BioExcel Summer School on Biomolecular Simulations 2018


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