Course outside EMBL-EBI

BioExcel Summer School on Biomolecular Simulations 2022

The summer school will include lectures and hands-on sessions on the following topics:

  • Molecular dynamics simulations
  • Biomolecular docking
  • Free energy calculations
  • Advanced sampling methods (Metadynamics)
  • BioExcel Building Blocks (BioBB)
  • Quantum mechanics/molecular mechanics (QM/MM)
  • Machine learning

During the hands-on computer practicals you will make use of the BioExcel flagship software and tools: e.g. GROMACS, HADDOCK, PMX, BioBB, and CP2K. The trainers, developers and/or experts in the use of the software, will provide guidance and support.

You can find more informatioan about the course on the BioExcel website: https://bioexcel.eu/events/bioexcel-summer-school-on-biomolecular-simulations-2022/

Who is this course for?

The BioExcel school is intended for primarily PhD and post-doctoral researchers using or planning to use biomolecular modeling and simulation in their everyday research. Familiarity with Linux and basic knowledge of molecular modelling software is a requirement.

What will I learn?

Learning outcomes

After this course you should be able to:

  • Use a range of biomolecular modeling and simulation software (GROMACS, HADDOCK, PMX, CP2K)
  • Discuss current trends and challenges in biomolecular simulation

Trainers

Adam Hospital
IRB Barcelona
Alessandra Villa
KTH Royal Institute of Technology in Stockholm
Alexandre Bonvin
University of Utrecht
Andrea Basciu
University of Cagliari
Attilio Vittorio Vargiu
University of Cagliari
Dmitry Morozov
University of Jyväskylä
Elisa Fadda
Maynooth University
Emiliano Ippoliti
FZ Jülich
Giuliano Malloci
University of Cagliari
Irina Moreira
Coimbra University
Vytautas Gapsys
Max Planck Institute

Programme

Note: The programme is still under development and subject to some changes

Time (CEST) Topic Trainer
Arrival day - Sunday 12 June 2022
19:00 - 20:00  Registrations  
20:00  Dinner at hotel  
Time (CEST) Topic Trainer
Day 1 - Monday 13 June 2022
08:30 - 9:00 Bus from the hotel to the venue  
09:00 - 9:30 Course introduction Marta Lloret Llinares
09:30 - 10:30 Molecular dynamics basics  Alessandra Villa
10:30 - 11:00 Coffee & tea break  
11:00 - 11:30 Molecular dynamics basics Alessandra Villa
11:30 - 12:30 Interoperable and reproducible biomolecular simulation workflows using BioBB - Introduction Adam Hospital
12:30 - 13:30 Lunch  
13:30 - 14:15 Flash talks  
14:15 - 15:45 Tutorial - GROMACS Alessandra Villa
15:45 - 16:15 Coffee & tea break  
16:15 - 17:45 Tutorial - Interoperable and reproducible biomolecular simulation workflows using BioBB Adam Hospital
17:45 - 18:15 Bus back to the hotel  
20:00 Dinner at hotel  
Time (CEST) Topic Trainer
Day 2 - Tuesday 14 June 2022
08:30 - 9:00 Bus from the hotel to the venue  
09:00 - 10:30 Modeling molecular recognition through enhanced-sampling methods Attilio Vittorio Vargiu
10:30 - 11:00 Coffee & tea break  
11:00 - 13:00 Tutorial - EDES - Guided introduction Attilio Vargiu, Giuliano Malloci & Andrea Basciu
13:00 - 14:00 Lunch  
1114:00 - 14:30 Flash talks  
14:30 - 16:00 Docking basics Alexandre Bonvin
16:00 - 16:30 Coffee & tea break  
16:30 - 18:00 Tutorial - HADDOCK Alexandre Bonvin
18:00 - 18:30 Bus back to the hotel  
19:30 Career session and dinner at hotel  
Time (CEST) Topic Trainer
Day 3 - Wednesday 15 June 2022
08:30 - 9:00 Bus from the hotel to the venue  
09:00 - 10:30 Introduction to QM/MM Emiliano Ippoliti
10:30 - 11:00 Coffee & tea break  
11:00 - 13:00 Tutorial - CP2K Dmitry Morozov
13:00 - 14:00 Lunch  
14:00 - 15:00 Poster session (even)  
15:00 - 16:00 Coffee & tea break  
15:30 - 16:30 Poster session (odd)  
16:30 - 20:00 Excursion to Nora and Pula  
20:00 Course dinner  
Time (CEST) Topic Trainer
Day 4 - Thursday 16 June 2022
08:30 - 9:00 Bus from the hotel to the venue  
09:00 - 10:30 Free energy calculations Vytautas Gapsys
10:30 - 11:00 Coffee & tea break  
11:00 - 13:00 Tutorial - PMX Vytautas Gapsys
13:00 - 14:00 Lunch  
14:00 - 15:00 Machine learning Irina Moreira
16:00 - 16:30 Coffee & tea break  
16:30 - 17:00 Career session  
17:00 - 18:00 Bring your own problem All speakers
18:00 - 18:30 Bus back to the hotel  
20:00 Dinner at hotel  
Time (CEST) Format Trainer
Day 5 - Friday 17 June 2022
08:30 - 9:00 Bus from the hotel to the venue  
09:00 - 10:30 MD for oligosaccharides Elisa Fadda
10:30 - 11:00 Coffee & tea break  
11:00 - 12:00 Round table / Get answers / Final remarks and feedback All speakers
12:00 - 13:00 Lunch  
13:00 Travel to the airport  

To apply you will need the following information:

  • Support letter from your supervisor or a senior co-worker explaining why you should be selected for this course (in word or pdf format)
  • Research Abstract (limit: 250 words – you will be able to present and discuss your research during the course)
  • A text with your biography and work history (limit: 200 words)

The support letter is attached to the application as a word or pdf file. The abstract and the text with the biography and work history are introduced in text boxes in the application form.

Please complete the application process by midnight (CET) on Monday 7 March. Incomplete applications will not be considered. All applicants will be informed of the status of their application (successful, waiting list, rejected) by Tuesday 22 March. If you have any questions regarding the application process, please contact Marta Lloret Llinares.

 

You can find tips on how to apply on the BioExcel website: https://bioexcel.eu/events/bioexcel-summer-school-on-biomolecular-simulations-2022/

The registration fee is 475 euros. You will only be required to pay if you are selected to participate in the event.

BioExcel will be providing a limited number of fixed amount travel bursaries for this event. If you would like to be considered for a travel bursary, check the information on travel grants on the BioExcel event website and email Marta Lloret Llinares after the submission of your application.

Applications closed
07 March 2022

12 - 17 June 2022
Science and technology park of Sardinia Italy
475 €
Contact
Jane Reynolds
Open application with selection
30 places

Organisers
  • Vera Matser
    EMBL-EBI
  • Marta Lloret Llinares
    EMBL-EBI
  • Alexandre Bonvin
    UNIVERSITY OF UTRECHT
  • Attilio Vittorio Vargiu
    UNIVERSITY OF CAGLIARI
  • Giuliano Malloci
    UNIVERSITY OF CAGLIARI

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