Projects full descriptions

Project details

Duration: From 1.12.2018 to 30.11.2022
Topic:  SC1-DTH-07-2018

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. This will be based on the use of novel imaging biomarkers, in silico tumour growth simulation, advanced visualisation of predictions with weighted confidence scores and machine-learning based translation of this knowledge into predictors for the most relevant, disease-specific, Clinical End Points.

PRIMAGE implements a hybrid cloud model, comprising the of use of open public cloud (based on EOSC services) and private clouds, enabling use by the scientific community (facilitating reuse of de-identified clinical curated data in Open Science) and also suitable for future commercial exploitation. The proposed data infrastructures, imaging biomarkers and models for in silico medicine research will be validated in the application context of two paediatric cancers, Neuroblastoma (NB, the most frequent solid cancer of early childhood) and the Diffuse Intrinsic Pontine Glioma (DIPG, the leading cause of brain tumour-related death in children). These two paediatric cancers are relevant validation cases given their representativeness of cancer disease, and their high societal impact, as they affect the most vulnerable and loved family members.

The European Society for Paediatric Oncology, two Imaging Biobanks and three of the most prominent European Paediatric oncology units are partners in this project, making retrospective clinical data (imaging, clinical, molecular and genetics) registries accessible to PRIMAGE, for training of machine learning algorithms and testing of the in silico tools´ performance. Solutions to streamline and secure the data pseudonymisation, extraction, structuring, quality control and storage processes, will be implemented and validated also for use on prospective data, contributing European shared data infrastructures.

Cyfronet tasks

The Cyfronet team will be involved directly in development, integration and support for high-performance execution environment for large-scale multi-model simulations. This solution will be provisioned by our team to the consortium members using the PLGrid Infrastructure for e-Science, and specifically, the Prometheus supercomputer. We will assist our partners in efficient usage of computational power and disk storage, and we will perform integration of Cyfronet tools and solutions with these provided by other technology providers within the project.

PRIMAGE Partners

• Instituto de Investigación Sanitaria La Fe
• Quibim SL
• Medexprim
• Konstanz University
• Universita di Pisa
• Universidad de Zaragoza
• The University of Sheffield
• Ansys France
• Matical Innovation SL
• St. Anna Kinderkrebsforschung e.V.
• Children´s Cancer Research Institute
• Uniklinik Koeln
• The European Society for Paediatric Oncology
• Institute for instrumentation on molecular imaging UPV-CSIC
• ACC Cyfronet AGH
• Chemotargets SL
• University of Bologna

PRIMAGE Papers

• 5 members of DICE Team are co-authors of a paper on the PRIMAGE project published in the European Radiology Experimental journal: Martí-Bonmatí, L., Alberich-Bayarri, Á., Ladenstein, R. et al.: PRIMAGE project: predictive in silico multiscale analytics to support childhood cancer personalised evaluation empowered by imaging biomarkers. Eur Radiol Exp 4, 22 (2020). https://doi.org/10.1186/s41747-020-00150-9

PRIMAGE Presentations

• M. Kasztelnik: Metody i narzędzia wspierające złożone symulacje na infrastrukturach HPC, presented at the Cyfronet Open Day in Krakow, Poland, 21.11.2022
• M. Kasztelnik, T. Gubała, P. Nowakowski, J. Meizner, P. Połeć, M. Malawski, M. Bubak: Reliable digital twin simulation development and execution on HPC infrastructures, presented at the VPH Conference, in Porto, Portugal, 6-9.09.2022
• K. Rycerz: Quantum Computing for HPC Problems, presented at the KU KDM 2022 conference, online, 7-8.04.2022

• M. Kasztelnik, T. Gubała, P. Nowakowski, J. Meizner, P. Połeć, M. Malawski, M. Bubak: High-level APIs for managing computations on the HPC systems, presented at the KU KDM 2022 conference, online, 7-8.04.2022
• Kasztelnik, M., Sosnowski, D., Nowakowski, P., Bubak, M.: Enabling organized computer simulations with patient cohort data, presented at CompBioMed Conference 2021, 15-17 September, 2021, https://cbmc21.vfairs.com/, talk available at https://www.youtube.com/watch?v=iZBmctHPBpE
• M. Bubak, M. Kasztelnik, J. Meizner, P. Nowakowski, T. Gubała, M. Malawski: Towards a Universal Platform for Large Scale Simulations on Prometheus (abstract, presentation), KUKDM 2020 Conference planned on 5-6.03.2020
• M. Bubak, T. Gubala, R. Hose, M. Kasztelnik, M. Malawski, J. Meizner, P. Nowakowski, S. Wood: Processing Complex Medical Workflows in the EurValve Environment, CompBioMed'19, London, UK, 25-27 September 2019
• M. Bubak, T. Gubala, M. Kasztelnik, M. Malawski, J. Meizner, P. Nowakowski: In quest for reproducibility of medical simulations on e-infrastructures, CompBioMed Workshop on Containers Technologies, Amsterdam, The Netherlands, 29.03.2019

First PRIMAGE Working Session, 28-30 April 2020

PRIMAGE Kick-off, Valencia, 19-20 December 2018

• ACC Cyfronet AGH, Krakow, PL - Distributed Computing Environments Team in PRIMAGE
• T2.3 (M1-M48) HPC Resources for PRIMAGE Simulations
• T2.5 (M1-M48) (HPC) User Interfaces and APIs
• T3.4 (M12-M36) Database for Clinical Data
• T5.6 (M13-M48) Integration with the HPC Execution Environment

PROCESS - PROviding Computing solutions for ExaScale ChallengeS

Duration: From 01.11.2017 to 31.10.2020
Topic: EINFRA-21-2017 Platform-driven e-infrastructure innovation

