uu.seUppsala University Publications
Change search
Refine search result
1234 1 - 50 of 173
CiteExportLink to result list
Permanent link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
Rows per page
  • 5
  • 10
  • 20
  • 50
  • 100
  • 250
Sort
  • Standard (Relevance)
  • Author A-Ö
  • Author Ö-A
  • Title A-Ö
  • Title Ö-A
  • Publication type A-Ö
  • Publication type Ö-A
  • Issued (Oldest first)
  • Issued (Newest first)
  • Created (Oldest first)
  • Created (Newest first)
  • Last updated (Oldest first)
  • Last updated (Newest first)
  • Disputation date (earliest first)
  • Disputation date (latest first)
  • Standard (Relevance)
  • Author A-Ö
  • Author Ö-A
  • Title A-Ö
  • Title Ö-A
  • Publication type A-Ö
  • Publication type Ö-A
  • Issued (Oldest first)
  • Issued (Newest first)
  • Created (Oldest first)
  • Created (Newest first)
  • Last updated (Oldest first)
  • Last updated (Newest first)
  • Disputation date (earliest first)
  • Disputation date (latest first)
Select
The maximal number of hits you can export is 250. When you want to export more records please use the Create feeds function.
  • 1.
    Abdulla, Parosh
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computer Systems.
    Aronis, Stavros
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    Jonsson, Bengt
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computer Systems.
    Sagonas, Konstantinos
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    Optimal dynamic partial order reduction2014In: Proc. 41st ACM SIGPLAN-SIGACT Symposium on Principles of Programming Languages, New York: ACM Press, 2014, p. 373-384Conference paper (Refereed)
    Abstract [en]

    Stateless model checking is a powerful technique for program verification, which however suffers from an exponential growth in the number of explored executions. A successful technique for reducing this number, while still maintaining complete coverage, is Dynamic Partial Order Reduction (DPOR). We present a new DPOR algorithm, which is the first to be provably optimal in that it always explores the minimal number of executions. It is based on a novel class of sets, called source sets, which replace the role of persistent sets in previous algorithms. First, we show how to modify an existing DPOR algorithm to work with source sets, resulting in an efficient and simple to implement algorithm. Second, we extend this algorithm with a novel mechanism, called wakeup trees, that allows to achieve optimality. We have implemented both algorithms in a stateless model checking tool for Erlang programs. Experiments show that source sets significantly increase the performance and that wakeup trees incur only a small overhead in both time and space.

  • 2.
    Abdulla, Parosh
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computer Systems.
    Aronis, Stavros
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    Jonsson, Bengt
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    Sagonas, Konstantinos
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    Source Sets: A Foundation for Optimal Dynamic Partial Order Reduction2017In: Journal of the ACM, ISSN 0004-5411, E-ISSN 1557-735X, Vol. 64, no 4, article id 25Article in journal (Refereed)
    Abstract [en]

    Stateless model checking is a powerful method for program verification that, however, suffers from an exponential growth in the number of explored executions. A successful technique for reducing this number, while still maintaining complete coverage, is Dynamic Partial Order Reduction (DPOR), an algorithm originally introduced by Flanagan and Godefroid in 2005 and since then not only used as a point of reference but also extended by various researchers. In this article, we present a new DPOR algorithm, which is the first to be provably optimal in that it always explores the minimal number of executions. It is based on a novel class of sets, called source sets, that replace the role of persistent sets in previous algorithms. We begin by showing how to modify the original DPOR algorithm to work with source sets, resulting in an efficient and simple-to-implement algorithm, called source-DPOR. Subsequently, we enhance this algorithm with a novel mechanism, called wakeup trees, that allows the resulting algorithm, called optimal-DPOR, to achieve optimality. Both algorithms are then extended to computational models where processes may disable each other, for example, via locks. Finally, we discuss tradeoffs of the source-and optimal-DPOR algorithm and present programs that illustrate significant time and space performance differences between them. We have implemented both algorithms in a publicly available stateless model checking tool for Erlang programs, while the source-DPOR algorithm is at the core of a publicly available stateless model checking tool for C/pthread programs running on machines with relaxed memory models. Experiments show that source sets significantly increase the performance of stateless model checking compared to using the original DPOR algorithm and that wakeup trees incur only a small overhead in both time and space in practice.

