BioExcel Summer School on Biomolecular Simulations 2019

Welcome to the 2019 BioExcel Summer school on Biomolecular Simulations

On this page you will find information about the Programme and logistics for the upcoming summer school.

Date: Sunday 30th June (arrival only) – Friday 5th July 2019

Venue: Sardegna Ricerche, Auditorium Building 2
Località Piscinamanna 09010 Pula (CA) Italy
Phone: +39 070 9243.1
www.sardegnaricerche.it/en/technologypark

Programme

– Note that the programme is subject to minor changes –

Time Topic Trainer / Speaker
Day 0 – Sunday 30th June 2019
18:30 Travel from airport to hotel  
19:30 Registration  
20:00 Dinner at Hotel Flamingo  
Day 1 – Monday 1st July 2019
08:30 – 09:00 Bus to the venue  
09:00 – 09:30 Welcome & Introduction to BioExcel Vera Matser & Alexandre Bonvin
09:30 – 10:30 Lecture – Introduction to molecular dynamics and its workflows  Mark Abraham
10:30 – 11:00 Coffee & tea break  
11:00 – 12:30 Lecture – Introduction to GROMACS and some of its algorithms  Christian Blau & Mark Abraham
12:30 – 13:30 Lunch  
13:30 – 14:30 Participant flashtalks  
14:30 – 15:30 Tutorial – First steps in using GROMACS Christian Blau & Mark Abraham
15:30 – 16:00 Coffee & tea break  
16:00 – 17:30 Tutorial – Using AWH enhanced sampling in GROMACS Christian Blau & Mark Abraham
17:30 – 18:00 Bus back to the hotel
20:00 Dinner at Hotel Flamingo
Day 2 – Tuesday 2nd July 2019
08:30 – 09:00 Bus to the venue
09:00 – 10:30 Lecture – Modeling molecular recognition through enhanced-sampling methods  Attilio Vargiu
10:30 – 11:00 Coffee & tea break  
11:00 – 12:30 Lecture – Integrative modelling of biomolecular complexes with HADDOCK  Alexandre Bonvin
12:30 – 13:30 Lunch  
13:30 – 14:30 Participant flashtalks  
14:30 – 15:30 Tutorial – HADDOCK  Alexandre Bonvin & Charlotte Van Noort
15:30 – 16:00 Coffee & tea break  
16:00 – 17:30 Tutorial – HADDOCK (continued)  Alexandre Bonvin & Charlotte Van Noort
17:30 – 18:00 Bus back to the hotel
20:00 Dinner at Hotel Flamingo
Day 3 – Wednesday 3rd July 2019
08:30 – 09:00 Bus to the venue
09:00 – 10:00 Lecture – QM/MM interfaces  Emiliano Ippoliti  
10:00 – 10:30 Coffee & tea break  
10:30 – 12:30 Tutorial – CP2K demonstration Vaibhav Modi
12:30 – 13:30 Lunch  
13:30 – 14:30 Poster session (even) – includes Coffee & Tea  
14:30 – 15:30 Poster session (odd) – includes Coffee & Tea  
16:00 – 20:00 Travel to Nora

Excursion to Nora and  Pula

20:00 – 22:00 Social dinner in Pula
22:00 – 22:30 Travel back to the hotel
Day 4 – Thursday 4th July 2019
08:30 – 09:00 Bus to the venue
09:00 – 10:30 Lecture – Alchemical free energy calculations using PMX  Bert de Groot
10:30 – 11:00 Coffee & tea break  
11:00 – 12:30 Tutorial – PMX  Bert de Groot & Vytautas Gapsys
12:30 – 13:30 Lunch  
13:30 – 14:30 Tutorial – PMX (continued)  Bert de Groot & Vytautas Gapsys
14:30 – 15:30 Tutorial – metadynamics / HADDOCK Charlotte van Noort & Andrea Basciu
15:30 – 16:00 Coffee & tea break  
16:00 – 17:30 Tutorial – metadynamics / HADDOCK Charlotte van Noort & Andrea Basciu
17:30 – 18:00 Bus back to the hotel
20:00 Dinner at Hotel Flamingo
Day 5 – Friday 5th July 2019 
08:30 – 09:00 Bus to the venue
09:00 – 10:30 Research highlights – short talks from selected participants  
10:30 – 11:00 Coffee & tea break  
11:00 – 12:15 Round table & Get answers session  
12:15 – 12:30 Final remarks and feedback  
12:30 – 13:15 Lunch  
13:30  Travel to the airport  

Instructions for posters

Poster

Please note that the poster board are 70 cm (width) X 100 cm (height).

Please print your posters in advance, as there will be limited access to printing facilities on site.

Transportation

Distance in km to Technology Park

48 km from Cagliari-Elmas Airport
42 km from Cagliari
9.5 km from Pula.

By shuttle

Shuttle services will be provided by the organizers from Cagliari Elmas Airport to the hotel (on Sunday), from the hotel to the Auditorium and return to the airport from the auditorium (on Friday).

You have received a detailed schedule over email  – Assembly point is in the arrivals hall close to the info-point (Sardegna Turismo) on the ground floor (close to the coffee shop).

By public transport

From Airport to the hotel

  • Proceed from Elmas Airport to Central Cagliari (piazza Matteotti) by taxi or train (Elmas Aeroport –> Cagliari – http://www.trenitalia.com/)
  • Bus 129 from Central station of Cagliari (piazza Matteotti) to Santa Margherita di Pula (ask the driver for the closest stop to Hotel Flamingo and Hotel Mare Pinate). On Sunday, only consider bus rides marked with GIOR (“giornaliero”) or FEST (“festivo”). See timetable here: 129

Accommodation and meals

Accommodation (shared) will be at Hotel Mare Pineta and evening meals (excl. dinner on day 3) at Hotel Flamingo, walking distance from Mare Pineta.

Hotel Flamingo is connected to Hotel Mare Pineta by an internal path, it takes 5-10 minutes.

Useful Links

Cagliari Transports, Port, Train Station and InfoPoints: http://www.cagliariturismo.it/en/get-to-cagliari
Cagliari Airport: http://www.sogaer.it/en/

Contacts

Michelle Mendonca
mmendonca@ebi.ac.uk
Tel: +44 (0)1223 49 4335