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  • 1. Abel, John H.
    et al.
    Drawert, Brian
    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.
    Petzold, Linda R.
    GillesPy: A Python package for stochastic model building and simulation2016In: IEEE Life Sciences Letters, E-ISSN 2332-7685, Vol. 2, p. 35-38Article in journal (Refereed)
  • 2.
    Ahmed, Laeeq
    et al.
    Royal Institute of Technology, KTH.
    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
    Royal Institute of Technology, KTH.
    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 prediction.2018In: Journal of Cheminformatics, ISSN 1758-2946, E-ISSN 1758-2946, Vol. 10, article id 8Article in journal (Refereed)
    Abstract [en]

    BACKGROUND: Docking and scoring large libraries of ligands against target proteins forms the basis of structure-based virtual screening. The problem is trivially parallelizable, and calculations are generally carried out on computer clusters or on large workstations in a brute force manner, by docking and scoring all available ligands.

    CONTRIBUTION: In this study we propose a strategy that is based on iteratively docking a set of ligands to form a training set, training a ligand-based model on this set, and predicting the remainder of the ligands to exclude those predicted as 'low-scoring' ligands. Then, another set of ligands are docked, the model is retrained and the process is repeated until a certain model efficiency level is reached. Thereafter, the remaining ligands are docked or excluded based on this model. We use SVM and conformal prediction to deliver valid prediction intervals for ranking the predicted ligands, and Apache Spark to parallelize both the docking and the modeling.

    RESULTS: We show on 4 different targets that conformal prediction based virtual screening (CPVS) is able to reduce the number of docked molecules by 62.61% while retaining an accuracy for the top 30 hits of 94% on average and a speedup of 3.7. The implementation is available as open source via GitHub ( https://github.com/laeeq80/spark-cpvs ) and can be run on high-performance computers as well as on cloud resources.

  • 3.
    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)
  • 4. Antolín, Roberto
    et al.
    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. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Gorjanc, Gregor
    Money, Daniel
    Hickey, John M.
    A hybrid method for the imputation of genomic data in livestock populations2017In: Genetics Selection Evolution, ISSN 0999-193X, E-ISSN 1297-9686, Vol. 49, article id 30Article in journal (Refereed)
  • 5. Anzt, Hartwig
    et al.
    Lukarski, Dimitar
    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.
    Tomov, Stanimire
    Dongarra, Jack
    Self-adaptive multiprecision preconditioners on multicore and manycore architectures2015In: High Performance Computing for Computational Science – VECPAR 2014, Springer, 2015, p. 115-123Conference paper (Refereed)
  • 6. 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)
  • 7. Arjmand, Doghonay
    et al.
    Engblom, Stefan
    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.
    Kreiss, Gunilla
    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, Numerical Analysis.
    Temporal upscaling in micromagnetism via heterogeneous multiscale methods2019In: Journal of Computational and Applied Mathematics, ISSN 0377-0427, E-ISSN 1879-1778, Vol. 345, p. 99-113Article in journal (Refereed)
  • 8.
    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)
  • 9.
    Bauer, Pavol
    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.
    Parallelism and efficiency in discrete-event simulation2015Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

    Discrete-event models depict systems where a discrete state is repeatedly altered by instantaneous changes in time, the events of the model. Such models have gained popularity in fields such as Computational Systems Biology or Computational Epidemiology due to the high modeling flexibility and the possibility to easily combine stochastic and deterministic dynamics. However, the system size of modern discrete-event models is growing and/or they need to be simulated at long time periods. Thus, efficient simulation algorithms are required, as well as the possibility to harness the compute potential of modern multicore computers. Due to the sequential design of simulators, parallelization of discrete event simulations is not trivial. This thesis discusses event-based modeling and sensitivity analysis and also examines ways to increase the efficiency of discrete-event simulations and to scale models involving deterministic and stochastic spatial dynamics on a large number of processor cores.

