Welcome to the 2018 BioExcel Summer school on Biomolecular Simulations
On this page you will find information about the Programme and logistics for the upcoming summer school
Note that this course is closed for registration. All successful applicants have been notified.
Date: Sunday 17th June (arrival only) – Friday 22nd June 2018
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 17th June 2018 | ||
| 19:30 | Registration | |
| 19:45 | Dinner at Hotel Flamingo | |
| Day 1 – Monday 18th June 2018 | ||
| 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 | Mark Abraham, Paul Bauer & Viveca Lindahl |
| 12:30 – 13:30 | Lunch | |
| 13:30 – 14:30 | Flashtalks | |
| 14:30 – 15:30 | Tutorial – First steps in using GROMACS | Mark Abraham & Paul Bauer |
| 15:30 – 16:00 | Coffee & tea break | |
| 16:00 – 17:30 | Tutorial – Using AWH enhanced sampling in GROMACS | Viveca Lindahl |
| 17:30 – 18:00 | Bus back to the hotel | |
| 19:30 – 21:30 | Dinner @ Hotel Flamingo | |
| Day 2 – Tuesday 19th June 2018 | ||
| 08:30 – 09:00 | Bus to the venue | |
| 09:00 – 10:30 | Lecture – Modeling molecular recognition through enhanced-sampling methods | Attilio Vargiu & Andrea Basciu |
| 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 | Flashtalks | |
| 14:30 – 15:30 | Tutorial – HADDOCK | Alexandre Bonvin & Adrien Melquiond |
| 15:30 – 16:00 | Coffee & tea break | |
| 16:00 – 17:30 | Tutorial – HADDOCK (continued) | Alexandre Bonvin & Adrien Melquiond |
| 17:30 – 18:00 | Bus back to the hotel | |
| 19:30 – 21:30 | Dinner @ Hotel Flamingo | |
| Day 3 – Wednesday 20th June 2018 | ||
| 08:30 – 09:00 | Bus to the venue | |
| 09:00 – 10:30 | Lecture – QM/MM interfaces in the CPMD code | Emiliano Ippoliti |
| 10:30 – 11:00 | Coffee & tea break | |
| 11:00 – 12:30 | Tutorial – CPMD | Emiliano Ippoliti & Viacheslav Bolnykh |
| 12:30 – 13:30 | Lunch | |
| 13:30 – 14:30 | Tutorial – CPMD (continued) | Emiliano Ippoliti & Viacheslav Bolnykh |
| 14:30 – 16:00 | Poster session & Coffee & tea break | |
| 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 21st June 2018 | ||
| 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 | Andrea Basciu & Adrien Melquiond |
| 15:30 – 16:00 | Coffee & tea break | |
| 16:00 – 17:30 | Tutorial – metadynamics / HADDOCK | Andrea Basciu & Adrien Melquiond |
| 17:30 – 18:00 | Bus back to the hotel | |
| 19:30 – 21:30 | Dinner @ Hotel Flamingo | |
| Day 5 – Friday 22nd June 2018 | ||
| 08:30 – 09:00 | Bus to the venue | |
| 09:00 – 10:00 | Research highlights – short talks from participants | Lara Callea, Joan Francesc Gilabert Navarro & Ksenia Korshunova |
| 10:00 – 10:30 | Talk – Dynamical structure-function relationship in bacterial transporters | Paolo Ruggerone |
| 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 – 13:30 | Lunch | |
| 14:30 | Travel to the airport | |
Instructions posters and flashtalks
Flashtalks
Using the following template (BioExcel_intro_participants) you are asked to send your flashtalk slides to Vera Matser (matser@ebi.ac.uk) by 1st June 2018
Poster
Please note that the poster board are 70 cm (width) X 100 cm (height).
You poster should be A1 portrait (594 x 841 mm) or Super A1 portrait (610 x 914 mm)
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 Pinate 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
Vera Matser
matser@ebi.ac.uk
Tel: +44 (0)1223 49 4149
