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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.
    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.
    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)
  • 4.
    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)
  • 5.
    Bouchnita, Anass
    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.
    Hellander, 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.
    A 3D multiscale model to explore the role of EGFR overexpression in tumourigenesis2019In: Bulletin of Mathematical Biology, ISSN 0092-8240, E-ISSN 1522-9602, Vol. 81, p. 2323-2344Article in journal (Refereed)
  • 6. 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)
  • 7.
    Coulier, Adrien
    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.
    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.
    Orchestral: a lightweight framework for parallel simulations of cell–cell communication2018In: Proc. 14th International Conference on e-Science, Los Alamitos, CA: IEEE Computer Society, 2018, p. 168-176Conference paper (Refereed)
  • 8. 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)
  • 9. 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)
  • 10. 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)
  • 11.
    Engblom, Stefan
    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.
    Ferm, Lars
    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.
    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, Numerical Analysis.
    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.
    Simulation of stochastic reaction-diffusion processes on unstructured meshes2008Report (Other academic)
  • 12.
    Engblom, Stefan
    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.
    Ferm, Lars
    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.
    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, Numerical Analysis.
    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.
    Simulation of stochastic reaction-diffusion processes on unstructured meshes2009In: SIAM Journal on Scientific Computing, ISSN 1064-8275, E-ISSN 1095-7197, Vol. 31, p. 1774-1797Article in journal (Refereed)
  • 13.
    Engblom, Stefan
    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.
    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.
    Multiscale simulation of stochastic reaction–diffusion networks2017In: Stochastic Processes, Multiscale Modeling, and Numerical Methods for Computational Cellular Biology, Springer, 2017, p. 55-79Chapter in book (Refereed)
  • 14.
    Ferm, Lars
    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.
    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, Numerical Analysis.
    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.
    An adaptive algorithm for simulation of stochastic reaction-diffusion processes2009Report (Other academic)
  • 15.
    Ferm, Lars
    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.
    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, Numerical Analysis.
    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.
    An adaptive algorithm for simulation of stochastic reaction-diffusion processes2010In: Journal of Computational Physics, ISSN 0021-9991, E-ISSN 1090-2716, Vol. 229, p. 343-360Article in journal (Refereed)
  • 16.
    Ferm, Lars
    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.
    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.
    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, Numerical Analysis.
    A hierarchy of approximations of the master equation scaled by a size parameter2007Report (Other academic)
  • 17.
    Ferm, Lars
    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.
    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.
    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, Numerical Analysis.
    A hierarchy of approximations of the master equation scaled by a size parameter2008In: Journal of Scientific Computing, ISSN 0885-7474, E-ISSN 1573-7691, Vol. 34, p. 127-151Article in journal (Refereed)
  • 18. Hegland, Markus
    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, Numerical Analysis.
    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.
    Sparse grids and hybrid methods for the chemical master equation2008In: BIT Numerical Mathematics, ISSN 0006-3835, E-ISSN 1572-9125, Vol. 48, p. 265-283Article in journal (Refereed)
  • 19.
    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, Numerical Analysis.
    Efficient computation of transient solutions of the chemical master equation based on uniformization and Quasi-Monte Carlo2007Report (Other academic)
  • 20.
    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, Numerical Analysis.
    Efficient computation of transient solutions of the chemical master equation based on uniformization and quasi-Monte Carlo2008In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 128, p. 154109:1-7Article in journal (Refereed)
  • 21.
    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, Numerical Analysis.
    Multiscale Stochastic Simulation of Reaction-Transport Processes: Applications in Molecular Systems Biology2011Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Quantitative descriptions of reaction kinetics formulated at the stochastic mesoscopic level are frequently used to study various aspects of regulation and control in models of cellular control systems. For this type of systems, numerical simulation offers a variety of challenges caused by the high dimensionality of the problem and the multiscale properties often displayed by the biochemical model.

    In this thesis I have studied several aspects of stochastic simulation of both well-stirred and spatially heterogenous systems. In the well-stirred case, a hybrid method is proposed that reduces the dimension and stiffness of a model. We also demonstrate how both a high performance implementation and a variance reduction technique based on quasi-Monte Carlo can reduce the computational cost to estimate the probability density of the system.