  • 3.
    Abdulla, Parosh Aziz
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computer Systems.
    Aronis, Stavros
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    Atig, Mohamed Faouzi
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computer Systems.
    Jonsson, Bengt
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computer Systems.
    Leonardsson, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computer Systems.
    Sagonas, Konstantinos
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    Stateless model checking for TSO and PSO2015In: Tools and Algorithms for the Construction and Analysis of Systems: TACAS 2015, Springer Berlin/Heidelberg, 2015, p. 353-367Conference paper (Refereed)
  • 4.
    Abdulla, Parosh Aziz
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computer Systems.
    Atig, Mohamed Faouzi
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computer Systems.
    Chen, Yu-Fang
    Academia Sinica.
    Leonardsson, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computer Systems.
    Rezine, Ahmed
    Linköping University.
    MEMORAX, a Precise and Sound Tool for Automatic Fence Insertion under TSO2013In: Tools and Algorithms for the Construction and Analysis of Systems, Springer Berlin/Heidelberg, 2013, p. 530-536Conference paper (Refereed)
  • 5. 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)
  • 6.
    Araujo, Hugo
    et al.
    Univ Fed Pernambuco, Recife, PE, Brazil.
    Carvalho, Gustavo
    Univ Fed Pernambuco, Recife, PE, Brazil.
    Mohaqeqi, Morteza
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computer Systems.
    Mousavi, Mohammad Reza
    Halmstad Univ, Halmstad, Sweden;Univ Leicester, Leicester, Leics, England.
    Sampaio, Augusto
    Univ Fed Pernambuco, Recife, PE, Brazil.
    Sound conformance testing for cyber-physical systems: Theory and implementation2018In: Science of Computer Programming, ISSN 0167-6423, E-ISSN 1872-7964, Vol. 162, p. 35-54Article in journal (Refereed)
    Abstract [en]

    Conformance testing is a formal and structured approach to verifying system correctness. We propose a conformance testing algorithm for cyber-physical systems, based on the notion of hybrid conformance by Abbas and Fainekos. We show how the dynamics of system specification and the sampling rate play an essential role in making sound verdicts. We specify and prove error bounds that lead to sound test-suites for a given specification and a given sampling rate. We use reachability analysis to find such bounds and implement the proposed approach using the CORA toolbox in Matlab. We apply the implemented approach on a case study from the automotive domain.

  • 7.
    Aronis, Stavros
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    Papaspyrou, Nikolaos
    Roukounaki, Katerina
    Sagonas, Konstantinos
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    Tsiouris, Yiannis
    Venetis, Ioannis E.
    A scalability benchmark suite for Erlang/OTP2012In: Proc. 11th ACM SIGPLAN Workshop on Erlang, New York: ACM Press, 2012, p. 33-42Conference paper (Refereed)
    Abstract [en]

    Programming language implementers rely heavily on benchmarking for measuring and understanding performance of algorithms, architectural designs, and trade-offs between alternative implementations of compilers, runtime systems, and virtual machine components. Given this fact, it seems a bit ironic that it is often more difficult to come up with a good benchmark suite than a good implementation of a programming language.

    This paper presents the main aspects of the design and the current status of bencherl, a publicly available scalability benchmark suite for applications written in Erlang. In contrast to other benchmark suites, which are usually designed to report a particular performance point, our benchmark suite aims to assess scalability, i.e., help developers to study a set of performance points that show how an application's performance changes when additional resources (e.g., CPU cores, schedulers, etc.) are added. We describe the scalability dimensions that the suite aims to examine and present its infrastructure and current set of benchmarks. We also report some limited set of performance results in order to show the capabilities of our suite.