The PROCESS demonstrators will pave the way towards exascale data services that will accelerate innovation and maximise the benefits of these emerging data solutions. The main tangible outputs of PROCESS are five very large data service prototypes, implemented using a mature, modular, generalizable open source solution for user friendly exascale data. The services will be thoroughly validated in real-world settings, both in scientific research and in industry pilot deployments. To achieve these ambitious objectives, the project consortium brings together the key players in the new data-driven ecosystem: top-level HPC and big data centres, communities – such as Square Kilometre Array (SKA) project – with unique data challenges that the current solutions are unable to meet and experienced e-Infrastructure solution providers with an extensive track record of rapid application development. In addition to providing the service prototypes that can cope with very large data, PROCESS addresses the work programme goals by using the tools and services with heterogeneous use cases, including medical informatics, airline revenue management and open data for global disaster risk reduction. This diversity of user communities ensures that in addition to supporting communities that push the envelope, the solutions will also ease the learning curve for broadest possible range of user communities. In addition, the chosen open source strategy maximises the potential for uptake and reuse, together with mature software engineering practices that minimise the efforts needed to set up and maintain services based on the PROCESS software releases.

PROCESS Consortium

• LUDWIG-MAXIMILIANSUNIVERSITAET MUENCHEN LMU MUENCHEN, Germany
• UNIVERSITEIT VAN AMSTERDAM UvA, The Netherlands
• STICHTING NETHERLANDS ESCIENCE CENTER NLESC, The Netherlands
• HAUTE ECOLE SPECIALISEE DE SUISSE OCCIDENTALE HES-SO, Switzerland
• LUFTHANSA SYSTEMS GMBH & CO KG LSY, Germany
• INMARK EUROPA SA INMARK EUROPA, Spain
• USTAV INFORMATIKY, SLOVENSKA AKADEMIA VIED UISAV, Slovakia
• Cyfronet AGH Krakow, Poland

PROCESS Presentations

• M. Bubak, J. Meizner, P. Nowakowski, M. Bobák, O. Habala, L. Hluchý, V. Tran, A. S. Z. Belloum, R. Cushing, M. Höb, D. Kranzlmüller, J. Schmidt: A hybrid HPC and Cloud platform for multidisciplinary scientific application (abstract, poster, presentation - slides, recorded presentation), Supercomputing Frontiers 2020 Conference, 23-25.03.2020
• J. Kapała, J. Meizner, P. Nowakowski, P.Wójtowicz, M. Bubak, Running Workloads on the Prometheus Cluster with Singularity (abstract, presentation), KUKDM 2020 Conference planned on 5-6.03.2020
• M. Bubak, M. Kasztelnik, J. Meizner, P. Nowakowski, T. Gubała, M. Malawski: Towards a Universal Platform for Large Scale Simulations on Prometheus (abstract, presentation), KUKDM 2020 Conference planned on 5-6.03.2020
• J. Meizner, M. Bubak, J. Kapała, P. Nowakowski, P. Wójtowicz: PROCESS - Compute Platform, Workshop: Platform-driven e-infrastructure innovations, Amsterdam, The Netherlands, 29.10.2018

PROCESS Posters

• K. Rycerz, P. Nowakowski, J. Meizner, B. Wilk, J. Bujas, Ł. Jarmocik, M. Krok, P. Kurc, S. Lewicki, M. Majcher, P. Ociepka, L. Petka, K. Podsiadło, P. Skalski, W. Zagrajczuk and M. Zygmunt, M. Bubak: A Survey of Interactive Execution Environments for Extreme Large-Scale Computations (PPT, PDF), KU KDM'18, Zakopane, 7-9.03.2018

PROCESS Kick-off: Garching, 20-21 November 2017

• M. Bubak, J. Meizner and P. Nowakowski: Cyfronet AGH DICE Team in the PROCESS Project
• M. Bubak, J. Meizner and P. Nowakowski: Extreme Large Computing Service-oriented Infrastructure

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. It is planned to develop a comprehensive diagnostic test based on analysis of the material obtained from the tumor via surgery or biopsy (targeted NGS of 700 genes). The Gliomed project will elaborate a liquid biopsy-type method based on tumor cfDNA in blood, which could be a quick and minimally invasive alternative to biopsy. The additional aims of the study are: comprehensive molecular characteristics of tumor genome and transcriptome as well as use of 3-D in vitro glioma cultures, i.a., under hypoxic conditions for screening of the content of stem cells and assessment of cells susceptibility to therapy in the environment of neoplastic niche.

The results will contribute to better understanding of glioma biology, will allow identification of new molecular biomarkers, potential therapeutic targets and will provide a practical model to investigate a response to treatment under hypoxia. Molecular diagnostic test would improve treatment results by therapy individualization and liquid biopsy will improve safety, comfort and enable to monitor disease course and treatment in a new way.

Cyfronet tasks

The Cyfronet team will undertake a series of bioinformatics and biostatistics analyses on tumor data. Information acquired from MR imaging and NGS sequencing of glioma cases will be thoroughly investigated to give answer to a set of challenging questions related to this type of tumor. The result of these analyses, collaboratively conducted with other project partners, will be the new liquid biopsy test validation.

Cyfronet will also act as the provider of adequate data storage space and computational power, to match the requirements of large-scale analyses to be undertaken in the course of the project. The tools available in the PLGrid Infrastructure will help the Gliomed researchers in efficient management of research data and analysis results.

