – 16:40 Practical session: Single cell microbial genomics with microfluidics
Tobias Wenzel – Institute for Biological and Medical Engineering, Chile
16:40 – 17:20Scientific discussion: Single cell microbial genomics
Tobias Wenzel – Institute for Biological and Medical Engineering, Chile
17:20 – 18:20 Networking time (Pub quiz)
17:20End of Day 3 – Continued access to networking and discussion platform, pre-recorded lectures and course materials on eCampus
Day 4 – Thursday 15 April 2021
Time (Europe/Berlin)Speaker
12:45 – 13:00Overview of the day
13:00 – 13:45Discussion Session based on pre-recorded talks
Moderator:
Giuseppe D’Auria – FISABIO, Spain
Josefa Antón Botella – University of Alicante, Spain
Giuseppe D’Auria – FISABIO, Spain
Kostas Konstantinidis – Georgia Institute of Technology, USA    
Georg Zeller – EMBL Heidelberg Germany
13:45 – 14:45Data analysis Practical session: Approaching Linux
Giuseppe D’Auria – FISABIO, SpainMariana Reyes Prieto – FISABIO, Spain
14:45 – 15:00Break
15:00 – 16:00Data analysis Practical session: Approaching Metataxonomy – QIIME2
Giuseppe D’Auria – FISABIO, Spain
Mariana Reyes Prieto – FISABIO, Spain
16:00 – 16:15Break
16:15 – 17:15Data analysis Practical session: Approaching Metagenomics
Giuseppe D’Auria – FISABIO, Spain
Mariana Reyes Prieto – FISABIO, Spain
17:15 – 17:30Break
17:30 – 18:30Students Presentations 
18:30End of Day 4 – Continued access to networking and discussion platform, pre-recorded lectures and course materials on eCampus
Day 5 – Friday 16 April 2021
Time (Europe/Berlin)Speaker
12:45 – 13:00Overview of the day
13:00 – 13:45Panel discussion: from bench to computer – Critical steps in Metagenomic annalyis controlls, standards 
Moderator:
Vladimir Benes – EMBL Heidelberg, Germany 
Giuseppe D’Auria – FISABIO, Spain
José Eduardo González Pastor – Center of Astrobiology (CSIC/INTA), Spain  
Kostas Konstantinidis – Georgia Institute of Technology, USA    
Tobias Wenzel – Institute for Biological and Medical Engineering, Chile
13:45 – 14:45Metagenomic analysis tools -INCA, MILC, MELP
Kristian Vlahovicek – University of Zagreb, Croatia
14:45 – 15:00Break
15:00 – 16:00Practical: MEGAN
Daniel Huson – University of Tübingen, Germany
16:00 – 16:15Break
16:15 – 17:15Students Presentations 
17:15 – 18:00Networking activity
18:00End of Day 5 – Continued access to networking and discussion platform, pre-recorded lectures and course materials on eCampus
Day 6 – Monday 19 April 2021
Time (Europe/Berlin)Speaker
12:45 – 13:00Overview of the day
13:00 – 14:45Interactive Session on Case Studies
Giuseppe D’Auria – FISABIO, Spain
José Eduardo González Pastor – Center of Astrobiology (CSIC/INTA), Spain
Kostas Konstantinidis – Georgia Institute of Technology, USA
Arantxa Lopez – FISABIO, Spain
Jan Provaznik – EMBL Heidelberg, Germany
Nayara Trevisan Doimo de Azevedo – EBML Heidelberg, Germany
Laura Villacorta – EMBL Heidelberg, Germany
Tobias Wenzel – Institute for Biological and Medical Engineering, Chile
14:45 – 15:00Break
15:00 – 15:45Interactive Session on Case Studies (Continuation)
Giuseppe D’Auria – FISABIO, Spain
José Eduardo González Pastor – Center of Astrobiology (CSIC/INTA), Spain
Kostas Konstantinidis – Georgia Institute of Technology, USA
Arantxa Lopez – FISABIO, Spain
Jan Provaznik – EMBL Heidelberg, Germany
Nayara Trevisan Doimo de Azevedo – EBML Heidelberg, Germany
Laura Villacorta – EMBL Heidelberg, Germany
Tobias Wenzel – Institute for Biological and Medical Engineering, Chile
15:45 – 16:15Break
16:15 – 16:50Discussion & Wrap-up
16:50 – 17:00Summary of the course and virtual farewell
17:00End of the course

Practical information

Registration Fees and Motivation Letter
Application is no longer possible. The course was limited to 16 participants.

The results will be announced approximately 2-3 weeks after the application deadline.

