PATC Course: Simulation Environments for Life Sciences

Date: 13/Mar/2014 Time: 09:00 - 14/Mar/2014 Time: 18:00


The course will take place in
Barcelona Supercomputing Centre,
within the UPC Campus Nord premises.

Room VS219, Vertex Building (green on the map)
S indicates that the room is 2 floors below the entrance level.

Target group: Level: for trainees with some theoretical and practical knowledge Prerequisites: Basic knowledge of structural bioinformatics Basic knowledge of parallelization strategies Material will be provided during the course, students are welcome to provide their own use cases.

Cost: There is no registration fee. The attendees would need to cover the expenses for travel, accommodation and meals.  

Primary tabs

Day 1 – March 13th, 2014
Session 1
09.00h – Welcome & Introduction (JLG)
10.30h – Break
11.00h – Atomistic MD Algorithm (JLG)
11.45h –  Algorithm improvements & HPC (JLG)
12.30h – Break

Session 2
14.00h – Simulation Setup (AH)
15.00h – Setup and Analysis Hands On (AH)
16.00h – Break
16.30h – Setup and Analysis Hands On (AH)  
18.00h – Adjourn

Day 2 – March 14th, 2014
Session 3
09.00h – Simulation DBs (MoDEL) (RG)
10.00h – Simulation Data Management (PA)
10.30h – Break
11.00h – Coarse Grained MD (AE)
12.00h – Application Examples (MO)
13.00h – Break

Session 4
14.00h – Coarse Grained MD manual slides Hands on (AE)
16.00h – Break
16.30h – Free  Hands-on
18.00h – End of the course

AE: Agustí Emperador (IRB) , AH: Adam Hospital (IRB), JLG: Josep Ll. Gelpi (BSC-IRB- UB), MO: Modesto Orozco (BSC-IRB-UB), PA: Pau Andrio (BSC), RG: Ramón Goñi (BSC)