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DIstributed Computing Environments (DICE) Team
We are a group of computer scientists and IT experts from the Department of Computer Science AGH and ACC Cyfronet AGH. We are a curiosity- and research-driven team, specializing in large-scale distributed computing, HPC, Web and Cloud technologies. We develop new methods, tools and environments and we apply these solutions in e-Science, healthcare and industrial domains.


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Projects full descriptions

Gliomed (2017-2020)

GLIOMED_LOGO_TRANS_354px.pngGliomas 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)

 

EurValve (2016-2019)

Paasage_logo_sEurValve 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

 

EurValve Reviews

WP2 presentation at the Review on 28.09.2017

 

Model Execution Environment

 

EurValve News

 

EurValve Presentations

 

EurValve Posters

 

PLGrid Core (2014-2015)

PLGrid Core Posters and Flyers

cgw2014-poster-wach-v2_s.png

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 (2012-2016)

Paasage_logo_sPaaSage 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

 

PaaSage Posters and Flyers

Workflow-Paasage-v6_s.pngTowards 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.

 

poster_1s

 

 

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

 

 

UCC-Workflow-Paasage-v2-alt_s.png

 

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

FedSM (2012-2015)

fedsmThe 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 (2011)

Collage Posters and Flyers

collage-poster-cgw12-v1_s.pngThe 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 (2011-2015)

vph-shareVPH-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 Presentations

 

VPH-Share Posters and Flyers

CGW2014_poster_koperek_s.pngScaling 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.

 

 

 

 

CGW14-poster_wis_oleksy_s.pngUse 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.

 

 

 

 

vph-cgw-poster-v4_s.pngFrom 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.

 

 

 

 

cloud-vnc-poster-v4_CGW14_s.pngAutoconfiguration 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_sEvaluation 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.

 

 

 

 

vph-poster-cloud_sCloud 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.

 

 

 

 

VPH-Share-poster_CGW11-A4_s.pngFederating 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 (2011-2014)

PLGrid Plus Presentations

 

PLGrid Plus Posters and Flyers

quantum_cgw14_a4_s.pngA 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.

 

cgw12-datanet-poster-v2_s.png

 

 

 

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 (2010-2013)

MAPPER Tutorials

 

MAPPER Presentations

 

MAPPER Posters and Flyers

simultech-semint-poster-v4_sSemantic 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.

 

 

 

 

ssrve_ulotka_sEfficient 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.

 

 

 

 

mapper-sztaki-28.05-v2_sComposing, 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.

 

 

 

 

MAPPER_cgw12_sProgramming 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.

 

 

 

 

mapper-cgw11v-final-A0_sProgramming 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

 

MAPPER Deliverables

 

MAPPER Movies

UrbanFlood (2010-2012)

urbanfloodThe 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

cgw11_poster-lb-ec2_sAn 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

 

UrbanFlood Movies

gSLM (2010-2012)

gslmThe 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/

PL-Grid (2009-2012)

pl-gridThe 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

ViroLab (2006-2009)

GREDIA (2006-2009)

grediaThe 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/

CoreGRID (2004-2008)

coregridThe 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

K-Wf Grid (2004-2007)

kwfgridThe 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

CrossGrid (2002-2005)

crossgridThe 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

CECM Teaming for Excellence (2017-2018)

cecmThe 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 Flyers

 

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)

 

 

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