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  • 1. Ahmed, Laeeq
    et al.
    Georgiev, Valentin
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences.
    Capuccini, Marco
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Toor, Salman
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Schaal, Wesley
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences.
    Laure, Erwin
    Spjuth, Ola
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences.
    Efficient iterative virtual screening with Apache Spark and conformal prediction2018In: Journal of Cheminformatics, ISSN 1758-2946, E-ISSN 1758-2946, Vol. 10, article id 8Article in journal (Refereed)
  • 2.
    Andrejev, Andrej
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    Toor, Salman
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Hellander, Andreas
    Holmgren, Sverker
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Risch, Tore
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    Scientific analysis by queries in extended SPARQL over a scalable e-Science data store2013In: Proc. 9th International Conference on e-Science, Los Alamitos, CA: IEEE Computer Society, 2013, p. 98-106Conference paper (Refereed)
  • 3. Appleton, Owen
    et al.
    Cameron, David
    Cernák, Jozef
    Dóbé, Péter
    Ellert, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, High Energy Physics.
    Frågåt, Thomas
    Grønager, Michael
    Johansson, Daniel
    Jönemo, Johan
    Kleist, Josva
    Kocan, Marek
    Konstantinov, Aleksandr
    Kónya, Balázs
    Márton, Iván
    Mohn, Bjarte
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, High Energy Physics.
    Möller, Steffen
    Müller, Henning
    Nagy, Zsombor
    Nilsen, Jon K.
    Ould-Saada, Farid
    Pajchel, Katarina
    Qiang, Weizhong
    Read, Alexander
    Rosendahl, Peter
    Röczei, Gábor
    Savko, Martin
    Skou Andersen, Martin
    Smirnova, Oxana
    Stefán, Péter
    Szalai, Ferenc
    Taga, Adrian
    Toor, Salman Z.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Wäänänen, Anders
    Zhou, Xin
    The next-generation ARC middleware2010In: Annales des télécommunications, ISSN 0003-4347, E-ISSN 1958-9395, Vol. 65, p. 771-776Article in journal (Refereed)
  • 4.
    Ausmees, Kristiina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    John, Aji
    Toor, Salman Z.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Hellander, Andreas
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Nettelblad, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    BAMSI: a multi-cloud service for scalable distributed filtering of massive genome data2018In: BMC Bioinformatics, ISSN 1471-2105, E-ISSN 1471-2105, Vol. 19, p. 240:1-11, article id 240Article in journal (Refereed)
  • 5. Drawert, Brian
    et al.
    Trogdon, Michael
    Toor, Salman
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Petzold, Linda
    Hellander, Andreas
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    MOLNs: A cloud platform for interactive, reproducible, and scalable spatial stochastic computational experiments in systems biology using PyURDME2016In: SIAM Journal on Scientific Computing, ISSN 1064-8275, E-ISSN 1095-7197, Vol. 38, p. C179-C202Article in journal (Refereed)
  • 6. Elmroth, Erik
    et al.
    Holmgren, Sverker
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Lindemann, Jonas
    Toor, Salman
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Östberg, Per-Olov
    Empowering a flexible application portal with a SOA-based grid job management framework2008Conference paper (Refereed)
  • 7. Jallow, Alieu
    et al.
    Hellander, Andreas
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Toor, Salman
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Cost-aware application development and management using CLOUD-METRIC2017In: Proc. 7th International Conference on Cloud Computing and Services Science, Setúbal, Portugal: SciTePress, 2017, p. 515-522Conference paper (Refereed)
  • 8.
    Jayawardena, Mahen
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Nettelblad, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Toor, Salman
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Östberg, Per-Olov
    Elmroth, Erik
    Holmgren, Sverker
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    A Grid-Enabled Problem Solving Environment for QTL Analysis in R2010In: Proc. 2nd International Conference on Bioinformatics and Computational Biology, Cary, NC: ISCA , 2010, p. 202-209Conference paper (Refereed)
  • 9.
    Jayawardena, Mahen
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Toor, Salman
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Holmgren, Sverker
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    A grid portal for genetic analysis of complex traits2009In: Proc. 32nd International Convention on Information and Communication Technology, Electronics and Microelectronics: Volume I, Rijeka, Croatia: MIPRO , 2009, p. 281-284Conference paper (Refereed)
  • 10.
    Jayawardena, Mahen
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Toor, Salman
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Holmgren, Sverker
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Computational and visualization tools for genetic analysis of complex traits2010Report (Other academic)
  • 11.
    Mahjani, Behrang
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Toor, Salman
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Software as a service in analysis of quantitative trait loci2016Report (Other academic)
  • 12.
    Mahjani, Behrang
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Toor, Salman
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Nettelblad, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Holmgren, Sverker
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    A flexible computational framework using R and Map-Reduce for permutation tests of massive genetic analysis of complex traits2017In: IEEE/ACM Transactions on Computational Biology & Bioinformatics, ISSN 1545-5963, E-ISSN 1557-9964, Vol. 14, p. 381-392Article in journal (Refereed)
  • 13.
    Mahjani, Behrang
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Toor, Salman
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Nettelblad, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Holmgren, Sverker
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    QTL as a service: PruneDIRECT for multi-dimensional QTL scans in cloud settings2016In: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811Article in journal (Other academic)
  • 14. Nilsen, Jon K.
    et al.
    Toor, Salman
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Nagy, Zsombor
    Mohn, Bjarte
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, High Energy Physics.
    Chelonia — a self-healing storage cloud2010In: Proc. 9th Cracow Grid Workshop, Kraków, Poland: ACC Cyfronet AGH , 2010, p. 5-12Conference paper (Refereed)
  • 15. Nilsen, Jon Kerr
    et al.
    Toor, Salman
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Nagy, Zsombor
    Mohn, Bjarte
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, High Energy Physics.
    Read, Alex
    Performance and stability of the Chelonia storage system2012In: Proc. International Symposium on Grids and Clouds 2012, Trieste, Italy: SISSA , 2012, p. 009:1-14Conference paper (Refereed)
  • 16. Nilsen, Jon Kerr
    et al.
    Toor, Salman
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Nagy, Zsombor
    Read, Alex
    Chelonia: A self-healing, replicated storage system2011In: Computing in High Energy and Nuclear Physics: CHEP 2010, Bristol, UK: Institute of Physics Publishing (IOPP), 2011, p. 062019:1-6Conference paper (Refereed)
  • 17.
    Toor, Salman
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Managing applications and data in distributed computing infrastructures2010Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

