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

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. In particular, it targeted the drug resistance problem in HIV (Human Immunodefficiency Virus) anti-viral therapy, using genetic information and computer modeling. GridSpace technology is used here as the main building block of the virtual laboratory, providing the core runtime, services and tools for programmers, computational scientists and virologists, enabling them to address important issues in modern treatment of infectious diseases through collaborative in-silico research.

Official project webpage

  • Optimization of Application Execution in Virtual Laboratory , Mikolaj Baranowski; Master of Science Thesis supervised by Marian Bubak; AGH University of Science and Technology, Krakow, Poland (presentation ) (2011)
  • M. Malawski, T. Gubala, M. Bubak: Wirtualne laboratorium dla chorob zakaznych - ViroLab. In: I. Roterman-Konieczna (eds.) Elementy Informatyki Medycznej: Sciezki kliniczne, wirtualny pacject, telekonsultacje, Wydawnictwo Universytetu Jagiellonskiego, vol. 3038, pp. 167-186, ISBN 978-83-233-2958-9 (2011)
  • M. Pomocka, P. Nowakowski, M. Bubak: Integrating the GridSpace Virtual Laboratory with EGEE Storage Services , abstract at e-Challenges in Warsaw, Poland (2010)
  • M. Malawski, T. Bartynski, M. Bubak: Invocation of operations from script-based grid applications (DOI ). In: Future Generation Computer Systems, vol. 26, Issue 1, pp. 138-146 (January 2010)
  • Data source registration in the Virtual Laboratory , Marek Pomocka, Master of Science Thesis supervised by Marian Bubak; reviewed by dr Piotr Gronek; AGH University of Science and Technology, Krakow, Poland (October 2009)
  • Security in Virtual Laboratory System , Jan Meizner, Master of Science Thesis supervised by Marian Bubak; reviewed by dr Dawid Kurzyniec; AGH University of Science and Technology, Krakow, Poland (presentation ) (September 2009)
  • Environment for management of experiments on the grid , Pawel Charkowski, Master of Science Thesis supervised by Marian Bubak; reviewed by dr Mariusz Sterzel; AGH University of Science and Technology, Krakow, Poland (presentation ) (September 2009)
  • Bioinformatics Applications in the Virtual Laboratory , Tomasz Jadczyk, Master of Science Thesis supervised by Marian Bubak; reviewed by prof. Irena Roterman and dr Monika Piwowar; AGH University of Science and Technology, Krakow, Poland (presentation ) (September 2009)
  • W. Funika, D. Caromel, P. Koperek, M. Kupisz: Towards semantic-based monitoring of ProActive distributed applications. In: CoreGRID 2009 Workshop in conjunction with EuroPar 2009, Delft, Netherlands (August 24, 2009)
  • E. Ciepiela, M. Malawski, M. Bubak: CompTalks – from a Meta-model Towards a Framework for Application-Level Interaction Protocols . In: Proceedings of the 2nd International Workshop on Real Time Online Interactive Applications on the Grid (ROIA 2009) in conjunction with Euro-Par 2009, LNCS, Springer (2009)
  • J. Meizner, M. Malawski, E. Ciepiela, M. Kasztelnik, D. Harezlak, P. Nowakowski, D. Krol, T. Gubala, W. Funika, M. Bubak, T. Mikolajczyk, P. Plaszczak, K. Wilk, M. Assel: ViroLab Security and Virtual Organization Infrastructure. In Y. Dou, R. Gruber, and J. Joller (eds.) Proceedings of APPT 2009, Advanced Parallel Processing Technologies 8th International Symposium, Rapperswil, Switzerland, August 24-25, 2009, LNCS 5737, pp. 230–245, Springer-Verlag, Berlin Heidelberg (2009)