Partners

• Medical University of Silesia (Katowice)
• Medical University of Warsaw
• Nencki Institute of Experimental Biology, Polish Academy of Sciences (Warsaw)
• Academic Computer Centre Cyfronet AGH (Krakow)
• Regional Science and Technology Center (Podzamcze)
• Oncogene Diagnostics Sp. z o.o. (Krakow)

	Strategiczny program badań naukowych i prac rozwojowych "Profilaktyka i leczenie chorób cywilizacyjnych - STRATEGMED"
Projekt współfinansowany przez Narodowe Centrum Badań i Rozwoju w ramach strategicznego programu badań naukowych i prac rozwojowych "Profilaktyka i leczenie chorób cywilizacyjnych - STRATEGMED"

The project will develop a Business Case to establish in Poland Europe's first Centre for simulation-driven healthcare Decision Support. The Centre's mission comprises development of new computation-based solutions for diagnostics and therapy in daily healthcare to improve personalised patient treatment, enhanced growth of SMEs which deal with technologies and services for novel personalised diagnostics and treatment strategies, as well as strong advancement of algorithms, models and technologies involved in personalised medicine.

The project aims to develop a Business Plan establishing the Centre and enabling it to achieve measurable success through introduction of a number of solutions based on computational models to clinical trials, development of a number of new market-ready products and services based on innovations, authoring highly cited scientific papers, obtaining patents and securing grants.

The Plan will be based on the Polish Specialisation Strategy and will be elaborated by two Polish partners: ACC Cyfronet AGH (experts in simulation and computing infrastructures for science) and Klaster LifeScience Kraków (top cluster of industry, academia and hospitals in the life sciences domain), in collaboration with the University of Sheffield and Insigneo Institute (experts in translation of in silico modelling and simulations to clinics), Forschungszentrum Jülich (experts in innovative HPC and data techniques for science and industry) and Fraunhofer ISI (experts in systemic multi-domain solutions and innovation in medicine).

CECM Documents

• CECM - abstract in Polish
• CECM - Teaming - abstract for kick off
• Centre for New Methods in Computational Diagnostics and Personalised Therapy - an overview presentation

CECM Flyers

• Towards a Centre for New Methods in Computational Diagnostics and Personalised Therapy (PPT, PDF)

CECM Posters

• M. Bubak, T. Gubała, M. Malawski, and P. Nowakowski: A Centre for New Methods in Computational Diagnostics and Personalised Therapy (PPT, PDF), KU KDM'18, Zakopane, 7-9.03.2018
  

CECM Presentations and Interviews

• M. Bubak and R. Hose: Sano: Personalized Computational Medicine, Hearing of Sano in front of the EU expert panel, Brussels, 21.02.2019
• M. Bubak: Interview about CECM for Newseria, 19.12.2017
• M. Bubak: Interview about CECM for Radio Krakow, 9.12.2017
• M. Bubak: "From the grid medical consortium, through virtual labs and bioinformatic environments, to the center of excellence for personalized diagnostics and medical therapy", the ACC Cyfronet AGH Open Day, Krakow, 27.11.2017.

CECM Kick-off in media

• 5.09.2017 - AGH to compete for a 15 million Euro grant to establish a new centre for IT and medicine (article in Polish in Gazeta Wyborcza) (English version)
• 5.09.2017 - Engineers will help in treating patients (article in Polish in Dziennik Polski)
• 5.09.2017 - AGH to help diagnose and treat patients (article in Polish in Gazeta Krakowska) (English version)
• 5.09.2017 - A modern medical center can be established in Krakow (article in Polish in Polska Agencja Prasowa)
• 4.09.2017 - AGH is counting on the appreciation of the European Commission (article in Polish in LoveKraków.pl)

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. In addition, the DSS will improve knowledge of disease mechanisms by applying a holistic assessment of cardiovascular function that includes haemodynamic data at all cardiovascular compartments (ventricle, valve, vessels) and multiscale components that couple organ with cell function.
The Cyfronet AGH team is responsile for elaboration of the Model Execution Environment, in particular:

1. To develop and provide the necessary infrastructure to:

• Collect, represent, annotate and publish core homogeneous data
• Store and give secure access to the participating clinical centres and to the development partners to the necessary data
• Execute the models in the most appropriate computational environment (private workstation, private cloud, public cloud) according to needs
• Support real-time multiscale visualisation.

2. To develop an integrated security system supporting:

• Authentication and authorisation
• Data encryption for secure processing in public clouds

3. To deploy and operate the developed infrastructure, ensuring:

• Quality of software components deployed and installed
• Quality of service, including such aspects as availability, responsiveness and cost efficiency

New: EurValve Video

EurValve Reviews

• M. Bubak and M. Kasztelnik: EurValve: Personalised Decision Support for Heart Valve Disease, Final review of the EurValve H2020 project, the Catharina Ziekenhuis in Eindhoven, 27.03.2019
• WP2 presentation at the Review on 28.09.2017

Model Execution Environment

• MB-WP2-EurValve-PB-GA-Berlin-June-2017-v2.pptx
• EurValve-WP2-Demo-29-July-2017.pptx
• MB-WP2-EurValve-PB-Lyon-Feb-2017-v10.pptx
• EurValve-WP2-Portal_v3.docx
• EurValve-WP2-Security_v3.docx
• EurValve-WP2-FileStore_v3.docx

EurValve News

• DICE at the Cloud Services for Synchronisation and Sharing Workshop in Amsterdam , 31.01.2017
• EurValve project meeting at the ACC Cyfronet AGH, 14.01.2017