Registration Fees (included admission, course materials, meals and coffee breaks):

Academia125 Euro
PhD Student125 Euro
Industry225 Euro

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Financial Assistance

Financial Assistance

Registration Fee Waivers

All academic and student registrants are invited to apply for a registration fee waiver, provided by the EMBL Advanced Training Centre Corporate Partnership Programme and EMBO. The registration fee waiver covers the registration sum that you have paid to attend the meeting. Conference participants are not required to pre-pay the registration fee to be selected for a fee waiver for a virtual meeting. If you have already paid the registration fee and are awarded a fee waiver, it will be reimbursed after the meeting. Course participants are required to pay the course fee in advance, which will then be reimbursed after the recipient has attended the course.

Childcare Grants 

For participants and speakers with childcare responsibilities there is the possibility to apply for a grant, provided by the EMBL Advanced Training Centre Corporate Partnership Programme and EMBO, to offset childcare costs incurred when participating at a virtual event. Eligible costs include fees for a babysitter or childcare facility or travel costs for a care giver. Please note that priority will be given to early stage researchers. Costs will be reimbursed after the meeting only once a reimbursement form and original receipts have been received. In order to apply for this grant, you must be registered by the abstract submission deadline.

Boehringer Ingelheim Fonds Travel Grant

Applies to selected courses only. Availability will be indicated during the abstract or motivation letter submission process.

This grant covers costs related to your attendance to the course (registration, travel and accommodation costs). The grant is restricted to PhD students and postdocs who conduct basic biomedical research.
Whether you are eligible to apply for a travel grant, depends on when you received your university entrance qualification (e.g. Abitur, A-Levels, High School Diploma, Final State Examination):

– for PhD and MD students, as well as graduates, the university entrance qualification must not have been obtained more than 11 years ago at the time of the envisaged course
– for postdocs, the university entrance qualification must not have been obtained more than 13 years ago at the time of the envisaged course

Application

Applications for financial assistance can be submitted via the submission portal* (for the submission of abstracts for conferences or the submission of motivation letters for courses) by completing the Financial Assistance Application Section (underneath the section for entering abstract/motivation letter information). The link to the portal can be found in the registration confirmation email that you will receive after registering for the conference or course.

For conferences, if you are not submitting an abstract, you can still apply for financial assistance in the submission portal by following the instructions here. Note that priority will be given to those submitting an abstract to present at the conference. In your application you will be asked to answer questions regarding your motivation for applying, and, for registration fee waivers, the reasons why your lab cannot fund your attendance and how your attendance will make a difference to your career. Application for financial support will not affect the outcome of your registration application.

*For some events, applications for Childcare Grants will still be done by email. Information about the grant will be sent out shortly after the abstract/motivation letter deadline. Please contact the event Conference Officer if you have any questions.

Selection

The scientific organisers will select the recipients of registration fee waivers during the abstract selection process for conferences and the participant selection process for courses. Results will be announced approximately 3 – 4 weeks before the event start date. Selection results do not impact your admission to the meeting. Registration fee waiver selection is based on your current work or study location, your motivation for applying, the reasons for needing financial support and the impact this event will have on your career. Childcare grants are allocated based on career stage, with priority given to early stage researchers.

Further details

A list of external funding opportunities can be found here, and information on attending a conference as an event reporter here.

For further information about financial assistance please refer to the FAQ page.

Sponsors

Event Supporters

Event Sponsor

Sponsorship Opportunities

We offer a variety of event sponsoring possibilities, with the flexibility to select a set sponsorship package or combine individual sponsorship options to suit your event budget. Discounts are available for companies sponsoring multiple events at EMBL Heidelberg. View other conferences, or contact sponsorship@embl.de for further information.

If you are interested in becoming a media partner of this event, please visit our media partnerships webpage.

Technical Requirements

Below you will find the software and technical requirements for this course. You will need admin rights to be able to install the software on your computer and we recommend you try this before the course. If you do not have admin rights, please contact your technical support team in advance to make sure the software can be installed.

Internet requirements

  • Client computer with fast and stable internet access for the live virtual sessions:
  • Minimum: 50 mbit download and 10 mbit upload (suitable for pre-recorded lectures)
  • Preferred: 100 mbit download and upload (at your host institute )

Additional Software

The EMBL eCampus learning platform will be used to collaborate, communicate and network with all of the course participants. All participants will receive information on how to join shortly before the course. We recommend using Chrome, Safari or Mozilla Firefox browsers for eCampus.

Zoom will be used for the live talks and Q&A sessions. More information will be provided closer to the start of the course

Other Information

While using the software during the course, please make sure you have nothing else using your bandwidth. We recommend using a wired connection.

Date: 12 - 19 Apr 2021

Location: Virtual


Deadline(s):

Closed


Contact: Maria Bacadare


EMBL Courses and Conferences are kindly supported by our Corporate Partnership Programme

Founder partners

Corporate partners

Associate partners

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