  • M. Dyrda, M. Malawski, M. Bubak, S. Naqvi: Providing security for MOCCA component environment . In: Parallel and Distributed Processing Symposium, International, pp. 1-7, 2009 IEEE International Symposium on Parallel&Distributed Processing (2009)
  • B. Balis, M. Bubak, M. Pelczar, J. Wach: Provenance Tracking and End-User Oriented Query Construction. In: M. Cannataro (ed.) Handbook of Research on Computational Grid Technologies for Life Sciences, Biomedicine and Healthcare , Chapter 4, pp. 60-75, Information Science Reference, IGI Global (2009)
  • T. Gubala, M. Bubak, P. M. A. Sloot: Semantic Integration of Collaborative Research Environments. In: M. Cannataro (ed.) Handbook of Research on Computational Grid Technologies for Life Sciences, Biomedicine and Healthcare , Chapter 26, pp. 514-530, Information Science Reference, IGI Global (2009)
  • M. Bubak, T. Gubala, M. Kasztelnik, M. Malawski: Building Collaborative Applications for System-level Science. In: W. Gentzsch, L. Grandinetti, G. Joubert (eds.) Advances in Parallel Computing, Vol. 18, 2009, High Speed and Large Scale Scientific Computing, ISBN 978-1-60750-073-5, doi: 10.3233/978-1-60750-073-5-299 (2009)
  • M. Assel, D. van de Vijver, P. Libin, K. Theys, D. Harezlak, B. O’Nuallain, P. Nowakowski, M. Bubak, A.-M. Vandamme, S. Imbrechts, R. Sangeda, T. Jiang, D. Frentz, P. Sloot: A Collaborative Environment Allowing Clinical Investigations on Integrated Biomedical Databases. In: T. Solomonides, M. Hofmann-Apitius, M. Fredigmann, S. Caludius Semler, Y. Legre, M. Kratz (eds.) Healthgrid Research, Innovation and Business Case, Proceedings of HealthGrid 2009, Studies in Health Technology and Informatics, vol. 147, pp. 51-61, IOS Press, ISSN 0926-9630 (2009)
  • P. M. A Sloot, Peter V. Coveney, G. Ertayalan, V. Mueller, C. A. Boucher, M. Bubak: HIV decision Support: from Molecule to Man. In: Philosophical Transactions of the Royal Society A, vol. 367, pp. 2691-2703, doi:10.1098/rsta.2009.0043 (2009)
  • Marian Bubak et al.: Virtual Laboratory for Collaborative Applications. In: M. Cannataro (ed.) Handbook of Research on Computational Grid Technologies for Life Sciences, Biomedicine and Healthcare , Chapter 27, pp. 531-551, Information Science Reference, IGI Global (2009)
  • B. Balis, M. Bubak: An ontology model for execution records of Grid scientific applications. In: 4th International Conference on Semantics, Knowledge and Grid SKG 2008, December 2008, Beijing, China, pp. 34-41, IEEE 2008, ISBN 978-0-7695-3401-5 (2008)
  • B. Balis, M. Bubak: Monitoring infrastructure for Grid scientific workflows . In: 3rd Workshop on Workflows in Support of Large-Scale Science during SuperComputing 08 The International Conference for High Performance Computing, Networking, Storage and Analysis , November 2008, Austin, Texas, IEEE 2008 (2008)
  • Recording application executions enriched with domain semantics of computations and data , Michal Pelczar, Master of Science Thesis supervised by Marian Bubak; reviewed by dr Maciej Zygmunt; AGH University of Science and Technology, Krakow, Poland (presentation ) (October 2008)
  • B. Balis, M. Bubak, M. Wegiel: LGF: A flexible framework for exposing legacy codes as services. In: Future Generation Computer Systems, vol. 24, Issue 7, July 2008, Elsevier, pp. 711-719 (2008)
  • Collection and Storage of Provenance Data , Jakub Wach; Master of Science Thesis supervised by Marian Bubak; reviewed by dr Dawid Kurzyniec, AGH University of Science and Technology, Krakow, Poland (presentation ) (July 2008)