EurValve Presentations and Interviews

• M. Bubak, T. Gubala, R. Hose, M. Kasztelnik, M. Malawski, J. Meizner, P. Nowakowski, S. Wood: Infrastructure for Personalised Medicine: It’s MEE that Matters!, Computational Models for the Clinic: Cardiac/Cardiovascular Application, EurValve Workshop, 25.01.2019, Krakow, Poland
• M. Bubak: Towards the Center of Excellence for Personalized Diagnostics and Medical Therapy, Computational Models for the Clinic: Cardiac/Cardiovascular Application, EurValve Workshop, 25.01.2019, Krakow, Poland

• M. Bubak: Interview about EurValve for Newseria, 11.12.2017
• M. Bubak: Interview about EurValve for Radio Krakow, 9.12.2017
• M. Bubak, T. Bartynski, T. Gubala, D. Harezlak, M. Kasztelnik, M. Malawski, J. Meizner, P. Nowakowski: Towards Model Execution Environment for Investigation of Heart Valve Diseases, CGW Workshop 2016,  24-26.10.2016, Krakow, Poland

EurValve Posters

• M. Bubak, T. Bartynski, T. Gubala, D. Harezlak, M. Kasztelnik, M. Malawski, J. Meizner, P. Nowakowski: Towards Model Execution Environment for Investigation of Heart Valve Diseases, CGW Workshop 2016,  24-26.10.2016, Krakow, Poland

EurValve Movies

• MEE EurValve movies on YouTube

PLGrid Core Posters and Flyers

Negative feedback based simulations of bio-systems (2014) (PDF) J. Wach, M. Bubak, L. Konieczny, I. Roterman-Konieczna; poster presented during CGW Workshop'14; 27-29 October, 2014, Krakow, Poland.

PaaSage delivers an open and integrated platform to support model based lifecycle management of Cloud applications. The platform and the accompanying methodology allow model-based development, configuration, optimisation and deployment of existing and new applications, independently of the existing Cloud infrastructures.

DICE Team developed and integrated HyperFlow worklfow engine with PaaSage framework. With the use of CAMEL the HyperFlow engine, the worker nodes and application executables can be described in a single model, which can be deployed on multiple clouds. The deployed application scales automatically based on the scalability rules defined in CAMEL. The workflow engine was successfully demonstrated together with MD application from HLRS project partner.

Publications related to PaaSage.

Official project website http://www.paasage.eu/

PaaSage Presentations

• M. Malawski: Deployment of scientific workflows into containers with PaaSage, Workshop on Container Strategies for Data & Software Preservation that Promote Open Science, May 19-20, 2016, Notre Dame, USA
• M. Bubak: Federating Cloud Computing Resources for Scientific Computing, SKG 2016 - the International Conference on Semantics, Knowledge and Grids, August 15-17, 2016, Beijing, China
• M. Bubak: Scientific Applications with HyperFlow and Scalarm on the PaaSage Platform, ESOCC 2016 Conference, September 5-7, 2016, Vienna, Austria

PaaSage Posters and Flyers

Towards Deployment and Autoscaling of Scientific Workflows with HyperFlow and PaaSage (PDF), B. Balis, M. Bubak, K. Figiela, M. Malawski, and M. Pawlik; poster presented during CGW Workshop'14; 27-29 October, 2014, Krakow, Poland.

PaaSage: Model-Based Cloud Platform Upperware (PDF), M. Bubak, B. Baliś, J. Kitowski, D. Król, B. Kryza, M. Malawski - Department of Computer Science AGH, Krakow, Poland 2014

Support for Scientific Workflows in a Model-based Cloud Platform (PDF), M. Malawski, B. Balis, K. Figiela, M. Pawlik and M. Bubak, Proceedings of 8th IEEE/ACM International Conference on Utility and Cloud Computing, December 07-10, 2015, Limassol, Cyprus, pp. 412-413, IEEE 2015

The FedSM project is funded by the European Commission in order to improve service management in federated e-Infrastructures such as Grids and Federated Clouds. The project has dual aims of making changes in three 'client' infrastructures to improve their service management maturity and developing material to assist other infrastructures in making their own improvements.

Publications related to FedSM.

Official project website http://fedsm.eu/

Collage Posters and Flyers

The Collage Authoring Environment: A Platform for Executable Publications  (PDF: A4), Eryk Ciepiela, Piotr Nowakowski, Daniel Harężlak, Marek Kasztelnik, Grzegorz Dyk, Jan Meizner, and Marian Bubak; poster presented during Cracow Grid Workshop 2012; 22-24 October 2012, Kraków, Poland.

VPH-Share develops the organisational fabric and integrates optimized services to (1) expose and share data and knowledge, (2) jointly develop multiscale models for the composition of new VPH workflows, (3) facilitate collaboration within the VPH community. Four flagship workflows (representing @neurIST, euHeart, VPHOP and Virolab projects) provide existing data, tools and models, engaging with the services developed by VPH-Share to drive the development of the infostructure and pilot its applications. Data sources are usually clinical data from individual patients – medical images and/or biomedical signals – sometimes with population information. Operations range from secure access and storage through annotation, data inference and assimilation, to complex image processing and physics-based mathematical modelling, to data reduction and representation.

We would be very grateful for your opinions. If you are using our ideas or tools, please cite appropriate papers from the list of Publications related to VPH-Share.

