Introduction for Simulation Environments for Life Sciences @ BSC
Date: 17 - 18 March 2021
All the PATC courses at BSC are free of charge.
Venue: Online via Zoom
Objectives: The course will make the attendants familiar with simulation technologies used in Life Sciences and their specific adaptation to HPC environment
Course convener: Josep Gelpi
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
Level: (All courses are designed for specialists with at least 1st cycle degree or similar background experience) INTERMEDIATE: for trainees with some theoretical and practical knowledge.
Further information:
In the context of virtual meetings, the Organiser may facilitate live webstreaming and audio recording. You have the option to opt out of inclusion in recordings by contacting our Education&Training team.
CONTACT US for further details about MSc, PhD, Post Doc studies, exchanges and collaboration in education and training with BSC.
For further details about Postgraduate Studies in UPC - Barcelona School of Informatics (FiB), visit the website
Sponsors: BSC and PRACE 6IP project are funding the PATC @ BSC training events.
If you want to learn more about PRACE Project, visit the website.
Agenda
17 March
18 March
09.00 - 10.30
Welcome & Introduction (JLG)
09.00 - 10.30
Simulation DBs and simulation data management patc.zip (PA)
10.30 - 11.00
Break
10.30 - 11.00
Break
11.00 - 11.45
Atomistic MD Algorithm (JLG)
11.00 - 11.45
MD a la carte (FC)
11.45 - 12.30
Algorithm improvements & HPC (JLG)
11.45 - 12.30
Introduction coarse-grained simulations (PDD)
12.30 - 14.00
Break
12.30 - 14.00
Break
14.00 - 15.30
Simulation Setup (FB)
14.00 - 15.00
Trajectory visualization (AH)
15.30 - 16.30
Break
15.00 - 16.00
Trajectory analysis (AH)
16.30 - 18.00
Setup and Analysis Hands On (AH)
16.00 - 16.30
Break
16.30 - 18.00
Survey and Report Writting
JLG: Josep Ll. Gelpi (BSC - IRB - UB)
FC: Francesco Colizzi (IRB)
PA: Pau Andrio (BSC)
FB: Federica Batistini (IRB - UB)
AH: Adam Hospital (IRB)
PDD: Pablo Dans (UDELAR - IP - IRB)
Event types:
- Workshops and courses
Activity log
