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Simulation Environments for Life Sciences @ BSC

12–13 Mar 2015
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

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.
PLEASE BRING YOUR OWN LAPTOP.
Starts
Ends
CET
BSC, Barcelona UPC, Campus Nord
Room VS 218, Vertex building
For details go to http://bsc.es/education
Course Program Outline:

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)
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