Short course on HPC-based Computational Bio-Medicine @ BSC

Room S208 (Barcelona BSC Campus Nord)

Room S208

Barcelona BSC Campus Nord

Vertex Building

The registration to this course is now open. Please, bring your own laptop. All the PATC courses at BSC are free of charge.

Course convener: Mariano Vazquez and Ruth Aris

Lecturers: Mariano Vázquez (BSC), Marco Verdicchio (SURFsara), Okba Hamitou (Bull), Gábor Závodszky (UvA), João Damas (ACELLERA), Adrià Perez (UPF), Phil Tooley (USFD), Ricard Borrell (BSC), Jazmín Aguado-Sierra (BSC), Dr Alexander Heifetz (EVOTEC), Andrea Townsend-Nicholson (UCL), Guillermo Marín (BSC) and Paul Melis (SURFsara)

Objectives:The objetive of this course is to give a panorama on the use of HPC-based computational mechanics in Engineering and Environment through the projects BSC are carrying on. This panorama includes the basics of what is behind the main tools: computational mechanics and parallelization. The training is delivered in collaboration with the center of excellence CompBioMed.

Learning outcomes: The course gives a wide perspective and the latest trends of how HPC helps in industrial, clinical and research applications allowing to achieve more realistic multiphysics simulations.  In addition, the student has the opportunity of running Jobs in Marenostrum supercomputer.

Level: INTERMEDIATE: For trainees with some theoretical and practical knowledge


Day 1 (Feb. 13)

Session 1 / 9:00am – 1:00 pm (4 h lectures)

9:00-9:15 Welcome (Mariano Vázquez, BSC)

9:15-11:00 Introduction to HPC in Computational Modelling (Marco Verdicchio, SURFsara)

11:00-13:00 Compilation and Optimization in the HPC environment (Okba Hamitou, Bull)

13:00-14:00 Lunch Break

Session 2 / 2:00pm – 6:00 pm (4 h lectures)

14:00-16:00 Zoom in on blood - Using supercomputers in hemodynamics (UvA) (Gábor Závodszky, UvA)

16:00-18:00 PlayMolecule: Cloud-based Applications for Molecular Discovery (João Damas, ACELLERA, Adrià Perez, UPF)


Day 2 (Feb. 14)

Session 3 / 9:00am – 1:00 pm (4 h lectures)

9:00-11:00 Hands on Image Registration with pFIRE (Phil Tooley, USFD)

11:00-12:00 Parallel algorithms for Computational Mechanics (Ricard Borrell, BSC)

12:00-13:00 HPC Multi-scale computational modelling using Alya Red (Jazmín Aguado-Sierra, BSC)

13:00-14:00 Lunch Break

Session 4 / 2:00pm – 6:00 pm (2 h lectures, 2 h practical)

14:00-15:00 Introduction to Computer-Aided Drug Design (CADD) and GPCR Modelling (Dr Alexander Heifetz, EVOTEC)

15:00-16:00 Innovations in HPC-training for medical, science and engineering students (Andrea Townsend-Nicholson, UCL)

16:00-18:00 Molecular Medicine: Hands On (Andrea Townsend-Nicholson, UCL)


Day 3 (Feb. 15)

Session 5 / 9:00am – 1:00 pm (4 h lectures)

9:00-10:00 Data Visulization for Researchers Crash Course (Guillermo Marín, BSC)

10:00-12:00 Visualization applied to 2D/3D scientific datasets (Paul Melis, SURFsara)

12:00-13:00 Molecular Medicine (UCL)

13:00-14:00 Lunch Break

Session 6 / 2:00pm – 4:00 pm

14:00-16:00 Visit to MareNostrum





The agenda of this meeting is empty