    List of papers
    1. Sensitivity estimation and inverse problems in spatial stochastic models of chemical kinetics
    Open this publication in new window or tab >>Sensitivity estimation and inverse problems in spatial stochastic models of chemical kinetics
    2015 (English)In: Numerical Mathematics and Advanced Applications: ENUMATH 2013, Springer, 2015, p. 519-527Conference paper, Published paper (Refereed)
    Place, publisher, year, edition, pages
    Springer, 2015
    Series
    Lecture Notes in Computational Science and Engineering ; 103
    National Category
    Computational Mathematics
    Identifiers
    urn:nbn:se:uu:diva-237184 (URN)10.1007/978-3-319-10705-9_51 (DOI)978-3-319-10704-2 (ISBN)
    Conference
    ENUMATH 2013
    Projects
    eSSENCEUPMARC
    Available from: 2014-10-31 Created: 2014-11-28 Last updated: 2018-11-12Bibliographically approved
    2. Fast event-based epidemiological simulations on national scales
    Open this publication in new window or tab >>Fast event-based epidemiological simulations on national scales
    2016 (English)In: The international journal of high performance computing applications, ISSN 1094-3420, E-ISSN 1741-2846, Vol. 30, p. 438-453Article in journal (Refereed) Published
    National Category
    Computer Sciences Computational Mathematics
    Identifiers
    urn:nbn:se:uu:diva-264751 (URN)10.1177/1094342016635723 (DOI)000387763100005 ()
    Projects
    UPMARCeSSENCE
    Available from: 2016-04-11 Created: 2015-10-16 Last updated: 2018-11-12Bibliographically approved
    3. Efficient inter-process synchronization for parallel discrete event simulation on multicores
    Open this publication in new window or tab >>Efficient inter-process synchronization for parallel discrete event simulation on multicores
    2015 (English)In: Proc. 3rd ACM SIGSIM Conference on Principles of Advanced Discrete Simulation, New York: ACM Press, 2015, p. 183-194Conference paper, Published paper (Refereed)
    Place, publisher, year, edition, pages
    New York: ACM Press, 2015
    National Category
    Computer Sciences
    Identifiers
    urn:nbn:se:uu:diva-260199 (URN)10.1145/2769458.2769476 (DOI)978-1-4503-3583-6 (ISBN)
    Conference
    SIGSIM-PADS 2015
    Projects
    UPMARC
    Available from: 2015-06-10 Created: 2015-08-17 Last updated: 2018-11-12Bibliographically approved
  • 10.
    Bauer, Pavol
    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.
    Parallelism in Event-Based Computations with Applications in Biology2017Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Event-based models find frequent usage in fields such as computational physics and biology as they may contain both continuous and discrete state variables and may incorporate both deterministic and stochastic state transitions. If the state transitions are stochastic, computer-generated random numbers are used to obtain the model solution. This type of event-based computations is also known as Monte-Carlo simulation.

    In this thesis, I study different approaches to execute event-based computations on parallel computers. This ultimately allows users to retrieve their simulation results in a fraction of the original computation time. As system sizes grow continuously or models have to be simulated at longer time scales, this is a necessary approach for current computational tasks.

    More specifically, I propose several ways to asynchronously simulate such models on parallel shared-memory computers, for example using parallel discrete-event simulation or task-based computing. The particular event-based models studied herein find applications in systems biology, computational epidemiology and computational neuroscience.

    In the presented studies, the proposed methods allow for high efficiency of the parallel simulation, typically scaling well with the number of used computer cores. As the scaling typically depends on individual model properties, the studies also investigate which quantities have the greatest impact on the simulation performance.

    Finally, the presented studies include other insights into event-based computations, such as methods how to estimate parameter sensitivity in stochastic models and how to simulate models that include both deterministic and stochastic state transitions.