Official project website http://www.vph-share.eu/

Tutorial for users: http://vph.cyfronet.pl/tutorial

Cloud live monitoring: http://149.156.10.132/ganglia

VPH-Share Deliverables

• VPH-Share-wp2-d2.1-v13.pdf
• VPH-Share_D22_1v3.pdf
• VPH-Share_D23_1v3.pdf
• VPH-Share_D24_10.pdf
• VPH-Share_D25_1v0.pdf

VPH-Share Presentations

• P. Nowakowski: Introduction to the VPH-Share Atmosphere cloud platform; lecture delivered at the FEIT WUT seminar, Warsaw University of Technology, November 2014
• M. Bubak, B. Baliś, T. Bartyński, T. Gubała, D. Harężlak, M. Kasztelnik, M. Malawski, J. Meizner, P. Nowakowski, B. Wilk, and P. Suder: From VPH-Share to PL-Grid: Atmosphere as as a Frontend to Cloud Resources in Research Infrastructures, Cracow Grid Workshop 2014, Kraków, Poland, 27-29 October 2014
• T. Bartyński, M. Kasztelnik, B. Wilk, and M. Bubak: Towards auto-scaling in the Atmosphere cloud platform, Cracow Grid Workshop 2014, Kraków, Poland, 27-29 October 2014
• M. Kasztelnik: Support for Taverna Workflows in VPH-Share Cloud Platform, Virtual Physiological Human Conference 2014, Trondheim, Norway, 9-12 September 2014
• P. Nowakowski: Execution and Sharing of VPH Applications in the Cloud with the Atmosphere Platform, Virtual Physiological Human Conference 2014, Trondheim, Norway, 9-12 September 2014
• P. Nowakowski: series of presentations of VPH-Share tools and services to CMUJ faculty and staff; September 2014
• M. Bubak: Federating cloud resources for building and execution of VPH applications, a keynote lecture at SKG2014 (The 10th International Conference on Semantics, Knowledge & Grids), Beijing, China, 27-29.08.2014
• A.A. Kononowicz, A.J. Narracott, J. Fenner, P. Nowakowski, M. Malawski, E. Mancini, P.V. Lawford, K. McCormack, N. Zary: Virtual Patients in the Cloud? Perspectives for Medical Education Offered by the Virtual Physiological Human Community, 20th SESAM, Poznan, Poland, 12 June 2014
• M. Malawski: VPH-Share demo at KUKDM'14, Zakopane, Poland, 14 March 2014
• M. Bubak: Federating cloud resources for building and execution of VPH applications, ACC Cyfronet AGH Open Day, Krakow, Poland, 25 November 2013
• M. Bubak, M. Kaszelnik: Towards a framework for creation, deployment and reliable operation of distributed, time-critical applications, High Performance Computing in Multidisciplinary Research, NIU ITMO, Saint Petersburg, 22 November 2013
• M. Bubak: Security in the Cloud Platform for VPH Applications, 3rd CIRRUS Workshop, ASI, Vienna, Austria, 19 November 2013
• J. Meizner: Public and private clouds as infrastructures for sharing data and computing services for VPH researchers, 2nd Summer School in Computational Oncology, Schloss Dagstuhl, June 23–28, 2013
• P. Nowakowski: Cloud-centric Development of Scientific Applications for the VPH Community, 2nd Summer School in Computational Oncology, Schloss Dagstuhl, June 23–28, 2013
• M. Bubak: Cloud Platform for VPH Applications, 2nd Summer School in Computational Oncology, Schloss Dagstuhl, June 23–28, 2013
• P. Nowakowski, T. Bartyński, T. Gubała, D. Harężlak, M. Kasztelnik, J. Meizner, M. Bubak: Managing Cloud Resources for Medical Applications, Cracow Grid Workshop 2012, Kraków, Poland, 22 October 2012

VPH-Share Posters and Flyers

Scaling Evolutionary Programming with use of Apache Spark (2014) (PDF) W. Funika and P. Koperek; poster presented during CGW Workshop'14; 27-29 October, 2014, Krakow, Poland.

Use of neural networks for managing the resources usage (2014) (PDF) W. Funika, P. Oleksy, and T. Wis; poster presented during CGW Workshop'14; 27-29 October, 2014, Krakow, Poland.

From VPH-Share to PL-Grid: Atmosphere as an Advanced Frontend to Cloud Resources in Research Infrastructures (2014) (PDF, PNG), M. Bubak, B. Baliś, T. Bartyński, T. Gubała, D. Harężlak, M. Kasztelnik, M. Malawski, J. Meizner, P. Nowakowski, B. Wilk, P. Suder; poster presented during CGW Workshop'14; 27-29 October, 2014, Krakow, Poland.

Autoconfiguration of remote desktop clients for cloud-based secure and interactive visualization (2014) (A1), D. Harężlak and M. Bubak; poster presented during CGW Workshop'14; 27-29 October, 2014, Krakow, Poland.

Evaluation of Cloud Providers for VPH Applications (2013) (A0), M. Bubak, M. Kasztelnik, M. Malawski, J. Meizner, P. Nowakowski - ACC Cyfronet AGH Krakow, PL, S. Varma - University of Sheffield, UK; poster presented during CCGrid2013 - 13th IEEE/ACM  International Symposium on Cluster, Cloud and Grid Computing; 13-16 May, 2013, Delft, the Netherlands.

Cloud Platform for Medical Applications (2012) (A4, A0), M. Bubak, P. Nowakowski, T. Bartynski, T. Gubala, D. Harezlak, M. Kasztelnik, M. Malawski, J. Meizner - ACC Cyfronet AGH Krakow, PL, A. Belloum, S. Koulouzis, D. Vasunin - University of Amsterdam, NL, P. Coveney, D. Chang - UCL London, UK, R. Diaz Rodriguez, D. Ruiz Lopez - ATOS Research, ES; October 2012.

Federating Cloud Resources in the VPH-Share Project (2011) (A4, A0), Piotr Nowakowski, Marian Bubak, Tomasz Bartyński, Daniel Harężlak, Marek Kasztelnik, Jan Meizner; poster presented during Cracow Grid Workshop 2011; 7-9 November 2011, Kraków, Poland.

