[ONLINE] PATC: Short course on HPC-based Computational Bio-Medicine

Tuesday 16th of February 2021: HPC-basics track

• 10:00-14:00hs CET. C. Teijeiro-Barjas (SURFsara) & Okba Hamitou (Atos). “First steps in the HPC environment”. This training provides information and tutorials about how to access and perform basic actions on a supercomputer. This session covers a wide range of topics: some theoretical aspects such as the description of the processor architecture, the several levels of code parallelization, and practical aspects such as the batch scheduler usage, compilation and optimization guidelines towards good performance achievements.

Wednesday 17th of February 2021: Molecular medicine track

• 10:00-12:55hs CET.  Andrea Townsend-Nicholson (UCL) & Art Hoti (UCL). “Molecular Medicine”. This workshop in molecular medicine aims to provide participants with a theoretical understanding of the importance of the relationship between human microbiomes – the microorganisms present in and on the human body – and human health and with the practical opportunity to use state of the art computational resources to run a metagenomics pipeline. Using marker gene abundance data and the QIIME2 computational workflow, the identity of the different bacterial taxa present in Next Generation Sequence data obtained from medically-relevant microbiome samples will be obtained and the statistical significance of the experimental hypothesis determined.
• 13:05-14:00hs CET. Alexander Heifetz (Evotec). “Introduction to Computer-Aided Drug Design (CADD)”. The subject of my presentation is application computer-aided drug design (CADD) methods in drug design. CADD is the application of computer modelling techniques to drug design process. I will provide a brief overview of these CADD approaches illustrated by the examples taken from real drug discovery campaigns. In my presentation, I will cover the basic theory behind these methods and describe various techniques like virtual screening, homology modeling, docking, structure- and ligand- based drug design, fragment-molecular orbital (FMO) quantum mechanics analysis of protein-water-ligand interactions, GPCR modeling, structure-activity analysis (SAR) and artificial intelligence/deep learning.

Thursday 18th of February 2021: Computational Mechanics track

• 10:00hs-11:55hs CET. David Oks(BSC) & Cristobal Samaniego(BSC). “Fluid-Structure Interaction methods for biomechanics”. During this hands-on course, different approaches for modelling fluid-structure interaction (FSI) couplings will be explored. The working principles of both boundary-conforming and immersed methods will be introduced in order to understand the benefits of using one or another in diverse applications. Relevant aspects of high-performance computing (HPC) will also be discussed during the course. Practical exercises will be carried out using Alya, a multi-physics HPC code developed at BSC designed from scratch to run efficiently on supercomputers. We will be running simulations on Marenostrum 4, BSC's supercomputer, in order to get familiarised with an HPC server environment.
• 12:05-14:00hs. Gabor  Zavodszky (UvA). “Zoom in on blood - Using supercomputers for blood flow simulations”. 1 mm^3 of human blood, that is less than a single drop, contains about 5 million cells. The interaction and deformation of these cells give rise to the unique properties of blood. Modern biomedical research (e.g. on drug delivery, effect of various diseases such as diabetic cells or sickle cell disease) builds on this information. Unravelling detailed biomechanical and rheological processes in flowing blood requires an accurate modelling of these deformable cells and the surrounding fluid on microscopic level. In this lecture an open-source package (www.hemocell.eu) will be discussed that on one hand allow us to model the behaviour of single cells accurately, and on the other hand can scale up to the level of large flows with millions of cells.

Friday 19th of February 2021: Visualization and life sciences

• 10:00-11:55hs CET. Eduardo Graells (BSC). “Effective Communication through Visualization”. In this talk we will learn methods and tools to create effective and coherent visualizations that deliver a message from your experimental results, where effective refers to the optimal usage of visual elements to encode information, and coherent refers to ensuring a rightful interpretation of our work.
• 12:05-13:30hs CET. Alfonso Valencia (BSC, PerMedCoE). “Personalised Medicine Centre of Excellence: how can HPC cell-level simulations help us fight against cancer and COVID”