BioExcel Summer School on Biomolecular Simulations 2022

Beach in cagliari with blue water and orange hues in skies

Date: 12  June  – 17 June 2022
Venue: Science and Technology Park of Sardinia, Pula, Italy
Applications open:  13 January 2022
Application deadline: 7 March 2022
Notification date: 22 March 2022 
Participation: Open application with a selection (30 applicants will be selected for the course)
Registration fee: 475 Euros (to be paid after the selection process)
Contact: Marta Lloret Llinares

The summer school is supported by Sardegna Ricerche. We plan to run this course face-to-face in Sardinia, Italy. This is subject to the COVID-19 pandemic situation.

We highly encourage applications from women and underrepresented groups.

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 in the BioExcel Travel Grant document.
  • Complete the application form for the course.
  • Email Marta Lloret Llinares after the submission of your application explaining why you should be considered for a travel grant.

Important Note: We are running a remote BioExcel school in March. If you are selected and accept a place in the BioExcel School in March, you will not be eligible for a place in the BioExcel Summer School in June.

Apply now>>

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.

Audience and Prerequisites

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.

Note: BioExcel is running a remote school in March. If you are selected and accept a place in the BioExcel School in March, you will not be elegible for a place in the BioExcel Summer School in June.

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.

Tips for a good application

1) During the selection process we focus on:
  • Do you have the pre-requisite knowledge?
  • Will your research and research group benefit from what you learn in this course?
So, please pay special attention to the following 3 questions on the application form:
  • Describe your research interests
  • Describe how this course will benefit your own research
  • Describe how this course will benefit the research of your group
2) You are asked to add an abstract about your research to be presented during the BioExcel school. If you do not have any results yet, you can write your abstract as a short introduction to the topic and a working plan.

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

The lectures and hands-on sessions will be given by internationally recognised leaders in the field of computational biomolecular research.

Speakers

  • Adam Hospital, BioExcel (IRB Barcelona)
  • Alessandra Villa, BioExcel (KTH)
  • Alexandre Bonvin, BioExcel (University of Utrecht)
  • Andrea Basciu, University of Cagliari
  • Attilio Vittorio Vargiu, University of Cagliari
  • Dmitry Morozov, BioExcel (University of Jyväskylä)
  • Elisa Fadda, Maynooth University
  • Emiliano Ippoliti, BioExcel (FZ Jülich)
  • Giuliano Malloci, University of Cagliari
  • Irina Moreira, Coimbra University
  • Vytautas Gapsys, BioExcel (Max Planck Institute)
Organisers
  • Vera Matser, BioExcel (EMBL-EBI)
  • Marta Lloret Llinares, BioExcel (EMBL-EBI)
  • Alexandre Bonvin, BioExcel (University of Utrecht)
  • Attilio Vittorio Vargiu, University of Cagliari
  • Giuliano Malloci, University of Cagliari

We plan to run this course face-to-face in Italy. This is subject to the pandemic situation, which we will monitor in the upcoming months. We will follow all applicable local regulations in relation to COVID-19.

Several measures will be in place during the course:

  • The EU COVID-19 certificate or equivalent will be checked at the venue
  • Body temperature will be checked at the venue
  • Proper cleaning and disinfection protocols will be followed
  • Rapid antigen tests will be available in case someone develops symptoms

More detailed information will be communicated to successful applicants.

As the situation is constantly evolving, the measures might change.

You can find information about requirements for travelling to Italy on the following website from their Ministry of Health: COVID-19, information for travellers


Date/Time
12 Jun, 2022 - 17 Jun, 2022
09:00 - 17:00

Location
Science and Technology Park of Sardinia

Categories