    List of papers
    1. Sensitivity estimation and inverse problems in spatial stochastic models of chemical kinetics
    Open this publication in new window or tab >>Sensitivity estimation and inverse problems in spatial stochastic models of chemical kinetics
    2015 (English)In: Numerical Mathematics and Advanced Applications: ENUMATH 2013, Springer, 2015, p. 519-527Conference paper, Published paper (Refereed)
    Place, publisher, year, edition, pages
    Springer, 2015
    Series
    Lecture Notes in Computational Science and Engineering ; 103
    National Category
    Computational Mathematics
    Identifiers
    urn:nbn:se:uu:diva-237184 (URN)10.1007/978-3-319-10705-9_51 (DOI)978-3-319-10704-2 (ISBN)
    Conference
    ENUMATH 2013
    Projects
    eSSENCEUPMARC
    Available from: 2014-10-31 Created: 2014-11-28 Last updated: 2018-11-12Bibliographically approved
    2. Multiscale modelling via split-step methods in neural firing
    Open this publication in new window or tab >>Multiscale modelling via split-step methods in neural firing
    2018 (English)In: Mathematical and Computer Modelling of Dynamical Systems, ISSN 1387-3954, E-ISSN 1744-5051, Vol. 24, p. 426-445Article in journal (Refereed) Published
    National Category
    Computational Mathematics Neurosciences
    Identifiers
    urn:nbn:se:uu:diva-332008 (URN)10.1080/13873954.2018.1488740 (DOI)000440605300005 ()
    Projects
    UPMARCeSSENCE
    Available from: 2018-08-01 Created: 2017-10-22 Last updated: 2018-11-19Bibliographically approved
    3. Fast event-based epidemiological simulations on national scales
    Open this publication in new window or tab >>Fast event-based epidemiological simulations on national scales
    2016 (English)In: The international journal of high performance computing applications, ISSN 1094-3420, E-ISSN 1741-2846, Vol. 30, p. 438-453Article in journal (Refereed) Published
    National Category
    Computer Sciences Computational Mathematics
    Identifiers
    urn:nbn:se:uu:diva-264751 (URN)10.1177/1094342016635723 (DOI)000387763100005 ()
    Projects
    UPMARCeSSENCE
    Available from: 2016-04-11 Created: 2015-10-16 Last updated: 2018-11-12Bibliographically approved
    4. Efficient inter-process synchronization for parallel discrete event simulation on multicores
    Open this publication in new window or tab >>Efficient inter-process synchronization for parallel discrete event simulation on multicores
    2015 (English)In: Proc. 3rd ACM SIGSIM Conference on Principles of Advanced Discrete Simulation, New York: ACM Press, 2015, p. 183-194Conference paper, Published paper (Refereed)
    Place, publisher, year, edition, pages
    New York: ACM Press, 2015
    National Category
    Computer Sciences
    Identifiers
    urn:nbn:se:uu:diva-260199 (URN)10.1145/2769458.2769476 (DOI)978-1-4503-3583-6 (ISBN)
    Conference
    SIGSIM-PADS 2015
    Projects
    UPMARC
    Available from: 2015-06-10 Created: 2015-08-17 Last updated: 2018-11-12Bibliographically approved
    5. Exposing inter-process information for efficient parallel discrete event simulation of spatial stochastic systems
    Open this publication in new window or tab >>Exposing inter-process information for efficient parallel discrete event simulation of spatial stochastic systems
    2017 (English)In: Proc. 5th ACM SIGSIM Conference on Principles of Advanced Discrete Simulation, New York: ACM Press, 2017, p. 53-64Conference paper, Published paper (Refereed)
    Place, publisher, year, edition, pages
    New York: ACM Press, 2017
    National Category
    Computer Sciences
    Identifiers
    urn:nbn:se:uu:diva-328367 (URN)10.1145/3064911.3064916 (DOI)978-1-4503-4489-0 (ISBN)
    Conference
    SIGSIM-PADS 2017
    Projects
    UPMARC
    Available from: 2017-05-16 Created: 2017-08-22 Last updated: 2018-11-12Bibliographically approved
  • 11.
    Bauer, Pavol
    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.