    Over the last few decades, the needs of computational power and data storage by collaborative, distributed scientific communities have increased very rapidly. Distributed computing infrastructures such as computing and storage grids provide means to connect geographically distributed resources and helps in addressing the needs of these communities. Much progress has been made in developing and operating grids, but several issues still need further attention. This thesis discusses three different aspects of managing large-scale scientific applications in grids:

    • Using large-scale scientific applications is often in itself a complex task, and to set them up and run experiments in a distributed environment adds another level of complexity. It is important to design general purpose and application specific frameworks that enhance the overall productivity for the scientists. The thesis present further development of a general purpose framework where existing portal technology is combined with tools for robust and middleware independent job management. Also, a pilot implementation of a domain-specific problem solving environment based on a grid-enabled R solution is presented.

    • Many current and future applications will need large-scale storage systems. Centralized systems are eventually not scalable enough to handle huge data volumes and also have can have additional problems with security and availability. An alternative is a reliable and efficient distributed storage system. In the thesis the architecture of a self-healing, grid-aware distributed storage cloud, Chelonia, is described and performance results for a pilot implementation are presented.

    • In a distributed computing infrastructure it is very important to manage and utilize the available resources efficiently. The thesis presents a review of different resource brokering techniques and how they are implemented in different production level middlewares. Also, a modified resource allocation model for the Advanced Resource Connector (ARC) middleware is described and performance experiments are presented.

  • 18.
    Toor, Salman
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Lindberg, Mathias
    Fällman, Ingemar
    Vallin, Andreas
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology.
    Mohill, Olof
    Freyhult, Pontus
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology.
    Nilsson, Linus
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology.
    Agback, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology.
    Viklund, Lars
    Zazzi, Henric
    Spjuth, Ola
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Capuccini, Marco
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Möller, Joakim
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences.
    Murtagh, Donal
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences.
    Hellander, Andreas
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    SNIC Science Cloud (SSC): A national-scale cloud infrastructure for Swedish academia2017In: Proc. 13th International Conference on e-Science, Los Alamitos, CA: IEEE Computer Society, 2017, p. 219-227Conference paper (Refereed)
  • 19.
    Toor, Salman
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Mohn, Bjarte
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, High Energy Physics.
    Cameron, David
    Holmgren, Sverker
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Case-study for different models of resource brokering in grid systems2010Report (Other academic)
  • 20.
    Toor, Salman
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Sabesan, Manivasakan
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    Holmgren, Sverker
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Risch, Tore
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    A scalable architecture for e-Science data management2011In: Proc. 7th International Conference on e-Science, Los Alamitos, CA: IEEE Computer Society, 2011, p. 210-217Conference paper (Refereed)
  • 21.
    Toor, Salman
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Töebbicke, Rainer
    Zotes Resines, Maitane
    Holmgren, Sverker
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Investigating an open source cloud storage infrastructure for CERN-specific data analysis2012In: Proc. 7th International Conference on Networking, Architecture, and Storage, Los Alamitos, CA: IEEE Computer Society, 2012, p. 84-88Conference paper (Refereed)
  • 22.
    Toor, Salman Zubair
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Managing Applications and Data in Distributed Computing Infrastructures2012Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    During the last decades the demand for large-scale computational and storage resources in science has increased dramatically. New computational infrastructures enable scientists to enter a new mode of science, e-science, which complements traditional theory and experiments. E-science is inherently interdisciplinary, involving researchers from several disciplines, and also opens up for large-scale collaborative efforts where physically distributed groups of scientists share software tools and data to make scientific progress. Within the field of e-science, new challenges are emerging in managing large-scale distributed computing efforts and distributed data sets. Different models, e.g. grids and clouds, have been introduced over the years, but new solutions built on these models are needed to enable easy and flexible use of distributed computing infrastructures by application scientists.