  • 8.
    Aronis, Stavros
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    Sagonas, Konstantinos
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    The shared-memory interferences of Erlang/OTP built-ins2017In: Proceedings Of The 16Th Acm Sigplan International Workshop On Erlang (Erlang '17) / [ed] Chechina, N.; Fritchie, SL., New York: Association for Computing Machinery (ACM), 2017, p. 43-54Conference paper (Refereed)
    Abstract [en]

    Erlang is a concurrent functional language based on the actor modelof concurrency. In the purest form of this model, actors are realizedby processes that do not share memory and communicate witheach other exclusively via message passing. Erlang comes quiteclose to this model, as message passing is the primary form of interprocesscommunication and each process has its own memoryarea that is managed by the process itself. For this reason, Erlangis often referred to as implementing “shared nothing” concurrency.Although this is a convenient abstraction, in reality Erlang’s mainimplementation, the Erlang/OTP system, comes with a large numberof built-in operations that access memory which is shared byprocesses. In this paper, we categorize these built-ins, and characterizethe interferences between them that can result in observabledifferences of program behaviour when these built-ins are usedin a concurrent setting. The paper is complemented by a publiclyavailable suite of more than one hundred small Erlang programsthat demonstrate the racing behaviour of these built-ins.

  • 9.
    Aronis, Stavros
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    Sagonas, Konstantinos
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    Lystig Fritchie, Scott
    VMware, Cambridge, MA, USA.
    Testing And Verifying Chain Repair Methods For CORFU Using Stateless Model Checking2017Conference paper (Refereed)
    Abstract [en]

    Corfu is a distributed shared log that is designed to be scalable and reliable in the presence of failures and asynchrony. Internally, Corfu is fully replicated for fault tolerance, without sharding data or sacrificing strong consistency. In this case study, we present the modeling approaches we followed to test and verify, using Concuerror, the correctness of repair methods for the Chain Replication protocol suitable for Corfu. In the first two methods we tried, Concuerror located bugs quite fast. In contrast, the tool did not manage to find bugs in the third method, but the time this took also motivated an improvement in the tool that reduces the number of traces explored. Besides more details about all the above, we present experiences and lessons learned from applying stateless model checking for verifying complex protocols suitable for distributed programming.

  • 10.
    Asada, Akira
    et al.
    Osaka Inst Technol, Fac Informat Sci & Technol, Osaka, Japan.
    Hayashi, Masaki
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Arts, Department of Game Design.
    Hirayama, Makoto J.
    Osaka Inst Technol, Fac Informat Sci & Technol, Osaka, Japan.
    TV production tool to make art programmes based on a simple scenario2019In: INTERNATIONAL WORKSHOP ON ADVANCED IMAGE TECHNOLOGY (IWAIT) 2019 / [ed] Kemao, Q Hayase, K Lau, PY Lie, WN Lee, YL Srisuk, S Yu, L, SPIE-INT SOC OPTICAL ENGINEERING , 2019, article id 1104921Conference paper (Refereed)
    Abstract [en]

    We have been studying and developing the real-time Computer Graphics (CG) based virtual museum where a user can walk through to appreciate artworks digitized in high-resolution. Our virtual museum also has a function to automatically create TV program-like CG animations using 3D CG models in the virtual space as it is so that the user can learn about individual works by watching the art shows. The CG animation is produced with TVML (TV program Making Language) engine implemented on the virtual museum. However, the current problem is that it requires a lot of work for a developer to write the complicated TVML scripts manually Therefore, this time we have developed a special tool to help the developer to prepare the TVML scripts easily. With this tool, the developer can produce the TVML-based art program simply by writing out a simple scenario on an ordinary text editor. In order to design this tool, TV art programs actually broadcasted are analyzed to determine the syntax of the simple scenario. Based on the analysis, we have developed the tool with TVML engine working on the Unity game Engine. We have also used this tool to imitate the broadcasted TV program to validate its usability.

  • 11.
    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)
  • 12.
    Axelsson, Veronica
    Gotland University, School of Game Design, Technology and Learning Processes.
    What technique is most appropriate for 3D modeling a chair for a movie production?2013Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Making 3D models with polygon modeling is the most common technique used for a 3D animated movie production, but there are also other good modeling techniques to work with. The aim of this thesis is to examine which of three chosen modeling technique is most appropriate to use for modeling a chair for a 3D animated movie production. I made three models of the same chair design and compared the results. The modeling technique used is polygon modeling, NURBS modeling and digital sculpting. A few factors were considered when I judged which one of the three techniques that was most suitable: The model's geometry, the workflow and the rendering (material and lightning).