    Engblom, Stefan
    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.
    Sensitivity estimation and inverse problems in spatial stochastic models of chemical kinetics2015In: Numerical Mathematics and Advanced Applications: ENUMATH 2013, Springer, 2015, p. 519-527Conference paper (Refereed)
  • 12.
    Bauer, Pavol
    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.
    Engblom, Stefan
    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.
    Mikulovic, Sanja
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Developmental Genetics.
    Senek, Aleksandar
    Multiscale modelling via split-step methods in neural firing2018In: Mathematical and Computer Modelling of Dynamical Systems, ISSN 1387-3954, E-ISSN 1744-5051, Vol. 24, p. 426-445Article in journal (Refereed)
  • 13.
    Bauer, Pavol
    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.
    Engblom, Stefan
    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.
    Widgren, Stefan
    Fast event-based epidemiological simulations on national scales2016In: The international journal of high performance computing applications, ISSN 1094-3420, E-ISSN 1741-2846, Vol. 30, p. 438-453Article in journal (Refereed)
  • 14.
    Bauer, Pavol
    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.
    Lindén, Jonatan
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computer Systems.
    Engblom, Stefan
    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.
    Jonsson, Bengt
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computer Systems.
    Efficient inter-process synchronization for parallel discrete event simulation on multicores2015In: Proc. 3rd ACM SIGSIM Conference on Principles of Advanced Discrete Simulation, New York: ACM Press, 2015, p. 183-194Conference paper (Refereed)
  • 15.
    Berglund, Anders
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computer Systems.
    Eckerdal, Anna
    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.
    Learning practice and theory in programming education: Students’ lived experience2015In: Proc. 3rd International Conference on Learning and Teaching in Computing and Engineering, Los Alamitos, CA: IEEE Computer Society, 2015, p. 180-186Conference paper (Refereed)
  • 16.
    Berglund, Anders
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computer Systems.
    Eckerdal, Anna
    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.
    Learning to program: A discussion on the interplay of theory and practice2015In: Proc. 1st Al Baha University and Uppsala University Symposium on Quality in Computing Education, 2015, p. 16-18Conference paper (Refereed)
  • 17.
    Blanc, Emilie
    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, Numerical Analysis.
    Engblom, Stefan
    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.
    Lötstedt, Per
    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, Numerical Analysis.
    Mesoscopic modeling of stochastic reaction–diffusion kinetics in the subdiffusive regime2016In: Multiscale Modeling & simulation, ISSN 1540-3459, E-ISSN 1540-3467, Vol. 14, p. 668-707Article in journal (Refereed)
  • 18. Boustedt, Jonas
    et al.
    Eckerdal, Anna
    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.
    McCartney, Robert
    Sanders, Kate
    Thomas, Lynda
    Zander, Carol
    Students' perceptions of the differences between formal and informal learning2011In: Proc. 7th International Computing Education Research Workshop, New York: ACM Press , 2011, p. 61-68Conference paper (Refereed)
  • 19. Brumm, Bernd
    et al.
    Kieri, Emil
    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 matrix-free Legendre spectral method for initial–boundary value problems2016In: Electronic Transactions on Numerical Analysis, ISSN 1068-9613, E-ISSN 1068-9613, Vol. 45, p. 283-304Article in journal (Refereed)
  • 20.
    Bull, Jonathan
    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, Numerical Analysis.
    Engblom, Stefan
    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 direct solver for the advection–diffusion equation using Green's functions and low-rank approximation2016In: Proc. 7th ECCOMAS Congress, European Community on Computional Methods in Applied Sciences (ECCOMAS), 2016, p. 7302-7316Conference paper (Refereed)
  • 21.
    Capuccini, Marco
    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.
    Ahmed, Laeeq
    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. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Large-scale virtual screening on public cloud resources with Apache Spark2017In: Journal of Cheminformatics, ISSN 1758-2946, E-ISSN 1758-2946, Vol. 9, article id 15Article in journal (Refereed)
  • 22.