VPH-Share Movies

PLGrid Plus Presentations

• E. Ciepiela, D. Harężlak, M. Kasztelnik, B. Wilk, M. Pawlik, J. Meizner, M. Bubak: GridSpace2: Virtual Laboratory in World Wide Web, EGI Community Forum 2013, Manchester, UK, 9 April 2013
• E. Ciepiela, B. Wilk, D. Harężlak, M. Kasztelnik, M. Pawlik, J. Meizner, M. Bubak: GridSpace2 – Towards Science-as-a-Service Model, KU KDM 2013, Zakopane, Poland, 28 February 2013
• W. Ziajka, M. Radecki, P. Szepieniec, T. Szepieniec: Benchmarking and normalization of compute resources in PL-Grid Infrastructure, Cracow Grid Workshop 2012, Kraków, Poland, 24 October 2012
• M. Golik, T. Szepieniec: BazaarSAT: SLA Translated to Local Resource Management System Configuration, Cracow Grid Workshop 2012, Kraków, Poland, 24 October 2012
• I. Roterman, M. Tomanek, M. Sterzel, T. Szepieniec, B. Kalinowska, Z. Baster, D. Dułak: Managing Protein Folding Process as Workflow Model with Wise Data Selection, Cracow Grid Workshop 2012, Kraków, Poland, 24 October 2012

• D. Harężlak, E. Ciepiela, M. Kasztelnik, B. Wilk, M. Bubak: DataNet – GridSpace Data Management Framework, Cracow Grid Workshop 2012, Kraków, Poland, 22 October 2012
• J. Meizner, M. Radecki, M. Pawlik, T. Szepieniec: Cloud Services in PL-Grid and EGI Infrastructures, Cracow Grid Workshop 2012, Kraków, Poland, 22 October 2012
• J. Kitowski, L. Dutka, T. Szepieniec, M. Sterzel, R. Pajak: PLGrid Plus Project - Status and Current Achievements, Cracow Grid Workshop 2012, Kraków, Poland, 22 October 2012
• T. Szepieniec: An NGI Sustainability Perspective: PL-Grid case study, EGI Technical Forum 2012, Prague, Czech Republic, 20 September 2012
• J. Kitowski, T. Szepieniec, M. Sterzel, L. Dutka: PLGrid Plus: Toward Domain-Specific Infrastructure for Supporting International Research Collaboration, EGI Community Forum 2012, Munich, Germany, 26 March 2012

PLGrid Plus Posters and Flyers

A Novel Environment for Simulation of Quantum Computing (2014) (PDF, PPT), J. Patrzyk, B. Patrzyk, K. Rycerz, M. Bubak; poster presented during CGW Workshop'14; 27-29 October, 2014, Krakow, Poland.

DataNet - GridSpace Data Management Framework  (PDF: A4), Daniel Harężlak, Eryk Ciepiela, Marek Kasztelnik, Bartosz Wilk and Marian Bubak; poster presented during Cracow Grid Workshop 2012; 22-24 October 2012, Kraków, Poland.

MAPPER Tutorials

• Tutorial 1: How to develop multiscale applications with MAD, MaMe and GridSpace Experiment Workbench?
• Tutorial 2: Bulding and running tightly coupled MUSCLE-based simulation on the example of Irrigation Canals

MAPPER Presentations

• K. Rycerz: Multiscale Application Support in the MAPPER project, ACC Cyfronet AGH Open Day, Krakow, Poland, 25 November 2013
• E. Ciepiela, D. Harężlak, M. Kasztelnik, B. Wilk, M. Pawlik, J. Meizner, M. Bubak: GridSpace2: Virtual Laboratory in World Wide Web, EGI Community Forum 2013, Manchester, UK, 9 April 2013
• E. Ciepiela, B. Wilk, D. Harężlak, M. Kasztelnik, M. Pawlik, J. Meizner, M. Bubak: GridSpace2 – Towards Science-as-a-Service Model, KU KDM 2013, Zakopane, Poland, 28 February 2013
• K. Rycerz, M. Bubak and WP8 team: MAPPER Multiscale Programming and Execution Tools. WP8 after year 2, 2nd Project Review, Amsterdam, The Netherlands, 28 November 2012
• K. Rycerz, D. Harężlak, G. Dyk, E. Ciepiela, T. Gubała, J. Meizner, M. Bubak: Programming and Execution of Multiscale Applications, Cracow Grid Workshop 2012, Kraków, Poland, 22 October 2012
• K. Rycerz (speaker), E. Ciepiela, G. Dyk, T. Gubała, D. Harężlak, J. Meizner, M. Bubak: Multiscale Programming and Execution Tools in the MAPPER project, EGI Technical Forum 2012, Workflow community workshop, Prague, Czech Republic, 21 September 2012
• M. Bubak (speaker), G. Harezlak, G. Dyk: Tools for programming and execution of multiscale applications, SCI-BUS, SHIWA, EDGI joint Summer School on Workflows and Gateways for Grids and Clouds - Introducing the latest developments in Grid and Cloud computing, Budapest, Hungary, 2-6 July 2012
• M. Bubak: Multiscale Applications on European e-Infrastructures, Chalmers e-Science initiative seminar, Göteborg, Sweden, 1-2 December, 2011
• M. Bubak, K. Rycerz and WP8 team: MAPPER Multiscale Programming and Execution Tools. WP8 after year 1, 24 November, 2011
• K. Rycerz and M. Bubak: Component Approach to Distributed Multiscale Simulations, SIMULTECH 2011, 1st International Conference on Simulation, Modeling Technologies and Applications, Noordwijkerhout, The Netherlands, 29-31 July, 2011
• K. Rycerz, E. Ciepiela, J. Kocot, M. Nowak, P. Pierzchała, M. Bubak: Towards an Environment for Multiscale Applications, KUKDM in Zakopane, Poland (2011)
• K. Rycerz, E. Ciepiela, D. Harezlak, M. Bubak: Towards Multiscale Computing Tools based on GridSpace, CGW'10 (2010)

MAPPER Posters and Flyers

Semantic Integration for Model-based Life Science Applications (PDF: A4), T. Gubala, K. Prymula, P. Nowakowski, M. Bubak. In: SIMULTECH 2013 Proceedings of the 3rd International Conference on Simulation and Modeling Methodologies, Technologies and Applications, Reykjavik, Iceland 29 - 31 July, 2013, pp. 74-81.

