8:45 - 9:00
9:00 - 9:40
Session Chair: Enrico Gobbetti, CRS4
9:00 - 9:25
Giacomo Cao, CRS4
Francesco Mola, Università di Cagliari
9:25 - 9:40
Introduction and program overview
9:40 - 11:00
SESSION 1: COMPUTATIONAL MODELING AND SIMULATION
Session Chair: Giorgio Fotia, CRS4
9:40 - 10:20
Mathematical models for the heart and the circulation
Politecnico di Milano and Ecole Polytechnique Fédérale de Lausanne
Abstract: Mathematical models based on first principles can describe the interaction between electrical, mechanical and fluid-dynamical processes occurring in the heart, as well as the coupling with the external circulation. This is a classical multi-physics problem featuring multi-scale solutions in space and time. Appropriate numerical strategies need to be devised to allow for an accurate and computationally effective simulation of these processes in both physiological and pathological regimes. This presentation will address some of these issues and a few representative applications of clinical interest. The work presented in this talk is part of the project iHEART that has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (grant agreement No 740132).
Speaker: Alfio Quarteroni is professor of Numerical Analysis at the Politecnico di Milano and professor emeritus at the EPFL (Swiss Federal Institute of Technology). Previously, he has been Researcher at the CNR (the Italian Research Council), professor at the University of Minnesota, Minneapolis, and Scientific Director of CRS4 (Cagliari, Sardinia). He is member of the Italian Academy of Science, the European Academy of Science, the Academia Europaea and the Lisbon Academy of Science. He received the NASA Group Achievement Award in 1992, the International Galileo Galilei prize for Sciences 2015, the doctorate Honoris Causa in Naval Engineering from University of Trieste, Italy, 2003; he is the Recipient of the Galileian Chair from the Scuola Normale Superiore, Pisa, Italy ,2001. He is author of 25 books, editor of 7 books, author of more than 350 papers published in international Scientific Journals and Conference Proceedings, member of the editorial board of 25 International Journals and Editor in Chief of two book series published by Springer. His research interests concern the application of Mathematical Modeling, Numerical Analysis and Scientific Computing to: fluid mechanics, geophysics, medicine and the improvement of sports performance. His group created and ran the mathematical simulation for the optimisation of performances of the Alinghi yacht, the winner of two editions (2003 and 2007) of the America's Cup.
10:20 - 11:00
Challenges in the multiscale analysis of multiphase flow
Institut Jean Le Rond d'Alembert, UMR7190, Sorbonne Université & CNRS, Paris, France
Abstract: I shall describe Direct Numerical Simulations (DNS) of multiphase flows using the Volume Of Fluid method (to which my collaboration with Gianluigi Zanetti gave an impulse in the 1990s), with particular emphasis on two phenomena: a large-scale, large-Reynolds case, the atomization of liquid jets, and a small-scale case, the moving contact line. For atomization, we extended a lot of efforts on the quasi planar setup of the Grenoble group to shed light on the statistics of droplet formation and the log-normal distribution observed, I will also describe an attempt to model the contact line, compared to the result of molecular dynamics.
Speaker: Stéphane Zaleski is Professor at Sorbonne Université in the Jean Le Rond d'Alembert Institute. He studied for his doctorate at the Physics Department of Ecole Normale Supérieure in Paris. He investigates various numerical methods for the simulation of multiphase flow with applications for atomization, cavitation, porous media flow, boiling, hydrometallurgy and droplet impact. The methods incorporate several variants of the Volume of Fluid method for interface tracking and the phase-field method for diffuse interfaces.
11:00 - 11:20
11:20 - 13:20
SESSION 2: DATA-INTENSIVE COMPUTING AND SCALABLE DATA ANALYSIS
Session Chair: Luca Pireddu, CRS4
11:20 - 12:00
OME’s Bio-Formats, OMERO, & IDR: Making BioImage Data FAIR on a Global Scale
Jason R. Swedlow
Centre for Gene Regulation and Expression, University of Dundee, UK ; Glencoe Software, Seattle, USA and Dundee, UK
Abstract: Despite significant advances in biological imaging and analysis, major informatics challenges remain unsolved: file formats are proprietary, storage and analysis facilities are lacking, as are standards for sharing image data and results. The Open Microscopy Environment (OME) is an open-source software framework developed to address these challenges by releasing specifications and software for managing image datasets and integrating them with other scientific data. OMEs Bio-Formats and OMERO are used in 1000’s of labs worldwide to enable discovery with imaging. We have used Bio-Formats and OMERO to build solutions for sharing and publishing imaging data. The Image Data Resource (IDR) includes image data linked to over 60 independent studies from genetic, RNAi, chemical, localisation and geographic high content screens, super-resolution microscopy, single cell profiling, light sheet microscopy of developing organisms and tissues, and digital pathology. Datasets range from several GBs to tens of TBs. Wherever possible, we have integrated image data with all relevant experimental, imaging and analytic metadata. These annotations make it possible to re-use IDR data, and to connect independent imaging datasets by molecular perturbations and phenotypes. We have also built cloud-based analysis tool portals to catalyse the re-use and re-analysis of published imaging data. These include notebooks and Docker containers that package well-known tools like ImageJ/Fiji, CellProfiler and Ilastik, making it is easy for anyone to view and interact with public data in IDR. We are now using notebooks to explore the phenotypes recorded in IDR data, and link them to genes and drugs used to target specific pathways in IDR data. I will include a few memories of the joy of working with Gianluigi on these critical, engaging problems.
