Registration for our Summer School this year is closed

The annual, flagship BioExcel Summer School provides a comprehensive combination of lectures and tutorial sessions on biomolecular modeling and simulations using modern core applications and tools. The School has been run very successfully multiple times between 2018 and 2022 and this year it will take place in Sardinia, Italy as an on-site event and supported by Sardegna Ricerche. Get a feel for what the School has to offer by accessing the collection of insights & highlights from our past events

Date: 10 – 15 September 2023
Venue: Science and Technology Park of Sardinia, Pula, Italy
Applications open:  30 March 2023
Application deadline: 28 May 2023
Notification date: 14 June 2023
Participation: Open application with a selection (30 applicants will be selected for the course). We can only accept participants from EuroHPC Joint Undertaking member institutions.
Registration fee: 500 Euros (to be paid after the selection process; includes accommodation, all meals and transport to/from the airport & course venue)
Deadline for registration fee if application is accepted: 29 June 2023

Registration

Audience and Prerequisites

  • The BioExcel School is intended primarily for 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.
  • We can only accept participants from EuroHPC Joint Undertaking member institutions.
  • We highly encourage applications from industrial entities, women and underrepresented groups.
  • For industrial application enquiries please contact info@bioexcel.eu as the registration fee might differ from the announced fee.

The BioExcel Code of Conduct will apply during the event.

Travel grants

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, please check the preliminary information in the BioExcel Travel Grant Guidelines for awarding travel grants.

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.

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. We can only accept applications from individuals based at  EuroHPC Joint Undertaking member institutions.

Please complete the application process by midnight (CEST) on Sunday 28 May. Incomplete applications will not be considered. All applicants will be informed of the status of their application (successful, waiting list, rejected) by Wednesday 31 May. If you have any questions regarding the application process, please contact event-support@csc.fi

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 10 September 2023
16:00 - 18:00 Pick-up at airport
18:00 - 19:00 Bus from airport to hotel
19:00 - 20:00 Registrations
20:00 Dinner at hotel
Time (CEST) Topic Trainer
Day 1 - Monday 11 September 2023
08:30 - 08:45 Bus from the hotel to the venue
08:45 - 09:00 Welcome and introduction
09:00 - 10:30 Lecture 1 - Molecular dynamics basics  Alessandra Villa
10:30 - 11:00 Coffee & tea break
11:00 - 12:45 Tutorial 1 - GROMACS Alessandra Villa
12:45 - 14:00 Lunch  
14:00 - 15:30 Lecture 2 - Interoperable and reproducible biomolecular simulation workflows using BioBB Adam Hospital
15:30 - 16:00 Coffee & tea break  
16:00 - 17:45 Tutorial 2 - BioBB Adam Hospital
17:45 - 18:00 Bus back to the hotel
20:00 Dinner at hotel
Time (CEST) Topic Trainer
Day 2 - Tuesday 12 September 2023
08:30 - 08:45 Bus from the hotel to the venue
08:45 - 09:00 Welcome and introduction
09:00 - 10:30 Lecture 3 - Integrative modelling with HADDOCK Rodrigo Vargas
10:30 - 11:00 Coffee & tea break
11:00 - 12:45 Tutorial 3 - HADDOCK Rodrigo Vargas
12:45 - 14:00 Lunch
14:00 - 15:00 Flash talks
15:00 - 18:00 Poster session I and II (with coffee break)
18:00 - 18:15 Bus back to the hotel
20:00 Dinner at hotel
Time (CEST) Topic Trainer
Day 3 - Wednesday 13 September 2023
08:30 - 08:45 Bus from the hotel to the venue
08:45 - 09:00 Welcome and introduction  
09:00 - 10:30 Lecture 4 - Enhanced sampling Erik Lindahl
10:30 - 11:00 Coffee & tea break
11:00 - 12:45 Tutorial 4 - GROMACS (enhanced sampling) Erik Lindahl
12:45 - 14:00 Lunch
14:00 - 15:30 Lecture 5 - Modeling molecular recognition through enhanced sampling methods Attilio Vargiu
15:30 - 16:00 Coffee & tea break
16:00 - 17:45 Tutorial 5 - EDES Attilio Vargiu
17:45 - 18:00 Bus back to the hotel  
20:00 Dinner at hotel  
Time (CEST) Topic Trainer
Day 4 - Thursday 14 September 2023
08:30 - 08:45 Bus from the hotel to the venue
08:45 - 09:00 Welcome and introduction  
09:00 - 10:30 Lecture 6 - Free energy calculation Bert de Groot
10:30 - 11:00 Coffee & tea break
11:00 - 12:45 Tutorial 6 - PMX Bert de Groot
12:45 - 14:00 Lunch
14:00 - 15:00 QM/MM Emiliano Ippoliti
15:00 - 16:00 Poster discussion (with coffee break)
16:00 - 19:00 Travel and excursion to Nora
19:00 - 20:00 Travel and visit to Pula
20:00 Social dinner
Time (CEST) Format Trainer
Day 5 - Friday 15 September 2023
08:30 - 08:45 Bus from the hotel to the venue
08:45 - 09:00 Welcome and introduction  
09:00 - 10:00 AI lecture (online remote) Ola Engkvist
10:00 - 10:30 Coffee & tea break
10:30 - 11:30 Career session All speakers
11:30 - 12:00 Final remarks
12:00 - 13:00 Lunch (take away for those leaving earlier
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, Spain)
  • Alessandra Villa, BioExcel (KTH, Sweden)
  • Erik Lindahl, BioExcel (KTH, Sweden)
  • Atte Sillanpää, BioExcel (CSC – IT Center for Science, Finland)
  • Attilio Vittorio Vargiu (University of Cagliari, Italy)
  • Bert de Groot, BioExcel (Max Planck Institute, Germany)
  • Emiliano Ippoliti (FZ Jülich, Germany)
  • Giuliano Malloci (University of Cagliari, Italy)
  • Ola Engkvist (AstraZeneca, Sweden)
  • Rodrigo Honorato, BioExcel (University of Utrecht, The Netherlands)
Organisers
  • Rossen Apostolov, BioExcel (KTH, Sweden)
  • Alessandra Villa, BioExcel (KTH, Sweden)
  • Atte Sillanpää, BioExcel (CSC – IT Center for Science, Finland)
  • Tiina Leiponen, BioExcel (CSC – IT Center for Science, Finland)
  • Otto Andersson, BioExcel (CSC – IT Center for Science, Finland)
  • Marina Bouianov, BioExcel (CSC – IT Center for Science, Finland)
  • Richard Norman, BioExcel (Norman Consulting, Norway)
  • Attilio Vittorio Vargiu (University of Cagliari, Italy)
  • Giuliano Malloci (University of Cagliari, Italy)
  • Alexandre Bonvin (University of Utrecht, The Netherlands)

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