    Capuccini, Marco
    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.
    Carlsson, Lars
    Norinder, Ulf
    Spjuth, Ola
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Conformal prediction in Spark: Large-scale machine learning with confidence2015In: Proc. 2nd International Symposium on Big Data Computing, Los Alamitos, CA: IEEE Computer Society, 2015, p. 61-67Conference paper (Refereed)
  • 23. Caulfield, Emmet
    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.
    CellMC: a multiplatform model compiler for the Cell Broadband Engine and x862010In: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811, Vol. 26, p. 426-428Article in journal (Refereed)
  • 24. Chevallier, Augustin
    et al.
    Engblom, Stefan
    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.
    Pathwise error bounds in multiscale variable splitting methods for spatial stochastic kinetics2018In: SIAM Journal on Numerical Analysis, ISSN 0036-1429, E-ISSN 1095-7170, Vol. 56, p. 469-498Article in journal (Refereed)
  • 25.
    Christoffer, Zakrisson
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Effektiva lösningsmetoder för Schrödingerekvationen: En jämförelse2013Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    In this paper the rate of convergence, speed of execution and symplectic properties of the time-integrators Leap-Frog (LF2), fourth order Runge-Kutta(RK4) and Crank-Nicholson (CN2) have been studied. This was done by solving the one-dimensional model for a particle in a box (Dirichlet-conditions). The results show that RK4 is the fastest in achieving higher tolerances, while CN2 is the fastest in achieving lower tolerances. Fourth order corrections of LF (LF4)and CN (CN4) were also studied, though these showed no improvements overLF2 and CN2. All methods were shown to exhibit symplectic behavior.

  • 26.
    Christoffersson, Gustaf
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Cell Biology.
    Lomei, Jalal
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Cell Biology.
    O'Callaghan, Paul
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Cell Biology.
    Kreuger, Johan
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Cell Biology.
    Engblom, Stefan
    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.
    Phillipson, Mia
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Cell Biology.
    Vascular sprouts induce local attraction of proangiogenic neutrophils2017In: Journal of Leukocyte Biology, ISSN 0741-5400, E-ISSN 1938-3673, Vol. 102, p. 741-751Article in journal (Refereed)
  • 27. Clear, Tony
    et al.
    Whalley, Jacqueline
    Robbins, Phil
    Philpott, Anne
    Eckerdal, Anna
    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.
    Laakso, Mikko-Jussi
    Lister, Raymond
    Report on the final BRACElet workshop: Auckland University of Technology, September 20102011In: Journal of Applied Computing and Information Technology, ISSN 2230-4398, Vol. 15, no 1:T1Article in journal (Other academic)
  • 28.
    Crooks, Lucy
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
    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.
    Carlborg, Örjan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
    An improved method for estimating chromosomal line origin in QTL analysis of crosses between outbred lines2011In: G3: Genes, Genomes, Genetics, ISSN 2160-1836, E-ISSN 2160-1836, Vol. 1, p. 57-64Article in journal (Refereed)
  • 29.
    Daniels, Mats
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computer Systems.
    Cajander, Åsa
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Eckerdal, Anna
    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.
    Lind, Mats
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Nylén, Aletta
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    Clear, Tony
    McDermott, Roger
    Competencies for paradigm shift "survival"2015In: Proc. 45th ASEE/IEEE Frontiers in Education Conference, Piscataway, NJ: IEEE Press, 2015, p. 1424-1429Conference paper (Refereed)
  • 30.
    Daurer, Benedikt J.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hantke, Max F.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    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. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Maia, Filipe R. N. C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hummingbird: monitoring and analyzing flash X-ray imaging experiments in real time2016In: Journal of applied crystallography, ISSN 0021-8898, E-ISSN 1600-5767, Vol. 49, p. 1042-1047Article in journal (Refereed)
  • 31.
    Daurer, Benedikt J.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Okamoto, Kenta
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Bielecki, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Maia, Filipe R. N. C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Mühlig, Kerstin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Seibert, M. Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hantke, Max F.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    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.