    In the spatially dependent case, the use of unstructured, tetrahedral meshes to sample realizations of the stochastic process is proposed. Using such meshes, we then extend the reaction-diffusion framework to incorporate active transport of cellular cargo in a seamless manner. Finally, two multilevel methods for spatial stochastic simulation are considered. One of them is a space-time adaptive method combining exact stochastic, approximate stochastic and macroscopic modeling levels to reduce the simualation cost. The other method blends together mesoscale and microscale simulation methods to locally increase modeling resolution.

    List of papers
    1. Hybrid method for the chemical master equation
    Open this publication in new window or tab >>Hybrid method for the chemical master equation
    2007 (English)In: Journal of Computational Physics, ISSN 0021-9991, E-ISSN 1090-2716, Vol. 227, p. 100-122Article in journal (Refereed) Published
    National Category
    Computational Mathematics Biochemistry and Molecular Biology
    Identifiers
    urn:nbn:se:uu:diva-26755 (URN)10.1016/j.jcp.2007.07.020 (DOI)000251140100006 ()
    Available from: 2007-10-26 Created: 2007-10-26 Last updated: 2017-12-07Bibliographically approved
    2. CellMC: a multiplatform model compiler for the Cell Broadband Engine and x86
    Open this publication in new window or tab >>CellMC: a multiplatform model compiler for the Cell Broadband Engine and x86
    2010 (English)In: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811, Vol. 26, p. 426-428Article in journal (Refereed) Published
    National Category
    Software Engineering Biochemistry and Molecular Biology
    Identifiers
    urn:nbn:se:uu:diva-111276 (URN)10.1093/bioinformatics/btp662 (DOI)000274342800026 ()
    Projects
    eSSENCE
    Available from: 2009-12-08 Created: 2009-12-08 Last updated: 2018-01-12Bibliographically approved
    3. Efficient computation of transient solutions of the chemical master equation based on uniformization and quasi-Monte Carlo
    Open this publication in new window or tab >>Efficient computation of transient solutions of the chemical master equation based on uniformization and quasi-Monte Carlo
    2008 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 128, p. 154109:1-7Article in journal (Refereed) Published
    National Category
    Computational Mathematics Biochemistry and Molecular Biology
    Identifiers
    urn:nbn:se:uu:diva-16105 (URN)10.1063/1.2897976 (DOI)000255228900011 ()
    Available from: 2008-04-22 Created: 2008-04-22 Last updated: 2017-12-08Bibliographically approved
    4. Simulation of stochastic reaction-diffusion processes on unstructured meshes
    Open this publication in new window or tab >>Simulation of stochastic reaction-diffusion processes on unstructured meshes
    2009 (English)In: SIAM Journal on Scientific Computing, ISSN 1064-8275, E-ISSN 1095-7197, Vol. 31, p. 1774-1797Article in journal (Refereed) Published
    National Category
    Computational Mathematics Computer Sciences
    Identifiers
    urn:nbn:se:uu:diva-97689 (URN)10.1137/080721388 (DOI)000267746200008 ()
    Available from: 2008-11-07 Created: 2008-11-07 Last updated: 2018-11-12Bibliographically approved
    5. Incorporating active transport of cellular cargo in stochastic mesoscopic models of living cells
    Open this publication in new window or tab >>Incorporating active transport of cellular cargo in stochastic mesoscopic models of living cells
    2010 (English)In: Multiscale Modeling & simulation, ISSN 1540-3459, E-ISSN 1540-3467, Vol. 8, p. 1691-1714Article in journal (Refereed) Published
    National Category
    Computational Mathematics Biochemistry and Molecular Biology
    Identifiers
    urn:nbn:se:uu:diva-131200 (URN)10.1137/100784709 (DOI)000285509300006 ()
    Projects
    eSSENCE
    Available from: 2010-09-23 Created: 2010-09-27 Last updated: 2017-12-12Bibliographically approved
    6. An adaptive algorithm for simulation of stochastic reaction-diffusion processes
    Open this publication in new window or tab >>An adaptive algorithm for simulation of stochastic reaction-diffusion processes
    2010 (English)In: Journal of Computational Physics, ISSN 0021-9991, E-ISSN 1090-2716, Vol. 229, p. 343-360Article in journal (Refereed) Published
    National Category
    Computational Mathematics Computer Sciences
    Identifiers
    urn:nbn:se:uu:diva-108918 (URN)10.1016/j.jcp.2009.09.030 (DOI)000272760500008 ()
    Projects
    eSSENCE
    Available from: 2009-10-04 Created: 2009-10-04 Last updated: 2018-01-13Bibliographically approved
    7. Coupled mesoscopic and microscopic simulation of stochastic reaction-diffusion processes in mixed dimensions
    Open this publication in new window or tab >>Coupled mesoscopic and microscopic simulation of stochastic reaction-diffusion processes in mixed dimensions
    2011 (English)Report (Other academic)
    Series
    Technical report / Department of Information Technology, Uppsala University, ISSN 1404-3203 ; 2011-005
    National Category
    Computational Mathematics Biochemistry and Molecular Biology
    Identifiers
    urn:nbn:se:uu:diva-152228 (URN)
    Projects
    eSSENCE
    Available from: 2011-04-04 Created: 2011-04-27 Last updated: 2011-11-18Bibliographically approved
  • 22.
