Marian Bubak

Cyfronet LMiM Team Leader

Projects

An Ecosystem for DIgital Twins in Healthcare

Mission EDITH is a Coordination and Support Action (CSA), funded by the European Commission, which will capitalise on the developments of digital technologies, high performance computing, availability and access to research and healthcare data in Europe, with the mission of defining a roadmap to go from separated single organ systems, to data-driven and knowledge-driven fully integrated multiscale and multiorgan whole-body twin.

CECM Teaming for Excellence

The project will develop a Business Case to establish in Poland Europe’s first Centre for simulation-driven healthcare Decision Support.

Centre for New Methods in Computational Diagnostics and Personalised Therapy

Sano Centre, created in Kraków, Poland, in the framework of Teaming for Excellence Phase 2 action, as well as the FNP International Research Agendas competition and with a financial support from the Polish Ministry of Science and Higher Education, will be a major driver for European advancement in rapidly growing field of computational medicine, developing sophisticated engineering methods for the prevention, diagnosis and treatment of disease, and meeting the overarching worldwide need for radically streamlined healthcare systems.

PRedictive In-silico Multiscale Analytics to support cancer personalized diaGnosis and prognosis, Empowered by imaging biomarkers

PRIMAGE proposes a cloud-based platform to support decision making in the clinical management of malignant solid tumours, offering predictive tools to assist diagnosis, prognosis, therapies choice and treatment follow up.

PROviding Computing solutions for ExaScale ChallengeS

The PROCESS demonstrators will pave the way towards exascale data services that will accelerate innovation and maximise the benefits of these emerging data solutions.

Competence Center for Distributed Grid Computing Infrastructures

The main objective of the PLGrid Core project is further, significant extension of the PL-Grid Infrastructure computing resources, especially in ACC Cyfronet AGH, as a specialized competence centre in the field of distributed computing infrastructures, with particular emphasis on grid technologies, cloud computing and platforms supporting computations on big data.

DevelOpment of GRID Environment for InteRaCtive ApplicationS

The CrossGrid project was oriented towards compute- and data-intensive applications characterized by the interaction with a person in a processing loop.

Diagnostics of gliomas based on circulating cell-free tumor DNA

Gliomas are incurable despite progress in surgery, radiotherapy and chemotherapy. Specific diagnosis of the type of glioma, early detection of molecular progression, characterization of critical mutations or epigenetic characteristics in individual patient give hope to improve treatment results.

Domain-oriented services and resources of Polish Infrastructure for Supporting Computational Science in the European Research Space

PLGrid Plus project served Polish scientific communities enabling extensive cooperation among them, as well as international cooperation in the scope of research activities in the area of e-Science.

European research network on foundations, software infrastructures and applications for large scale distributed, grid and peer-to-peer technologies

The European Research Network on Foundations, Software Infrastructures and Applications for large scale distributed, GRID and Peer-to-Peer Technologies.

GRid enabled access to rich mEDIA content

Grid technology has achieved significant advances in the past few years with a plethora of prestigious organisations contributing to middleware that opens the horizons for new exploitation opportunities.

ICT for environmental services and climate change adaptation

The mission of the UrbanFlood project was investigating the use of sensors within flood embankments to support an online early warning system, real time emergency management and routine asset management.

Knowledge is power, especially in industry

PaaSage delivers an open and integrated platform to support model based lifecycle management of Cloud applications.

Knowledge-based Workflow System for Grid Applications

The Knowledge-based Workflow System for Grid Applications (K-Wf Grid) project addressed the need for a better infrastructure for the future Grid environment.

Multiscale Applications on European e-Infrastructures

The MAPPER project responded to the critical need by developing computational strategies, software and services for distributed multiscale simulations across disciplines, exploiting existing and evolving European e-Infrastructure.

Personalised Decision Support for Heart Valve Disease

EurValve will implement, test and validate a modelling based decision support system (DSS) for aortic and mitral valve diseases that allows simulating, comparing and understanding the effects (outcomes) and risks of different treatment strategies.

Polish Infrastructure for Information Technology Support of Science in the European Research Area

The goal of the PL-Grid project was to provide the Polish scientific community with an IT supercomputing platform and a set of advanced tools to enable e-science research in various fields.

ViroLab: A virtual laboratory for decision support in viral diseases treatment

The ViroLab Project developed a virtual laboratory for research in the area of infectious diseases.

Virtual Physiological Human: Sharing for Healthcare - A Research Environment

VPH-Share develops the organisational fabric and integrates optimized services to:

Heterogeneous Exascale Computing

In Levente Kovács, Tamás Haidegger & Anikó Szakál: Recent Advances in Intelligent Engineering: Volume Dedicated to Imre J. Rudas’ Seventieth Birthday. 6 81--110. Cham: Springer International Publishing https://doi.org/10.1007/978-3-030-14350-3_5. ISBN: 978-3-030-14350-3

Towards a European Health Research and Innovation Cloud (HRIC)

Genome Medicine, 122 (1) 18. https://doi.org/10.1186/s13073-020-0713-z

Application of Continuous Time Quantum Walks to Image Segmentation

In João M. F. Rodrigues, Pedro J. S. Cardoso, Jânio Monteiro, Roberto Lam, Valeria V. Krzhizhanovskaya, Michael H. Lees, Jack J. Dongarra & Peter M.A. Sloot: Computational Science – ICCS 2019. 1 17--30. Cham: Springer International Publishing https://doi.org/10.1007/978-3-030-22741-8_2. ISBN: 978-3-030-22741-8

