Supercomputing Frontiers Europe 2022

SCFE20 ICM Seminar Computational Developmental Biology
19th October, 2020

Virtual ICM Seminar with Ivo F. Sbalzarini: “Computational Developmental Biology”

3D microscopy Bioinformatics genetics genomics Ivo F. Sbalzarini Machine Learning Numerical Simulations Parallel Computing systems biology Virtual ICM Seminars Virtual Reality (VR)

The lecture on scientific computing for systems biology is opening the new series of ICM (virtual) seminars on significant developments and problems in computer and computational science. Save the date on October 22nd 2020.

The Virtual ICM Seminar with prof. Sbalzarini will take place on Thursday, October 22, 2020 (4 pm CEST) and is open for all. The free registration ticket is available here. The organizer of the lecture is the Interdisciplinary Centre for Mathematical and Computational Modelling (ICM) University of Warsaw.

The seminar is especially aimed at students and researchers involved in bioinformatics and systems biology, as well as genetics and genomics, and new methods of discovery critical in those studies: Machine Learning, Numerical Simulations and Parallel Computing, Virtual Reality (VR) and visualization in real time for 3D microscopy.


Our vision is to develop a computer simulation of a developing embryo, incorporating the known biochemistry and biophysics into a computational model in 3D-space and time, which predicts the emerging shape and function of the tissue. Development and morphogenesis of tissues, organs, and embryos emerges from the collective self-organization of cells that communicate though chemical and mechanical signals. Decisions about growth, division, and migration are taken locally by each cell based on the collective information. In this sense, a developing tissue is akin to a massively parallel computer system, where each cell computes robust local decisions, integrating communication with other cells.

Mechanistically understanding and reprogramming this system is a grand challenge. While the “hardware” (proteins, lipids, etc.) and the “source code” (genome) are increasingly known, we known virtually nothing about the algorithms that this code implements on this hardware. Using examples from our work, I highlight computational challenges along the way. These range from content-adaptive data representations for machine learning, to novel languages for parallel high-performance computing, to virtual reality and real-time visualization for 3D microscopy and numerical simulations of nonlinear and non-equilibrium mechanical models. This cooperative interdisciplinary effort contributes to all involved disciplines.

Ivo Sbalzarini is the Chair of Scientific Computing for Systems Biology on the faculty of computer science of TU Dresden, a professor of mathematics at TU Dresden, and director of the TUD-Department in the Center for Systems Biology Dresden. He also is a permanent Senior Research Group Leader with the Max Planck Institute of Molecular Cell Biology and Genetics in Dresden.


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Virtual ICM Seminars in Computer and Computational Science are a continuation of the Supercomputing Frontiers Europe conference, which took place virtually in March this year.

Worldwide Open Science online meetings in HPC, Artificial Intelligence, Quantum Computing, BigData, IoT, computer and data networks are a place to meet and discuss with such personalities as Stephen Wolfram (Founder & CEO, Wolfram Research), Alan Edelman (MIT), Aneta Afelt (ICM, Espace-DEV, IRD Montpellier France), Simon Mutch (University of Melbourne) or Scott Aaronson (University of Texas at Austin). For the listing of all ICM seminars please check this link with recordings.

So far, over 2,000 people from all over the world have participated in both initiatives. The organizer of meetings with outstanding scientists is the Interdisciplinary Centre for Mathematical and Computational Modelling – ICM University of Warsaw.