    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, Numerical Analysis.
    Numerical simulation of well stirred biochemical reaction networks governed by the master equation2008Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

    Numerical simulation of stochastic biochemical reaction networks has received much attention in the growing field of computational systems biology. Systems are frequently modeled as a continuous-time discrete space Markov chain, and the governing equation for the probability density of the system is the (chemical) master equation. The direct numerical solution of this equation suffers from an exponential growth in computational time and memory with the number of reacting species in the model. As a consequence, Monte Carlo simulation methods play an important role in the study of stochastic chemical networks. The stochastic simulation algorithm (SSA) due to Gillespie has been available for more than three decades, but due to the multi-scale property of the chemical systems and the slow convergence of Monte Carlo methods, much work is currently being done in order to devise more efficient approximate schemes.

    In this thesis we review recent work for the solution of the chemical master equation by direct methods, by exact Monte Carlo methods and by approximate and hybrid methods. We also describe two conceptually different numerical methods to reduce the computational time when studying models using the SSA. A hybrid method is proposed, which is based on the separation of species into two subsets based on the variance of the copy numbers. This method yields a significant speed-up when the system permits such a splitting of the state space. A different approach is taken in an algorithm that makes use of low-discrepancy sequences and the method of uniformization to reduce variance in the computed density function.

    List of papers
    1. Hybrid method for the chemical master equation
    Open this publication in new window or tab >>Hybrid method for the chemical master equation
    2007 (English)In: Journal of Computational Physics, ISSN 0021-9991, E-ISSN 1090-2716, Vol. 227, p. 100-122Article in journal (Refereed) Published
    National Category
    Computational Mathematics Biochemistry and Molecular Biology
    Identifiers
    urn:nbn:se:uu:diva-26755 (URN)10.1016/j.jcp.2007.07.020 (DOI)000251140100006 ()
    Available from: 2007-10-26 Created: 2007-10-26 Last updated: 2017-12-07Bibliographically approved
    2. Sparse grids and hybrid methods for the chemical master equation
    Open this publication in new window or tab >>Sparse grids and hybrid methods for the chemical master equation
    2008 (English)In: BIT Numerical Mathematics, ISSN 0006-3835, E-ISSN 1572-9125, Vol. 48, p. 265-283Article in journal (Refereed) Published
    National Category
    Computational Mathematics Biochemistry and Molecular Biology
    Identifiers
    urn:nbn:se:uu:diva-17747 (URN)10.1007/s10543-008-0174-z (DOI)000258527500007 ()
    Available from: 2008-08-21 Created: 2008-08-21 Last updated: 2017-12-08Bibliographically approved
    3. Efficient computation of transient solutions of the chemical master equation based on uniformization and quasi-Monte Carlo
    Open this publication in new window or tab >>Efficient computation of transient solutions of the chemical master equation based on uniformization and quasi-Monte Carlo
    2008 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 128, p. 154109:1-7Article in journal (Refereed) Published
    National Category
    Computational Mathematics Biochemistry and Molecular Biology
    Identifiers
    urn:nbn:se:uu:diva-16105 (URN)10.1063/1.2897976 (DOI)000255228900011 ()
    Available from: 2008-04-22 Created: 2008-04-22 Last updated: 2017-12-08Bibliographically approved
  • 23.
    Hellander, Andreas
    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.
    Ferm, Lars
    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.
    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.
    Adaptive stochastic hybrid simulation of biochemical reaction-diffusion models2009In: Proc. 3rd International Conference on Foundations of Systems Biology in Engineering, The Systems Biology Institute , 2009, p. 4-Conference paper (Refereed)
  • 24.
    Hellander, Andreas
    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.
    Hellander, 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, Numerical Analysis.
    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.
    Coupled mesoscopic and microscopic simulation of stochastic reaction-diffusion processes in mixed dimensions2011Report (Other academic)
  • 25.