  • M. Assel, P. Nowakowski, M. Bubak: Integrating and Accessing Medical Data Resources within the ViroLab Virtual Laboratory. In: M. Bubak, G. D. v. Albada, J. Dongarra, P. M. A. Sloot (eds.) Proceedings ICCS 2008, Krakow, Poland, LNCS 5103, pp. 90-99, Springer (2008)
  • B. Balis, M. Bubak, M. Pelczar, J. Wach: Provenance Querying for End-Users: A Drug Resistance Case Study. In: M. Bubak, G. D. v. Albada, J. Dongarra, P. M. A. Sloot (eds.) Proceedings ICCS 2008, Krakow, Poland, LNCS 5103, pp. 80-89, Springer (2008)
  • B. Kowalewski, M. Bubak, B. Balis: An Event-Based Approach to Reducing Coupling in Large-Scale Applications. In: M. Bubak, G. D. v. Albada, J. Dongarra, P. M. A. Sloot (eds.) Proceedings ICCS 2008, Krakow, Poland, LNCS 5103, pp. 358-367, Springer (2008)
  • W. Funika, D. Harezlak, D. Krol, M. Bubak: Environment for Collaborative Development and Execution of Virtual Laboratory Applications. In: M. Bubak, G. D. v. Albada, J. Dongarra, P. M. A. Sloot (eds.), Proceedings ICCS 2008, Krakow, Poland, LNCS 5103, pp. 246-458, Springer (2008)
  • M. Malawski, T. Bartynski, M. Bubak: A Tool for Building Collaborative Applications by Invocation of Grid Operations. In: M. Bubak, G. D. v. Albada, J. Dongarra, P. M. A. Sloot (eds.) Proceedings ICCS 2008, Krakow, Poland, LNCS 5103, pp. 243-252, Springer (2008)
  • T. Gubala, M. Kasztelnik, M. Malawski, M. Bubak: Towards a System-Level Science Support. In: Bubak, M., Albada, G.D.v., Dongarra, J., Sloot, P.M.A. (eds.) Proceedings ICCS 2008, Krakow, Poland, June 23-25, 2008, LNCS, Springer, vol. 5101, pp. 56-65 (2008)
  • M. Bubak, T. Gubala, M. Malawski, B. Balis, W. Funika, T. Bartynski, E. Ciepiela, D. Harezlak, M. Kasztelnik, J. Kocot, D. Krol, P. Nowakowski, M. Pelczar, J. Wach, M. Assel, A. Tirado-Ramos: Virtual Laboratory for Development and Execution of Biomadical Collaborative Applications. In: S. Puuronen, M. Pechenizkiy, A. Tsymbal, D-J. Lee (eds.) Proc. 21st IEEE International Symposium on Computer-Based Medical Systems, June 17-19, 2008, Jyvaskyla, Finland, p. 373 - 378, doi: 10.1109/CBMS.2008.47 (2008)
  • Security in Component Grid Systems , Michal Dyrda; Master of Science Thesis supervised by Marian Bubak; reviewed by dr Dawid Kurzyniec; AGH University of Science and Technology, Krakow, Poland (presentation ) (June 2008)
  • B. Balis, M. Bubak, M. Pelczar, J. Wach: Provenance Tracking and Querying in the ViroLab Virtual Laboratory. In: Proceedings of the 8th IEEE International Symposium on Cluster Computing and the Grid 2008 (CCGRID), pp. 675-680, IEEE Computer Society (2008)
  • M. Malawski, T. Gubala, M. Kasztelnik, T. Bartynski, M. Bubak, F. Baude, L. Henrio: High-level Scripting Approach for Building Component-based Applications on the Grid. In: M. Danelutto, P. Fragopoulou, V. Getov (eds.) Making Grids Work, Springer-Verlag, pp. 307-320, ISBN 978-0-387-78447-2 (2008)
  • B. Balis, M. Bubak, M. Pelczar, J. Wach: Provenance Tracking and Querying in ViroLab. In Cracow Grid Workshop 2007 - Workshop Proceedings, ACC CYFRONET AGH, pp. 71-76 (2008)
  • M. Malawski, J. Kocot, E. Ciepiela, M. Bubak: Optimization of Application Execution in the ViroLab Virtual Laboratory . In Cracow Grid Workshop 2007 - Workshop Proceedings, ACC CYFRONET AGH, pp. 65-70 (2008)
  • E. Ciepiela, J. Kocot, T. Gubala, M. Malawski, M. Kasztelnik, M. Bubak: Virtual Laboratory Engine – GridSpace Engine . In Cracow Grid Workshop 2007 - Workshop Proceedings, ACC CYFRONET AGH, pp. 53-58 (2008)
  • T. Bartynski, M. Malawski, M. Bubak: Invocation of Grid Operations in the ViroLab Virtual Laboratory . In: Cracow Grid Workshop 2007 Workshop Proceedings, ACC CYFRONET AGH, pp. 59-64 (2008)
