BioExcel Summer School on Biomolecular Simulations 2022

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 eligible 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
14:00 – 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
20:00	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 – 11:00	Tutorial – PMX	Vytautas Gapsys
11:00 – 11:30	Coffee & tea break
11:30 – 13:00	Poster session (even)
13:00 – 14:00	Lunch
14:00 – 15:30	Poster session (odd)
15:30 – 16:00	Coffee & tea break
16:00 – 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	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 – 16:00	Machine learning	Irina Moreira
16:00 – 16:30	Coffee & tea break
16:30 – 17:30	Career session
17:30 – 18:00	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

Introduction

At BioExcel we are committed to the safety of our participants and trainers. Both BioExcel and our community of participants need to take new precautions when planning how we come together again in person for learning and scientific exchange. BioExcel continuously monitors local and international guidelines and regulations relating to the COVID-19 pandemic. Due to the changing nature of the pandemic and in order to be compliant with relevant national and international regulations, it may be necessary for BioExcel to update, from time to time, these COVID-19 specific safety rules. We will inform registered participants about substantial changes to this document.

 

COVID-19 vaccination status as a condition of attendance

BioExcel requires that all participants in its on-site conferences and courses – including standard participants, speakers, trainers– are fully vaccinated or carry a valid form of exemption from vaccination. Please note that only Proof of vaccination or medical exemption as defined by the Italian Government will be accepted. For more information, please see the Italian Government website.

 

COVID-19 testing during your stay as an additional layer of protection

BioExcel is seeking to provide a periodic self-testing regime for participants and staff as an additional layer of safety. By registering you declare that you will make every reasonable effort to participate in any such testing. You are requested to self-test for COVID-19 on the morning of your first day of attendance, shortly before leaving your accommodation or travelling to the course venue. For this you are encouraged to obtain and bring with you the self-test rapid-antigen / lateral flow kits, readily and affordably available in most countries.

Safe conduct at the event

By attending, you agree to abide by applicable Italian regulations at the hotel and at the Science and Technology Park of Sardinia, and to conduct yourself in accordance with all provided instructions. This will include, but is not limited to:

• Refraining from attending the event, or leaving promptly, if you develop symptoms associated with COVID-19;
• Complying with the prevailing mask-wearing policy communicated at the event: FFP2 masks to be worn in the bus and at the course venue;
• Participating in temperature checks when required by the venue;
• Following instructions on physical distancing and crowd circulation at the event;
• Following distancing and circulation instructions on-site to minimise contact;
• Observing good hand-washing and hygiene etiquette;
• Filling in and signing a self-declaration form, in which you will be asked to confirm that:
  • You have not been in close contact with a person with suspected or confirmed SARS-CoV-2 infection;
  • You have not shown any symptoms of a SARS-CoV-2 infection yourself;
  • You have valid proof of vaccination or recovery when coming on site. You will present this for verification to the course organisers.

Commitment to COVID-19 safety at our courses

BioExcel has a comprehensive on-site COVID-19 safety plan that consists of a range of precautions to reduce the risk of COVID-19 transmission. Underpinned by the limitation of access to immunised (i.e. vaccinated) persons, the plan is adapted over time and, if necessary, on an event-by-event basis, to ensure that it remains proportionate to the trajectory of the pandemic and to the latest developments.

• Periodic testing, as described above, may be in place if deemed appropriate;
• FFP2 masks will be required in the buses and at the course venue to comply with local and national regulations at the time of the event. Participants will need to bring their own supply of FFP2 masks.

Proper cleaning and disinfection protocols and workplace practices are in place as a standard, and hand sanitising stations are present throughout the building for use by all.

Participants accept that they may be asked to leave the event should they fail to meet the obligations contained herein.