    Hellander, Andreas
    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.
    Hellander, 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, Numerical Analysis.
    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.
    Coupled mesoscopic and microscopic simulation of stochastic reaction-diffusion processes in mixed dimensions2012In: Multiscale Modeling & simulation, ISSN 1540-3459, E-ISSN 1540-3467, Vol. 10, p. 585-611Article in journal (Refereed)
  • 26.
    Hellander, Andreas
    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.
    Klosa, Jan
    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.
    MacNamara, Shev
    Robustness analysis of spatiotemporal models in the presence of extrinsic fluctuations2017In: SIAM Journal on Applied Mathematics, ISSN 0036-1399, E-ISSN 1095-712X, Vol. 77, p. 1157-1183Article in journal (Refereed)
  • 27.
    Hellander, Andreas
    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.
    Lawson, Michael J.
    Drawert, Brian
    Petzold, Linda
    Local error estimates for adaptive simulation of the reaction–diffusion master equation via operator splitting2014In: Journal of Computational Physics, ISSN 0021-9991, E-ISSN 1090-2716, Vol. 266, p. 89-100Article in journal (Refereed)
  • 28.
    Hellander, Andreas
    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.
    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.
    Hybrid method for the chemical master equation2006Report (Other academic)
  • 29.
    Hellander, Andreas
    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.
    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.
    Hybrid method for the chemical master equation2007In: Journal of Computational Physics, ISSN 0021-9991, E-ISSN 1090-2716, Vol. 227, p. 100-122Article in journal (Refereed)
  • 30.
    Hellander, Andreas
    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.
    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.
    Incorporating active transport of cellular cargo in stochastic mesoscopic models of living cells2010Report (Other academic)
  • 31.
    Hellander, Andreas
    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.
    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.
    Incorporating active transport of cellular cargo in stochastic mesoscopic models of living cells2010In: Multiscale Modeling & simulation, ISSN 1540-3459, E-ISSN 1540-3467, Vol. 8, p. 1691-1714Article in journal (Refereed)
  • 32.
    Hellander, Stefan
    et al.
    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, Computational Science.
    Petzold, Linda
    University of California, Department of Computer Science.
    Mesoscopic-microscopic spatial stochastic simulation with automatic system partitioning2017In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 147, no 23, article id 234101Article in journal (Refereed)
    Abstract [en]

    The reaction-diffusion master equation (RDME) is a model that allows for efficient on-lattice simulation of spatially resolved stochastic chemical kinetics. Compared to off-lattice hard-sphere simulations with Brownian dynamics or Green's function reaction dynamics, the RDME can be orders of magnitude faster if the lattice spacing can be chosen coarse enough. However, strongly diffusion-controlled reactions mandate a very fine mesh resolution for acceptable accuracy. It is common that reactions in the same model differ in their degree of diffusion control and therefore require different degrees of mesh resolution. This renders mesoscopic simulation inefficient for systems with multiscale properties. Mesoscopic-microscopic hybrid methods address this problem by resolving the most challenging reactions with a microscale, off-lattice simulation. However, all methods to date require manual partitioning of a system, effectively limiting their usefulness as "black-box" simulation codes. In this paper, we propose a hybrid simulation algorithm with automatic system partitioning based on indirect a priori error estimates. We demonstrate the accuracy and efficiency of the method on models of diffusion-controlled networks in 3D.

  • 33. Hellander, Stefan
    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.
    Petzold, Linda
    Reaction rates for mesoscopic reaction-diffusion kinetics2015In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics, ISSN 1539-3755, E-ISSN 1550-2376, Vol. 91, p. 023312:1-12, article id 023312Article in journal (Refereed)
  • 34.
    Hellander, Stefan
    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.
    Hellander, Andreas
    Petzold, Linda
    Reaction-diffusion master equation in the microscopic limit2012In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics, ISSN 1539-3755, E-ISSN 1550-2376, Vol. 85, p. 042901:1-5Article in journal (Refereed)
  • 35. Horuk, Christopher B.
    et al.
    Douglas, Geoffrey
    Gupta, Anand
    Krintz, Chandra
    Bales, Ben
    Bellesia, Giovanni
    Drawert, Brian
    Wolski, Rich
    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.
    Automatic and portable cloud deployment for scientific simulations2014In: Proc. 12th International Conference on High Performance Computing and Simulation, Piscataway, NJ: IEEE , 2014, p. 374-381Conference paper (Refereed)
  • 36. 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)
  • 37. Kaucka, Marketa
    et al.