Efficient Execution of Grid-based Multiscale Applications for Metallurgical Industry (PDF: A4), Łukasz Rauch, Mateusz Ambroziński, Krzysztof Bzowski, Maciej Pietrzyk, Eryk Ciepiela, Katarzyna Rycerz, Bartosz Wilk, Marian Bubak; Summer School on Grid and Cloud Workflows and Gateways 2013, SZTAKI, Budapest, Hungary, 1-6 July 2013.

Composing, Executing and Sharing Multiscale Applications in an Integrated Environment (PDF: A4), Katarzyna Rycerz, Eryk Ciepiela, Daniel Harężlak, Maciej Pawlik, Tomasz Gubała, Jan Meizner, Marian Bubak; Summer School on Grid and Cloud Workflows and Gateways 2013, SZTAKI, Budapest, Hungary, 1-6 July 2013.

Programming and Execution of Multiscale Applications (PDF: A4), Katarzyna Rycerz, Eryk Ciepiela, Tomasz Gubała, Daniel Harężlak, Grzegorz Dyk, Jan Meizner, and Marian Bubak; poster presented during Cracow Grid Workshop 2012; 22-24 October 2012, Kraków, Poland.

Programming and Execution of Multiscale Applications on Distributed Infrastructures (PDF: A4, A0; PPT: A4, A0), Katarzyna Rycerz, Eryk Ciepiela, Tomasz Gubała, Daniel Harężlak, Joanna Kocot, Grzegorz Dyk, Jan Meizner and Marian Bubak; poster presented during Cracow Grid Workshop 2011; 7-9 November 2011, Kraków, Poland (see related presentation).

MAPPER Manuals

• MaMe User Manual
• MaMe Administrator Manual
• GridSpace2 Experiment Workbench – User Guide
• GridSpace2 Experiment Workbench – Tutorials
• GridSpace2 Experiment Workbench - Administrator Manual
• MAD Administrator Manual
• MAD User Manual

MAPPER Deliverables

• D8.1-ArchitectureInterfaces-CYF-v2.13.pdf
• D8.2-FirstPrototypeWithDemonstration-CYF-v1.7.pdf
• D8.3-SecondPrototype-CYF-v1.1.pdf
• D8.4-FinalValidation-CYF-v1.5.pdf

MAPPER Movies

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. The Common Information Space (CIS) provides a means for integration, over the Internet, of Early Warning Systems, sensors and application programs for public information and decision support.

We would be very grateful for your opinions. If you are using our ideas or tools, please cite appropriate papers from the list of Publications related to UrbanFlood.

Official project website http://urbanflood.eu/

Meeting in Krakow, 30-31 May 2012

See pictures from the meeting ...

UrbanFlood Presentations

See presentations in the CIS section ...

UrbanFlood Posters

An application scaling system in Elastic Compute Cloud (PDF: A4), W. Funika, K. Mazurek, and W. Kruczkowski; poster presented during Cracow Grid Workshop 2011; 7-9 November 2011, Kraków, Poland.

UrbanFlood Press Articles

• A. Ślązak (PAP - Nauka w Polsce), Zdążyć przed wielką falą (in Polish), an article at the Polish Ministry of Science and Higher Education web site, 30 March, 2012
• D. Merecik (TVP.pl), W Krakowie otwarto Centrum Informatyki AGH (in Polish), an article and a video at the TVP.pl web site, 28 March, 2012

UrbanFlood Movies

The gSLM project aimed to improve Service Level Management (SLM) in the grid domain. SLM is a set of tools and processes widely used in the commercial sector to agree, define and measure the provision of a service. In the grid domain SLM can make it easier for grid resource owners, operators and representatives of user groups to agree upon, document and manage the many agreements between stakeholders required to make the grid run smoothly. By bringing together experts in grid operations and management with leading members of the IT Service Management community, the project aimed to generate new approaches and concepts for grid SLM.

Publications related to gSLM.

Official project website http://gslm.eu/

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. This infrastructure is compatible with existing worldwide Grid frameworks. GridSpace2 is positioned as the basis for an advanced virtual laboratory environment for in-silico processing by Polish scientists, state authorities and crisis management teams. More on PL-Grid Virtual Laboratory ...

We would be very grateful for your opinions. If you are using our ideas or tools, please cite appropriate papers from the list of Publications related to PL-Grid.

Official project website http://projekt.plgrid.pl/en

The GREDIA Project prepared a system for access to multimedia data on the Grid, in the context of business applications. GREDIA focused on media and banking sectors. Here, GridSpace is applied as a core of the Appea platform, which enables users to quickly develop and deploy application scenarios, making use of the available Grid services and data resources. Moreover, GridSpace is capable of interfacing end users and present them with custom user interfaces, adapted to the needs of individual application domains.

Publications related to GREDIA.

Official project website http://www.gredia.eu/

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

The programme of the Project was structured around six complementary research areas that have been selected on the basis of their strategic importance, their research challenges and the recognised European expertise to develop next generation Grid middleware, namely: (1) Knowledge & Data Management, (2) Programming Models, (3) System Architecture Grid, (4) Information and Monitoring Services, (5) Resource Management and Scheduling, (6) Problem Solving Environments, Tools and GRID systems.