    In the first part of the thesis, application execution environments are studied. The goal is to hide technical details of the underlying distributed computing infrastructure and expose secure and user-friendly environments to the end users. First, a general-purpose solution using portal technology is described, enabling transparent and easy usage of a variety of grid systems. Then a problem-solving environment for genetic analysis is presented. Here the statistical software R is used as a workflow engine, enhanced with grid-enabled routines for performing the computationally demanding parts of the analysis. Finally, the issue of resource allocation in grid system is briefly studied and certain modifications in the distributed resource-brokering model for the ARC middleware are proposed.

    The second part of the thesis presents solutions for managing and analyzing scientific data using distributed storage resources. First, a new reliable and secure file-oriented distributed storage system, Chelonia, is presented. The architectural design of the system is described and implementation issues are considered. Also, the stability and scalable performance of Chelonia is verified using several test scenarios. Then, tools for providing an efficient and easy-to-use platform for data analysis built on Chelonia are presented. Here, a database driven approach is explored. An extended architecture where Chelonia is combined with the Web-Service MEDiator (WSMED) system is implemented, providing web service tools to query data without any further programming. This approach is then developed further and Chelonia is combined with SciSPARQL, a query language that extends SPARQL to queries over numeric scientific data. This results in a system that is capable of interactive analysis of distributed data sets. Writing customized modules in Java, Python or C can fulfill advanced application-specific analysis requirements. The viability of the approach is demonstrated by applying the system to data produced by URDME, a computational environment in systems biology and results for sample queries expressed in SciSPARQL are presented.

    Finally, the use of an open source storage cloud, Openstack – SWIFT, for analysis of data from CERN experiments is considered. Here, a pilot implementation for the ROOT data analysis framework is presented together with a performance evaluation.