    The three chairs were rendered in the same scene with the same lightning and settings. The results showed that the model's geometry and how smooth it is to work with the modeling technique matter most for judging which technique is the most appropriate. In addition, the results show that how the light falls and reflects the surface depends on how the geometry was placed on the model rather than which of the other modeling techniques that was used.

  • 13.
    Aziz, Yama
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Computing Science.
    Exploring a keyword driven testing framework: a case study at Scania IT2017Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    The purpose of this thesis is to investigate organizational quality assurance through the international testing standard ISO 29119. The focus will be on how an organization carries out testing processes and designs and implements test cases. Keyword driven testing is a test composition concept in ISO 29119 and suitable for automation. This thesis will answer how keyword driven testing can facilitate the development of maintainable test cases and support test automation in an agile organization.

    The methodology used was a qualitative case study including semi-structured interviews and focus groups with agile business units within Scania IT. Among the interview participants were developers, test engineers, scrum masters and a unit manager.

    The results describe testing practices carried out in several agile business units, maintainability issues with test automation and general ideas of how test automation should be approached. Common issues with test automation were test cases failing due to changed test inputs, inexperience with test automation frameworks and lack of resources due to project release cycle.

    This thesis concludes that keyword driven testing has the potential of solving several maintainability issues with test cases breaking. However, the practicality and effectiveness of said potential remain unanswered. Moreover, successfully developing an automated keyword driven testing framework requires integration with existing test automation tools and considering the agile organizational circumstances.

  • 14. Bangerth, Wolfgang
    et al.
    Burstedde, Carsten
    Heister, Timo
    Kronbichler, Martin
    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.
    Algorithms and data structures for massively parallel generic adaptive finite element codes2011In: ACM Transactions on Mathematical Software, ISSN 0098-3500, E-ISSN 1557-7295, Vol. 38, no 2, p. 14:1-28Article in journal (Refereed)
  • 15.
    Barot, Camille
    et al.
    N Carolina State Univ, Dept Comp Sci, Raleigh, NC 27695 USA..
    Buro, Michael
    Univ Alberta, Dept Comp Sci, Edmonton, AB, Canada..
    Cook, Michael
    Univ London, Goldsmiths, London WC1E 7HU, England..
    Eladhari, Mirjam
    Stockholm Univ, Dept Comp & Syst Sci, S-10691 Stockholm, Sweden.;Univ Malta, Inst Digital Games, Msida, Malta..
    Johansson, Magnus
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Arts, Department of Game Design.
    Li, Boyang
    Disney Res, Pittsburgh, PA USA..
    Liapis, Antonios
    Univ Malta, Inst Digital Games, Msida, Malta..
    McCoy, Josh
    Amer Univ, Dept Comp, Washington, DC 20016 USA..
    Ontanon, Santiago
    Drexel Univ, Dept Comp Sci, Philadelphia, PA 19104 USA..
    Rowe, Jonathan
    N Carolina State Univ, Dept Comp Sci, Raleigh, NC 27695 USA..
    Tomai, Emmett
    Univ Texas Rio Grande Valley, Dept Comp Sci, Brownsville, TX USA..
    Verhagen, Harko
    Stockholm Univ, Dept Comp & Syst Sci, S-10691 Stockholm, Sweden..
    Zook, Alexander
    Georgia Inst Technol, Sch Interact Comp, Atlanta, GA 30332 USA..
    The AIIDE 2015 Workshop Program2016In: The AI Magazine, ISSN 0738-4602, Vol. 37, no 2, p. 91-94Article in journal (Refereed)
    Abstract [en]

    The workshop program at the 11th Annual AAAI Conference on Artificial Intelligence and Interactive Digital Entertainment was held November 14-15, 2015, at the University of California, Santa Cruz, USA. The program included four workshops (one of which was a joint workshop): Artificial Intelligence in Adversarial Real-Time Games, Experimental AI in Games, Intelligent Narrative Technologies and Social Believability in Games, and Player Modeling. This article contains the reports of three of the four workshops.