Publications related to CoreGRID.

Project website

The Knowledge-based Workflow System for Grid Applications (K-Wf Grid) project addressed the need for a better infrastructure for the future Grid environment. The Grid as a vast space of partially-cooperating, partially-competing Grid services will be a very dynamic and complex environment. In order to address the complexity in using and controlling the next generation Grid, the consortium adopted the approaches envisioned by semantic Web and Grid communities in a novel, generic infrastructure. The K-Wf Grid system assists its users in composing powerful Grid workflows by means of a rule-based expert system.

Publications related to K-Wf Grid.

Project website

The CrossGrid project was oriented towards compute- and data-intensive applications characterized by the interaction with a person in a processing loop. Such applications require a response from the Grid to an action by a human agent in different time scales.

Publications related to CrosGrid.

Project website

Project details

Fullname: Centre for New Methods in Computational Diagnostics and Personalised Therapy
Short name: Sano
Duration: From 1.08.2019 to 31.07.2026
Grant number: 857533

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.

The Sano's area of operation is computational medicine:

• clinician-led activity can be radically reduced by migrating the majority of routine clinical assessments toward computationally-driven,
• entirely new approaches to disease diagnosis and management follow the development of novel computed biomarkers of disease, personalised to the individual patient, and typically leading to dramatically reduced costs.

The Sano Centre combines expertise in machine-learning based decision science with fundamental biomarker identification using advanced simulation and data analysis methods.

When fully developed, the Centre will act as a core technology provider for industry, fostering modernisation, innovation and increasing productivity, and additionally it will act as a catalyst, attracting new investment and businesses. It will provide an essential link between computational, medical sciences and the industrial sector, thus fostering knowledge and technology transfer and accelerating innovation.

Sano was established in Kraków because of several local advantages with regard to the education and research infrastructure, the high concentration of research hospitals and a dynamic entrepreneurial community in life sciences, so being embedded in a highly dynamic and competitive ecosystem.

The Centre will provide a fully sustainable mix of three advanced technical services, loosely categorised as education, project participation and industrial product development, with these three strands ultimately contributing approximately equally to the Centre’s income stream.

Sano Partners

• Sano - Centre for Computational Personalised Medicine - International Research Foundation
• Academic Computer Centre Cyfronet AGH
• LifeScience Cluster Kraków – a Key National Cluster
• University of Sheffield and Insigneo Institute
• Forschungszentrum Jülich
• Fraunhofer Institute for Systems and Innovation Research ISI
• National Center for Research and Development (left the project in 2Q2021, according to the work plan)
• RWTH Aachen University (Linked Third Party)
• Sheffield Teaching Hospital (Linked Third Party)

Cyfronet personnel involved in the project

1. Marian Bubak: Cyfronet Teaming project leader
2. Maciej Malawski: Work Package 3 leader
3. Sabina Lichołai
4. Piotr Nowakowski
5. Tomasz Gubała
6. Karolina Jarosińska

The list of current Sano Centre Personnel

Former Cyfronet Teaming for Excellence project members

Jan Meizner, Tomasz Michalczyk, Tadeusz Satława

Sano presentations

• Sano overview presentation (PPT, PDF), 13.08.2020

• Sano extended EU Hearing presentation (PPT, PDF)
• Sano presentation at the Cracow Tech Week (PPT, PDF), 22.05.2019
• Sano presentation at the CompBioMed2 Kick-off: (PPT, PDF), 22.10.2019
• Sano presentation at the Conference International Cooperation: (PPT, PDF), 24.10.2019
• Sano presentation at the PRIMAGE Workshop "Advanced ICT for Medical Imaging Research and Innovation": (PPT, PDF), 31.10.2019
• M. Bubak, M. Kasztelnik, J. Meizner, P. Nowakowski, T. Gubała, M. Malawski: "Towards a Universal Platform for Large Scale Simulations on Prometheus" (abstract, presentation), KUKDM 2020 Conference planned on 5-6.03.2020
• M. Bubak: "Sano after one year of operation" (PPT, PDF), presented on 23.11.2020 at LSOS 2020 and Cyfronet AGH Open Day

Sano leaflets

• Sano leaflet (PDF)
• SanoCentre and the COVID-19 pandemic leaflet (PDF), 9.04.2020

Sano documents

• Extended abstract
• Extended abstract in Polish

Deliverables

Teaming deliverables elaborated

Teaming deliverables planned for 2021

EuroHPC PL

Duration: 01.01.2021 – 31.12.2023
Aim: The aim is to build a specialized general-purpose infrastructure for large-scale computing, enabling the undertaking of research challenges in key areas from the point of view of Polish society, the scientific community and the economy. The project is the Polish stage of development of the EuroHPC program. Cyfronet is the project coordinator and the leader of the Consortium.

Our team is involved in task III.1 "Laboratory for the use of supercomputers in medicine". In this part of the EuroHPC PL project we are designing and developing a set of tools which will assist scientists involved in computational medicine in more efficient use of HPC resources. Furthermore, our intent is to equip medical researchers in ability to compose their complex applications, configure them to execute efficiently on computational clusters, manage versions of code and data to support result provenance, and share the effects of their work with their collaborators, inside their institute or externally.

We are collaborating with medical domain specialists, both medicine doctors and engineers involved in medical technology, in order to create solutions which fit their interactive way of conducting computational experiments, e.g. through Jupiter notebooks. Other tools which are being improved or developed in the course of this project are Rimrock, PLGData and Model Execution Environment.