Speaker: Jason Swedlow earned a BA in Chemistry from Brandeis (1982) and PhD in Biophysics from UCSF (1994). After postdocs at UCSF and Harvard, he established his laboratory at Dundee, focussed on mitotic chromosome dynamics and cell and tissue imaging informatics (1998). He was awarded several prestigious fellowships and named Professor of Quantitative Cell Biology (2007). He founded the Open Microscopy Environment (OME) and Glencoe Software, Inc. His awards include BBSRC's Innovator of the Year (2011) and Fellow of the Royal Society of Edinburgh (2012).
12:00 - 12:40
Provenance information in medical research - quest for dealing with reproducibility issues
Masaryk University, Czech Republic; BBMRI-ERIC, Austria
Abstract: Medical research is known to be plagued with reproducibility issues in the last two decades, raising substantial concerns about effectiveness of research funding flowing into the domain (estimates being 50-90% of research being not reproducible). Research infrastructures play central role to change this as they act as guardians of the biological material and data to be shared for medical research purposes. In 2016, together with Gianluigi Zanetti, Jörg Geiger, and Heimo Müller, we have started work on developing a common machine-readable and machine-actionable model of provenance information, that is able to describe the complete history of biological data, including provenance that spans multiple organizations. This activity has been adopted by ISO TC/276 (Biotechnology) WG5 (Data Integration) and we are striving to make it an international standard, so that vendors of hardware and software used for laboratory automation and data generation can adopt and automate generation of provenance information. This talk will summarize state of the development of the standard and anticipated outlook of its applications.
Speaker: Petr Holub, Ph.D., is an Associate Professor of computer science at Masaryk University, in the Czech Republic. Since 2015, he has been Senior IT/Data Protection Manager with BBMRI-ERIC. Since 2011, he has also been responsible for the IT infrastructure of the Czech BBMRI. He is a co-founder of Comprimato Systems company, which develops and commercializes research results in acceleration of compression algorithms. Previously, he was head of the Division of Communication Technologies at the Institute of Computer Science in Masaryk University, architect of advanced multimedia and collaborative systems of the Czech national e-infrastructure operated by CESNET, and chief architect and team leader of the UltraGrid high-performance media processing and distribution framework, which received Best Open-Source Software Award by ACM Multimedia SIG. He has been a contributor to a number of international and national projects linking computer science and biomedicine, such as EU ITHANET or MediGrid, as well as a number of other international computer science oriented projects such as EU GridLab, EU CoreGRID.
12:40 - 13:20
Electroencephalographic (EEG) signals in pharmaco-resistant epilepsy after Vagus Nerve Stimulation (VNS) treatment: a computational approach
Faculty of Medicine, University of Cagliari, Italy
Abstract: The treatment of epilepsy, despite the impetuous advancement of neurosciences, remains an excruciating unsolved problem. Indeed, more than 30% of epileptic subjects are pharmacoresistant. The Vagus Nerve Stimulation (VNS) is a low-impact surgical solution which improves the incidence of episodes and their severity, though its mechanism of action is still unclear. In a collaborative study, Santoni and Zanetti from CRS4 calculated the modifications of EEG signals recorded in Clinical Neurology, University of Cagliari, in a population of epileptic patients treated with VNS. The results obtained show that the EEG signals were already modulated towards a physiological pattern in subjects successfully treated. By suggesting a relationship between VNS and EEG for the first time, this work paved the way for the most recent studies on the modifications of brain networks and VNS.
Speaker: Professor of Neurology at the Faculty of Medicine University of Cagliari (2000-2017). Main field of research: epilepsy, neurophysiology of sleep, degenerative diseases
13:20 - 15:00
15:00 - 15:20
APERTURA E SALUTI
Session Chair: Enrico Gobbetti, CRS4
15:00 - 15:10
Saluti istituzionali e apertura lavori pomeridiani
Giacomo Cao, CRS4
Francesco Mola, Università di Cagliari
15:10 - 15:20
15:20 - 16:20
SESSION 3: INNOVAZIONE E TRASFERIMENTO TECNOLOGICO
Session Chair: Francesca Frexia, CRS4
15:20 - 15:40
Ricerca industriale in automazione e tracciabilità dei processi clinici per migliorare i percorsi di diagnosi e cura
Speaker: Andrea Costaglioli è Direttore dell’Innovation Hub di Inpeco.
15:40 - 16:00
La telemedicina tra ricerca e pratica clinica: l'esperienza per la Cardiologia Pediatrica
ARNAS "G. Brotzu"
Speaker: Roberto Tumbarello è Direttore della Struttura Complessa Cardiologia Pediatrica e Cardiopatie Congenite, ARNAS "G. Brotzu" (Cagliari)
16:00 - 16:20
Next Generation Pathology meets Next Generation Microbiology
Facoltà di Medicina e Chirurgia, Università degli Studi di Sassari
Speaker: Sergio Uzzau è Professore di Microbiologia e Microbiologia Clinica alla Facoltà di Medicina e Chirurgia dell'Università di Sassari.
16:20 - 16:40
16:40 - 18:00
SESSION 4: INCIDENTALLY...
Session Chair: Andrea Giachetti, University of Verona
16:40 - 17:30
By the way...
Short talks with personal memories. / Brevi interventi con ricordi personali.
17:30 - 18:00
Open mic session. / Microfono aperto.
18:00 - 18:20