    Benner, W. Henry
    Svenda, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Tîmneanu, Nicuşor
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Ekeberg, Tomas
    Loh, N. Duane
    Pietrini, Alberto
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Zani, Alessandro
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Rath, Asawari D.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Westphal, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Kirian, Richard A.
    Awel, Salah
    Wiedorn, Max O.
    van der Schot, Gijs
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Carlsson, Gunilla H.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hasse, Dirk
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Sellberg, Jonas A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Barty, Anton
    Andreasson, Jakob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Boutet, Sebastian
    Williams, Garth
    Koglin, Jason
    Andersson, Inger
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Larsson, Daniel S. D.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Experimental strategies for imaging bioparticles with femtosecond hard X-ray pulses2017In: IUCrJ, ISSN 0972-6918, E-ISSN 2052-2525, Vol. 4, p. 251-262Article in journal (Refereed)
  • 32. Do-Quang, Minh
    et al.
    Engblom, Stefan
    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.
    Tornberg, Anna-Karin
    Amberg, Gustav
    The well-posedness of diffuse interface modeling of surfactants in two-phase fluid flow2013In: Wetting and Evaporation: Droplets of Pure and Complex Fluids, France: Aix-Marseille Université , 2013, p. 80-81Conference paper (Refereed)
  • 33.
    Dorostkar, Ali
    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, Numerical Analysis.
    Lukarski, Dimitar
    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.
    Lund, Björn
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, Geophysics.
    Neytcheva, Maya
    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, Numerical Analysis.
    Notay, Yvan
    Schmidt, Peter
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, Geophysics.
    CPU and GPU performance of large scale numerical simulations in Geophysics2014In: Euro-Par 2014: Parallel Processing Workshops, Part I, Springer, 2014, p. 12-23Conference paper (Refereed)
  • 34.
    Dorostkar, Ali
    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, Numerical Analysis.
    Lukarski, Dimitar
    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.
    Lund, Björn
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, Geophysics.
    Neytcheva, Maya
    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, Numerical Analysis.
    Notay, Yvan
    Schmidt, Peter
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, Geophysics.
    Parallel performance study of block-preconditioned iterative methods on multicore computer systems2014Report (Other academic)
  • 35. Drawert, Brian
    et al.
    Engblom, Stefan
    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
    URDME: a modular framework for stochastic simulation of reaction-transport processes in complex geometries2012In: BMC Systems Biology, ISSN 1752-0509, E-ISSN 1752-0509, Vol. 6, p. 76:1-17Article in journal (Refereed)
  • 36. Drawert, Brian
    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.
    Bales, Ben
    Banerjee, Debjani
    Bellesia, Giovanni
    Daigle Jr., Bernie J.
    Douglas, Geoffrey
    Gu, Mengyuan
    Gupta, Anand
    Hellander, Stefan
    Horuk, Chris
    Nath, Dibyendu
    Takkar, Aviral
    Wu, Sheng
    Lötstedt, Per
    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, Numerical Analysis.
    Krintz, Chandra
    Petzold, Linda R.
    Stochastic Simulation Service: Bridging the gap between the computational expert and the biologist2016In: PloS Computational Biology, ISSN 1553-734X, E-ISSN 1553-7358, Vol. 12, no 12, article id e1005220Article in journal (Refereed)
  • 37. 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)
  • 38.
    Eckerdal, Anna
    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.
    Relating theory and practice in laboratory work: a variation theoretical study2015In: Studies in Higher Education, ISSN 0307-5079, E-ISSN 1470-174X, Vol. 40, p. 867-880Article in journal (Refereed)
  • 39.
    Eckerdal, Anna
    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.
    Kinnunen, Päivi
    Thota, Neena
    Nylén, Aletta
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    Sheard, Judy
    Malmi, Lauri
    Teaching and learning with MOOCs: Computing academics' perspectives and engagement2014In: Proc. 19th Conference on Innovation and Technology in Computer Science Education, New York: ACM Press , 2014, p. 9-14Conference paper (Refereed)
  • 40.