  • 16.
    Bauer, Paul
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Barrozo, Alexandre
    Department of Chemistry, University of Southern California, SGM 418, 3620 McClintock Ave., Los Angeles, CA 90089-1062, United StatesDepartment of Chemistry, University of Southern California, SGM 418, 3620 McClintock Ave., Los Angeles, CA 90089-1062, United States.
    Purg, Miha
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Amrein, Beat Anton
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Esguerra, Mauricio
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Wilson, Philippe Barrie
    Leicester School of Pharmacy, De Montfort University, The Gateway, Leicester LE1 9BH, UK.
    Major, Dan Thomas
    Department of Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel.
    Åqvist, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational Biology and Bioinformatics.
    Kamerlin, Shina C. Lynn
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structural Biology.
    Q6: A comprehensive toolkit for empirical valence bond and related free energy calculations2018In: SoftwareX, ISSN 2352-7110, p. 388-395Article in journal (Refereed)
    Abstract [en]

    Atomistic simulations have become one of the main approaches to study the chemistry and dynamicsof biomolecular systems in solution. Chemical modelling is a powerful way to understand biochemistry,with a number of different programs available to perform specialized calculations. We present here Q6, anew version of the Q software package, which is a generalized package for empirical valence bond, linearinteraction energy, and other free energy calculations. In addition to general technical improvements, Q6extends the reach of the EVB implementation to fast approximations of quantum effects, extended solventdescriptions and quick estimation of the contributions of individual residues to changes in the activationfree energy of reactions.

  • 17.
    Beecham, Sarah
    et al.
    Lero, Limerick, Ireland..
    Clear, Tony
    Auckland Univ Technol, Sch Engn Comp & Math Sci, Auckland, New Zealand..
    Barr, John
    Ithaca Coll, Dept Comp Sci, Ithaca, NY USA..
    Daniels, Mats
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computer Systems.
    Oudshoorn, Michael
    Northwest Missouri State Univ, Sch Comp Sci & Informat Syst, Maryville, MO USA..
    Noll, John
    Univ East London, London, England..
    Preparing tomorrow's software engineers for work in a global environment2017In: IEEE Software, ISSN 0740-7459, E-ISSN 1937-4194, Vol. 34, no 1, p. 9-12Article in journal (Refereed)
  • 18. Behrmann, Gerd
    et al.
    David, Alexandre
    Larsen, Kim Guldstrand
    Pettersson, Paul
    Yi, Wang
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computer Systems.
    Developing UPPAAL over 15 years2011In: Software, practice & experience, ISSN 0038-0644, E-ISSN 1097-024X, Vol. 41, no 2, p. 133-142Article in journal (Refereed)
  • 19.
    Bernström, Kristian
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Computing Science.
    Näsman, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Computing Science.
    Utredning och implementering av en prototyp för integration av Prevas FOCS och ABB 800xA2014Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    ABB and Prevas have initiated a collaboration to sell a system to optimize steel industry furnaces, called FOCS. The purpose of this thesis is to investigate possibilities for integrating Prevas FOCS and ABB 800xA.

    The result of the investigation is used for an implementation of a prototype of the integrated system. The study shows a general method that can be used when implementing two software systems. The prototype of the integrated systems is made with usability principles in mind. This is a very important aspect in order to create a good working environment for the operators of a steel plant. It is also important to follow communication standards when integrating software systems. In an industrial network used in the steel industry OPC is a standard for communication. We recommend ABB and Prevas to follow this standard when possible to make the integration smoother. To keep the cost of the integration to a minimum it is also recommended to reuse existing resources. This can however have a negative effect on usability and it is therefore important to keep a balance between cost and usability.

    The prototype made in this thesis accomplishes the goal of transferring the functionalities used by operators of Prevas FOCS to 800xA so that operators can control the processes using only one integrated system.