    List of papers
    1. Empowering a flexible application portal with a SOA-based grid job management framework
    Open this publication in new window or tab >>Empowering a flexible application portal with a SOA-based grid job management framework
    Show others...
    2008 (English)Conference paper, Published paper (Refereed)
    Place, publisher, year, edition, pages
    Trondheim, Norway: Norwegian University of Science and Technology, 2008
    National Category
    Software Engineering
    Identifiers
    urn:nbn:se:uu:diva-173381 (URN)
    Conference
    PARA 2008: State of the Art in Scientific and Parallel Computing
    Available from: 2012-04-23 Created: 2012-04-23 Last updated: 2018-01-12Bibliographically approved
    2. A Grid-Enabled Problem Solving Environment for QTL Analysis in R
    Open this publication in new window or tab >>A Grid-Enabled Problem Solving Environment for QTL Analysis in R
    Show others...
    2010 (English)In: Proc. 2nd International Conference on Bioinformatics and Computational Biology, Cary, NC: ISCA , 2010, p. 202-209Conference paper, Published paper (Refereed)
    Place, publisher, year, edition, pages
    Cary, NC: ISCA, 2010
    National Category
    Software Engineering Genetics
    Identifiers
    urn:nbn:se:uu:diva-111594 (URN)978-1-880843-76-5 (ISBN)
    Projects
    eSSENCE
    Available from: 2010-01-12 Created: 2009-12-17 Last updated: 2018-01-12Bibliographically approved
    3. Chelonia — a self-healing storage cloud
    Open this publication in new window or tab >>Chelonia — a self-healing storage cloud
    2010 (English)In: Proc. 9th Cracow Grid Workshop, Kraków, Poland: ACC Cyfronet AGH , 2010, p. 5-12Conference paper, Published paper (Refereed)
    Place, publisher, year, edition, pages
    Kraków, Poland: ACC Cyfronet AGH, 2010
    National Category
    Software Engineering
    Identifiers
    urn:nbn:se:uu:diva-129188 (URN)978-83-61433-01-9 (ISBN)
    Projects
    eSSENCE
    Available from: 2010-03-01 Created: 2010-08-06 Last updated: 2018-01-12Bibliographically approved
    4. Chelonia: A self-healing, replicated storage system
    Open this publication in new window or tab >>Chelonia: A self-healing, replicated storage system
    2011 (English)In: Computing in High Energy and Nuclear Physics: CHEP 2010, Bristol, UK: Institute of Physics Publishing (IOPP), 2011, p. 062019:1-6Conference paper, Published paper (Refereed)
    Place, publisher, year, edition, pages
    Bristol, UK: Institute of Physics Publishing (IOPP), 2011
    Series
    Journal of Physics: Conference Series ; 331
    National Category
    Software Engineering
    Identifiers
    urn:nbn:se:uu:diva-173392 (URN)10.1088/1742-6596/331/6/062019 (DOI)000301120500019 ()
    Projects
    eSSENCE
    Available from: 2011-12-23 Created: 2012-04-23 Last updated: 2018-01-12Bibliographically approved
    5. Performance and stability of the Chelonia storage system
    Open this publication in new window or tab >>Performance and stability of the Chelonia storage system
    Show others...
    2012 (English)In: Proc. International Symposium on Grids and Clouds 2012, Trieste, Italy: SISSA , 2012, p. 009:1-14Conference paper, Published paper (Refereed)
    Place, publisher, year, edition, pages
    Trieste, Italy: SISSA, 2012
    Series
    Proceedings of Science, ISSN 1824-8039 ; 153
    National Category
    Software Engineering
    Identifiers
    urn:nbn:se:uu:diva-129189 (URN)
    Conference
    ISGC 2012
    Projects
    eSSENCE
    Available from: 2012-03-01 Created: 2010-08-06 Last updated: 2018-01-12Bibliographically approved
    6. A scalable architecture for e-Science data management
    Open this publication in new window or tab >>A scalable architecture for e-Science data management
    2011 (English)In: Proc. 7th International Conference on e-Science, Los Alamitos, CA: IEEE Computer Society, 2011, p. 210-217Conference paper, Published paper (Refereed)
    Place, publisher, year, edition, pages
    Los Alamitos, CA: IEEE Computer Society, 2011
    National Category
    Computer Sciences
    Identifiers
    urn:nbn:se:uu:diva-166258 (URN)10.1109/eScience.2011.37 (DOI)978-1-4577-2163-2 (ISBN)
    Projects
    eSSENCE
    Available from: 2012-01-09 Created: 2012-01-11 Last updated: 2018-01-12Bibliographically approved
    7. Scientific analysis by queries in extended SPARQL over a scalable e-Science data store
    Open this publication in new window or tab >>Scientific analysis by queries in extended SPARQL over a scalable e-Science data store
    Show others...
    2013 (English)In: Proc. 9th International Conference on e-Science, Los Alamitos, CA: IEEE Computer Society, 2013, p. 98-106Conference paper, Published paper (Refereed)
    Place, publisher, year, edition, pages
    Los Alamitos, CA: IEEE Computer Society, 2013
    National Category
    Computer Sciences
    Identifiers
    urn:nbn:se:uu:diva-173448 (URN)10.1109/eScience.2013.19 (DOI)000330195500012 ()978-0-7695-5083-1 (ISBN)
    Projects
    eSSENCE
    Available from: 2013-10-25 Created: 2012-04-24 Last updated: 2018-01-12Bibliographically approved
    8. Investigating an open source cloud storage infrastructure for CERN-specific data analysis
    Open this publication in new window or tab >>Investigating an open source cloud storage infrastructure for CERN-specific data analysis
    2012 (English)In: Proc. 7th International Conference on Networking, Architecture, and Storage, Los Alamitos, CA: IEEE Computer Society, 2012, p. 84-88Conference paper, Published paper (Refereed)
    Place, publisher, year, edition, pages
    Los Alamitos, CA: IEEE Computer Society, 2012
    National Category
    Software Engineering
    Identifiers
    urn:nbn:se:uu:diva-173388 (URN)10.1109/NAS.2012.14 (DOI)978-1-4673-1889-1 (ISBN)
    Conference
    NAS 2012
    Projects
    eSSENCE
    Available from: 2012-09-24 Created: 2012-04-23 Last updated: 2018-01-12Bibliographically approved
  • 23. Torruangwatthana, Preechakorn
    et al.
    Wieslander, Håkan
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction.
    Blamey, Ben
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Hellander, Andreas
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Toor, Salman
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    HarmonicIO: Scalable data stream processing for scientific datasets2018In: Proc. 11th International Conference on Cloud Computing, Los Alamitos, CA: IEEE Computer Society, 2018, p. 879-882Conference paper (Refereed)
1 - 23 of 23
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