  • M. Kasztelnik, T. Gubala, M. Malawski, M. Bubak: Development and Execution of Collaborative Application on the ViroLab Virtual Laboratory . In: Cracow Grid Workshop 2007 Workshop Proceedings, ACC CYFRONET AGH, pp. 41-46 (2008)
  • T. Gubala, B. Balis, M. Malawski, M. Kasztelnik, P. Nowakowski, M. Assel, D. Harezlak, T. Bartynski, J. Kocot, E. Ciepiela, D. Krol, J. Wach, M. Pelczar, W. Funika, M. Bubak: ViroLab Virtual Laboratory . In: Cracow Grid Workshop 2007 Workshop Proceedings, pp. 35-40, ACC CYFRONET AGH (2008)
  • Remote execution of delegated operations with support for automatic selection among multiple communication protocols , Tomasz Bartynski; Master of Science Thesis supervised by Marian Bubak; reviewed by dr Dawid Kurzyniec; AGH University of Science and Technology, Krakow, Poland (presentation ) (February 2008)
  • T. Bartynski, M. Malawski, T. Gubala, M. Bubak: Universal Grid Client: Grid Operation Invoker. In: 7-th International Conference on Parallel Processing and Applied Mathematics PPAM'2007, LNCS 4967, Springer, pp. 1068-1077 (2008). (Presentation given at the conference.)
  • B. Balis, M. Bubak, M. Pelczar: From Monitoring Data to Experiment Information - Monitoring of Grid Scientific Workflows. In: G. Fox, K. Chiu, R. Buyya (eds.) Third IEEE International Conference on e-Science and Grid Computing, e-Science 2007, Bangalore, India, IEEE Computer Society, pp. 187-194 (2007)
  • B. Balis, M. Bubak, J. Wach: User-Oriented Querying over Repositories of Data and Provenance. In: G. Fox, K. Chiu, R. Buyya (eds.) Third IEEE International Conference on e-Science and Grid Computing, e-Science 2007, Bangalore, India, IEEE Computer Society, pp. 77-84 (2007)
  • M. Bubak, T. Gubala, M. Kasztelnik, M. Malawski, P. Nowakowski, P.M.A. Sloot: Collaborative Virtual Laboratory for e-Health . In: P. Cunningham and M. Cunningham (eds.) Expanding the Knowledge Economy: Issues, Applications, Case Studies, eChallenges e-2007 Conference Proceedings, IOS Press, Amsterdam, pp. 537-544 (2007)
  • Monitoring of Component-Based Applications , Eryk Ciepiela; Master of Science Thesis supervised by Marian Bubak; reviewed by dr Dominik Radziszowski; AGH University of Science and Technology, Krakow, Poland (presentation ) (June 2007)
  • Optimization of Grid Application Execution , Joanna Kocot, Iwona Ryszka; Master of Science Thesis supervised by Marian Bubak; reviewed by dr Katarzyna Rycerz; AGH University of Science and Technology, Krakow, Poland (presentation ) (June 2007)
  • P. M. A. Sloot, A. Tirado-Ramos, M. Bubak: Multi-Science Decision Support for HIV Drug Resistance Treatment. In: P. Cunningham, M. Cunningham (eds.) Expanding the Knowledge Economy: Issues, Applications, Case Studies, IOS Press, pp. 597-606 (2007)
  • P. M. A. Sloot, I. Altintas, M. Bubak, Ch. A. Boucher: From Molecule to Man: Decision Support in Individualized E-Health , IEEE Computer Society, vol 39, no.11, pp. 40-46 (Nov. 2006)
  • M. Bubak, T. Gubala, M. Malawski, M. Kasztelnik, T. Bartynski, P. Nowakowski: Virtual Laboratory in ViroLab, poster presentation at Cracow Grid Workshop CGW'06 (2006)
  • W. Funika, P. Pegiel: GScript Editor as a Part of the ViroLab Presentation Layer, poster presentation at the Cracow Grid Workshop CGW'06 (2006)
  • M. Malawski, M. Bubak, M. Placek, D. Kurzyniec, V. Sunderam: Experiments with distributed component computing across Grid boundaries . In: Proceedings of the HPC-GECO/CompFrame workshop in conjunction with HPDC 2006, Paris (2006)
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