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
