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Simulation Environments for Life Sciences @ BSC

Mar 14 – 15, 2016
BSC, Barcelona UPC, Campus Nord
CET timezone

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Objectives: The course will make the attendants familiar with simulation technologies used in Life Sciences and their specific adaptation to HPC environment

Detailed outline:
Introduction to biomolecular simulation
Coarse-grained and atomistic simulation strategies
Automated setup for simulation

HPC specifics: Large scale parallelization, use of GPU’s
Storage and strategies for large scale trajectory analysis

Learning Outcomes: Setup, execute, and analyze standard simulations in HPC environment

Starts
Ends
CET
BSC, Barcelona UPC, Campus Nord
TBD
For details go to http://bsc.es/education

Course Program Outline:

Day 1

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

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Day 2
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)

 

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