    Eckerdal, Anna
    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.
    Laakso, Mikko-Jussi
    Lopez, Mike
    Sarkar, Amitrajit
    Relationship between text and action conceptions of programming: a phenomenographic and quantitative perspective2011In: Proc. 16th Conference on Innovation and Technology in Computer Science Education, New York: ACM Press , 2011, p. 33-37Conference paper (Refereed)
  • 41.
    Eckerdal, Anna
    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.
    Thuné, Michael
    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.
    Analysing the enacted object of learning in lab assignments in programming education2013In: Proc. 1st International Conference on Learning and Teaching in Computing and Engineering, Los Alamitos, CA: IEEE Computer Society, 2013, p. 208-211Conference paper (Refereed)
  • 42.
    Ekeberg, Tomas
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Engblom, Stefan
    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.
    Liu, Jing
    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.
    Machine learning for ultrafast X-ray diffraction patterns on large-scale GPU clusters2015In: The international journal of high performance computing applications, ISSN 1094-3420, E-ISSN 1741-2846, Vol. 29, p. 233-243Article in journal (Refereed)
  • 43.
    Ekeberg, Tomas
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Svenda, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Abergel, Chantal
    Maia, Filipe R. N. C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Seltzer, Virginie
    Claverie, Jean-Michel
    Hantke, Max
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Jönsson, Olof
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    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.
    van der Schot, Gijs
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Liang, Mengning
    DePonte, Daniel P.
    Barty, Anton
    Seibert, M. Marvin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Iwan, Bianca
    Andersson, Inger
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Loh, N. Duane
    Martin, Andrew V.
    Chapman, Henry
    Bostedt, Christoph
    Bozek, John D.
    Ferguson, Ken R.
    Krzywinski, Jacek
    Epp, Sascha W.
    Rolles, Daniel
    Rudenko, Artem
    Hartmann, Robert
    Kimmel, Nils
    Hajdu, Janos
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics.
    Three-dimensional reconstruction of the giant mimivirus particle with an X-ray free-electron laser2015In: Physical Review Letters, ISSN 0031-9007, E-ISSN 1079-7114, Vol. 114, no 9, p. 098102:1-6, article id 098102Article in journal (Refereed)
  • 44.
    Elmgren, Maja
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry.
    Andersson, Staffan
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Physics Didactics.
    Pears, Arnold
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computer Systems.
    Pålsson, Stefan
    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.
    Scaffolding pedagogic excellence in higher education2013In: Improving Student Learning through Research and Scholarship, UK: Oxford Brookes University , 2013, p. 164-176Conference paper (Refereed)
  • 45. 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)
  • 46.
    Engblom, Stefan
    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.
    On the stability of stochastic jump kinetics2014In: Applied Mathematics, ISSN 2152-7385, E-ISSN 2152-7393, Vol. 5, p. 3217-3239Article in journal (Refereed)
  • 47.
    Engblom, Stefan
    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.
    On the stability of stochastic jump kinetics2012Report (Other academic)
  • 48.
    Engblom, Stefan
    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.
    On well-separated sets and fast multipole methods2011In: Applied Numerical Mathematics, ISSN 0168-9274, E-ISSN 1873-5460, Vol. 61, p. 1096-1102Article in journal (Refereed)
  • 49.
    Engblom, Stefan
    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.
    Stability and strong convergence for spatial stochastic kinetics2017In: Stochastic Processes, Multiscale Modeling, and Numerical Methods for Computational Cellular Biology, Springer, 2017, p. 109-125Chapter in book (Refereed)
  • 50.
    Engblom, Stefan
    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.
    Stochastic simulation of pattern formation in growing tissue: A multilevel approach2019In: Bulletin of Mathematical Biology, ISSN 0092-8240, E-ISSN 1522-9602, Vol. 81Article in journal (Refereed)
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