Exascale Computing and Data Architectures for Brownfield Applications

2018 14th International Conference on Natural Computation, Fuzzy Systems and Knowledge Discovery (ICNC-FSKD). 1 450--457. https://doi.org/10.1109/FSKD.2018.8686900

Composing, Execution and Sharing of Multiscale Applications

Future Generation Computer Systems, 532 77--87. https://doi.org/10.1016/j.future.2015.06.002

Teaching Quantum Computing with the QuIDE Simulator

Procedia Computer Science, 512 1724--1733. https://doi.org/10.1016/j.procs.2015.05.374

Towards A Novel Environment for Simulation of Quantum Computing

Computer Science, 162 (1) 103--103. https://doi.org/10.7494/csci.2015.16.1.103

Applying Workflow as a Service Paradigm to Application Farming

Concurrency and Computation: Practice and Experience, 262 (6) 1297--1312. https://doi.org/10.1002/cpe.3073

Cost Optimization of Execution of Multi-Level Deadline-Constrained Scientific Workflows on Clouds

In Roman Wyrzykowski, Jack Dongarra, Konrad Karczewski & Jerzy Waśniewski: Parallel Processing and Applied Mathematics. 1 251--260. Berlin, Heidelberg: Springer https://doi.org/10.1007/978-3-642-55224-3_24. ISBN: 978-3-642-55224-3

Secure Storage and Processing of Confidential Data on Public Clouds

In Roman Wyrzykowski, Jack Dongarra, Konrad Karczewski & Jerzy Waśniewski: Parallel Processing and Applied Mathematics. 1 272--282. Berlin, Heidelberg: Springer https://doi.org/10.1007/978-3-642-55224-3_26. ISBN: 978-3-642-55224-3

Distributed Computing on an Ensemble of Browsers

IEEE Internet Computing, 172 (05) 54--61. IEEE Computer Society https://doi.org/10.1109/MIC.2013.3

Evaluation of Cloud Providers for VPH Applications

2013 13th IEEE/ACM International Symposium on Cluster, Cloud, and Grid Computing. 1 200--201. https://doi.org/10.1109/CCGrid.2013.54

MapReduce Operations with WS-VLAM Workflow Management System

Procedia Computer Science, 182 2599--2602. https://doi.org/10.1016/j.procs.2013.05.449

OIntEd: Online Ontology Instance Editor Enabling a New Approach to Ontology Development

Software: Practice and Experience, 432 (11) 1319--1335. https://doi.org/10.1002/spe.2141

Support for Multiscale Simulations with Molecular Dynamics

Procedia Computer Science, 182 1116--1125. https://doi.org/10.1016/j.procs.2013.05.277

The Collage Authoring Environment: From Proof-of-Concept Prototype to Pilot Service

Procedia Computer Science, 182 769--778. https://doi.org/10.1016/j.procs.2013.05.241

Component-Based Approach for Programming and Running Scientific Applications on Grids and Clouds

The International Journal of High Performance Computing Applications, 262 (3) 275--295. SAGE Publications Ltd STM https://doi.org/10.1177/1094342011422924

Computations of Protein Hydrophobicity Profile as Virtual Experiment in Gridspace Virtual Laboratory

Bio-Algorithms and Medical-Systems, 82 (4) 361--372. De Gruyter https://doi.org/10.1515/bams-2012-0026

Constructing Workflows from Script Applications

Scientific Programming, 202 (4) 359--377. IOS Press https://doi.org/10.3233/SPR-120358

Flexible and Extendable Mechanism Enabling Secure Access to E-Infrastructures and Storage of Confidential Data for the GridSpace2 Virtual Laboratory

In Marian Bubak, Tomasz Szepieniec & Kazimierz Wiatr: Building a National Distributed E-Infrastructure–PL-Grid: Scientific and Technical Achievements. 6 89--101. Berlin, Heidelberg: Springer https://doi.org/10.1007/978-3-642-28267-6_7. ISBN: 978-3-642-28267-6

Implementation of Service Level Management in PL-Grid Infrastructure

In Marian Bubak, Tomasz Szepieniec & Kazimierz Wiatr: Building a National Distributed E-Infrastructure–PL-Grid: Scientific and Technical Achievements. 6 171--181. Berlin, Heidelberg: Springer https://doi.org/10.1007/978-3-642-28267-6_13. ISBN: 978-3-642-28267-6

Managing Entire Lifecycles of E-Science Applications in the GridSpace2 Virtual Laboratory – From Motivation through Idea to Operable Web-Accessible Environment Built on Top of PL-Grid e-Infrastructure

In Marian Bubak, Tomasz Szepieniec & Kazimierz Wiatr: Building a National Distributed E-Infrastructure–PL-Grid: Scientific and Technical Achievements. 6 228--239. Berlin, Heidelberg: Springer https://doi.org/10.1007/978-3-642-28267-6_18. ISBN: 978-3-642-28267-6

Scripting Language Extensions Offered by the GridSpace Experiment Platform

In Marian Bubak, Tomasz Szepieniec & Kazimierz Wiatr: Building a National Distributed E-Infrastructure–PL-Grid: Scientific and Technical Achievements. 6 217--227. Berlin, Heidelberg: Springer https://doi.org/10.1007/978-3-642-28267-6_17. ISBN: 978-3-642-28267-6