  • 20.
    Black-Schaffer, David
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computer Systems.
    Dally, William J.
    Stanford University, Department of Computer Science.
    Block-Parallel Programming for Real-time Embedded Applications2010In: Proc. 39th International Conference on Parallel Processing, Piscataway, NJ: IEEE , 2010, p. 297-306Conference paper (Refereed)
    Abstract [en]

    Embedded media applications have traditionally used custom ASICs to meet their real-time performance requirements. However, the combination of increasing chip design cost and availability of commodity many-core processors is making programmable devices increasingly attractive alternatives. Yet for these processors to be successful in this role, programming systems are needed that can automate the task of mapping the applications to the tens-to-hundreds of cores on current and future many-core processors, while simultaneously guaranteeing the real-time throughput constraints. This paper presents a block-parallel program description for embedded real-time media applications and automatic transformations including buffering and parallelization to ensure the program meets the throughput requirements. These transformations are enabled by starting with a high-level, yet intuitive, application description. The description builds on traditional stream programming structures by adding simple control and serialization constructs to enable a greater variety of applications. The result is an application description that provides a balance of flexibility and power to the programmer, while exposing the application structure to the compiler at a high enough level to enable useful transformations without heroic analysis.

  • 21.
    Blom, Johan
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Mathematics and Computer Science, Department of Information Technology. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Mathematics and Computer Science, Department of Information Technology, Computer Systems. Datorteknik.
    Jonsson, Bengt
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Mathematics and Computer Science, Department of Information Technology. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Mathematics and Computer Science, Department of Information Technology, Computer Systems. Datorteknik.
    Automated test generation for industrial Erlang applications2003In: Erlang Workshop 2003: Proceedings of the 2003 ACM SIGPLAN Workshop on Erlang, Uppsala, Sweden, August 29, 2003., 2003, p. 8-14Conference paper (Refereed)
  • 22.
    Boustedt, Jonas
    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 student perspective on software development and maintenance2010Report (Other academic)
  • 23. Broy, Manfred
    et al.
    Jonsson, BengtUppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Mathematics and Computer Science, Department of Information Technology. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Mathematics and Computer Science, Department of Information Technology, Computer Systems. datorteknik.Katoen, Joost-PieterLeucker, MartinUppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Mathematics and Computer Science, Department of Information Technology. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Mathematics and Computer Science, Department of Information Technology, Computer Systems. datorteknik.Pretschner, Alexander
    Model-Based Testing of Reactive Systems: Advanced Lectures2005Collection (editor) (Other scientific)
  • 24.
    Bäcklund, Emil
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology.
    Survailability planning App2012Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
  • 25.
    Bäärnhielm, Arvid
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences.
    Utveckling av applikation till plattformen Android2015Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [sv]

    Målet med detta projekt var att utveckla en applikation för Android för lagring av tillagade matlådor. Utifrån beräknad hållbarhetstid för matlådan skulle en notifikation ges innan matlådan blev dålig. Då idén byggde på att hållbarhetstider skulle beräknas utifrån ingående ingredienser så kunde projektet inte färdigställas när det visade sig att detta inte var ett genomförbart sätt att beräkna hållbarhetstid. En till stora delar fungerande applikation utifrån grundidén har ändå skapats.

  • 26. 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)
  • 27. Clear, Tony
    et al.
    Beecham, Sarah
    Barr, John
    Daniels, Mats
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computer Systems.
    McDermott, Roger
    Oudshoorn, Michael
    Savickaite, Airina
    Noll, John
    Challenges and recommendations for the design and conduct of global software engineering courses: A systematic review2015In: Proc. 20th ITiCSE Working Group Reports, New York: ACM Press, 2015, p. 1-39Conference paper (Refereed)
  • 28.
    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)
  • 29.
    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)
  • 30. 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)
  • 31. 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)
  • 32. 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)
  • 33.
    Edvinsson, Marcus
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Implementing the circularly polarized light method for determining wall thickness of cellulosic fibres2012Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    The wall thickness of pulp fibers plays a major role in the paper industry, but it is currently not possible to measure this property without manual laboratory work. In 2007, researcher Ho Fan Jang patented a technique to automatically measure fiber wall thickness, combining the unique optical properties of pulp fibers with image analysis. In short, the method creates images through the use of an optical system resulting in color values which demonstrate the retardation of a particular wave length instead of the intensity. A device based on this patent has since been developed by Eurocon Analyzer. This thesis investigates the software aspects of this technique, using sample images generated by the Eurocon Analyzer prototype.