    Ivashkin, Evgeny
    Gyllborg, Daniel
    Zikmund, Tomas
    Tesarova, Marketa
    Kaiser, Jozef
    Xie, Meng
    Petersen, Julian
    Pachnis, Vassilis
    Nicolis, Silvia K.
    Yu, Tian
    Sharpe, Paul
    Arenas, Ernest
    Brismar, Hjalmar
    Blom, Hans
    Clevers, Hans
    Suter, Ueli
    Chagin, Andrei S.
    Fried, Kaj
    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.
    Adameyko, Igor
    Analysis of neural crest-derived clones reveals novel aspects of facial development2016In: Science Advances, ISSN 2375-2548, Vol. 2, no 8, p. e1600060:1-16, article id e1600060Article in journal (Refereed)
  • 38. Kaucka, Marketa
    et al.
    Zikmund, Tomas
    Tesarova, Marketa
    Gyllborg, Daniel
    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.
    Jaros, Josef
    Kaiser, Jozef
    Petersen, Julian
    Szarowska, Bara
    Newton, Phillip T.
    Dyachuk, Vyacheslav
    Li, Lei
    Qian, Hong
    Johansson, Anne-Sofie
    Mishina, Yuji
    Currie, Josh
    Tanaka, Elly M.
    Erickson, Alek
    Dudley, Andrew
    Brismar, Hjalmar
    Southam, Paul
    Coen, Enrico
    Chen, Min
    Weinstein, Lee S.
    Hampl, Ales
    Arenas, Ernest
    Chagin, Andrei S.
    Fried, Kaj
    Adameyko, Igor
    Oriented clonal cell dynamics enables accurate growth and shaping of vertebrate cartilage2017In: eLIFE, E-ISSN 2050-084X, Vol. 6, article id e25902Article in journal (Refereed)
  • 39.
    Lawson, Michael J.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
    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.
    Accuracy of the Michaelis–Menten approximation when analysing effects of molecular noise2015In: Journal of the Royal Society Interface, ISSN 1742-5689, E-ISSN 1742-5662, Vol. 12, no 106, p. 20150054:1-10, article id 20150054Article in journal (Refereed)
  • 40.
    Meinecke, Lina
    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.
    Analysis and design of jump coefficients in discrete stochastic diffusion models2016In: SIAM Journal on Scientific Computing, ISSN 1064-8275, E-ISSN 1095-7197, Vol. 38, p. A55-A83Article in journal (Refereed)
  • 41.
    Singh, Prashant
    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.
    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.
    Hyperparameter optimization for approximate Bayesian computation2018In: Proc. 50th Winter Simulation Conference, Piscataway, NJ: IEEE, 2018, p. 1718-1729Conference paper (Refereed)
  • 42.
    Singh, Prashant
    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.
    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.
    Multi-objective optimization driven construction of uniform priors for likelihood-free parameter inference2018In: Proc. 32nd European Simulation and Modelling Conference, EUROSIS , 2018, p. 22-27Conference paper (Refereed)
  • 43.
    Singh, Prashant
    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.
    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.
    Surrogate assisted model reduction for stochastic biochemical reaction networks2017In: Proc. 49th Winter Simulation Conference, Piscataway, NJ: IEEE, 2017, p. 1773-1783Conference paper (Refereed)
  • 44.
    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)
  • 45. 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)
  • 46.
    Wrede, Fredrik
    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.
    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.
    Smart computational exploration of stochastic gene regulatory network models using human-in-the-loop semi-supervised learning2019In: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811, Vol. 35Article in journal (Refereed)
  • 47. Östberg, Per-Olov
    et al.
    Hellander, Andreas
    Drawert, Brian
    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.
    Petzold, Linda
    Abstractions for scaling eScience applications to distributed computing environments: A StratUm integration case study in molecular systems biology2012In: Proc. 3rd International Conference on Bioinformatics Models, Methods and Algorithms, Setúbal, Portugal: SciTePress , 2012, p. 290-294Conference paper (Refereed)
  • 48. Östberg, Per-Olov
    et al.
    Hellander, Andreas
    Drawert, Brian
    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.
    Petzold, Linda
    Reducing complexity in management of eScience computations2012In: Proc. 12th International Symposium on Cluster, Cloud and Grid Computing, Los Alamitos, CA: IEEE Computer Society, 2012, p. 845-852Conference paper (Refereed)
1 - 48 of 48
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