    The software developed in this thesis has been subdivided into three groups for independent consideration. First being the problem of solving wall thickness for colors in the images. Secondly, the image analysis process of identifying fibers and good points for measuring them. Lastly, it is investigated how statistical analysis can be applied to improve results and derive other useful properties such as fiber coarseness.

    With the use of this technique there are several problems which need to be overcome. One such problem is that it may be difficult to disambiguate the colors produced by fibers of different thickness. This complication may be reduced by using image analysis and statistical analysis. Another challenge can be that theoretical values often differ greatly from the observed values which makes the computational aspect of the method problematic. The results of this thesis show that the effects of these problems can be greatly reduced and that the method offers promising results.

    The results clearly distinguish between and show the expected characteristics of different pulp samples, but more qualitative reference measurements are needed in order to draw conclusions on the correctness of the results.

  • 34. 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)
  • 35.
    Engquist, Björn
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Numerical Analysis.
    Smedsaas, Tom
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Numerical Analysis.
    Automatic analysis in PDE software1984In: PDE Software: Modules, Interfaces and Systems, Amsterdam, The Netherlands: Elsevier Science , 1984, p. 399-409Conference paper (Refereed)
  • 36.
    Engquist, Björn
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Numerical Analysis.
    Smedsaas, Tom
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Numerical Analysis.
    Automatic computer code generation for hyperbolic and parabolic differential equations1980In: SIAM Journal on Scientific and Statistical Computing, ISSN 0196-5204, Vol. 1, p. 249-259Article in journal (Refereed)
  • 37.
    Hayashi, Masaki
    et al.
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Arts, Department of Game Design.
    Shishikui, Yoshiaki
    Meiji Univ, Frontier Media Sci Dept, Nakano Ku, 4-21-1 Nakano, Tokyo 1648525, Japan..
    Bachelder, Steven
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Arts, Department of Game Design.
    Nakajima, Masayuki
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Arts, Department of Game Design.
    An Attempt of Mimicking TV News Program with Full 3DCG-Aiming at the Text-Generated TV System -2016In: 2016 Ieee International Symposium On Broadband Multimedia Systems And Broadcasting (BMSB), 2016Conference paper (Refereed)
    Abstract [en]

    We have been studying and developing a new television system based on a methodology which delivers text-based scripts through the Internet representing visual contents instead of transmitting visual content in a format of video data. Such a Text-Generated TV System is achieved by the technology called TVML (TV program Making Language) enabling to create TV-program-like computer graphics animation automatically from script. One of the problems in our development is how to establish the scheme of TV program production with TVML to get quality contents like in a real TV broadcast. Our approach to the problem is to analyze the real TV program and to mimic it with TVML. We first choose a reference TV program then analyze it in many aspects. Based on the acquired knowledge, we then transfer those findings to CG production made using TVML to make a copy of the original TV show as faithful as possible. The objective of the attempt is to reveal the essential elements which would be needed to obtain a full-CG TV program with quality. In this paper, we describe the mimicking process of the news show, the result of the TVML production with a comparison to the original and the evaluation result that we conducted with testers. Finally, we discuss the pros and cons of the CG production applied to produce news show and have shed light on the problems.

  • 38. Heister, Timo
    et al.
    Kronbichler, Martin
    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.
    Bangerth, Wolfgang
    Generic finite element programming for massively parallel flow simulations2010In: Proc. ECCOMAS CFD Conference 2010, Portugal: Tech. Univ. Lisbon , 2010, p. 10-Conference paper (Refereed)
  • 39.
    Henderson-Sellers, Brian
    et al.
    University of Technology, Sydney, Australia.
    Ralyté, Jolita
    University of Geneva, Carouge, Switzerland.
    Ågerfalk, Pär J.
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Social Sciences, Department of Informatics and Media.
    Rossi, Matti
    Aalto University, Aalto, Finland.
    Situational Method Engineering2014Book (Other academic)
    Abstract [en]

    While previously available methodologies for software – like those published in the early days of object technology – claimed to be appropriate for every conceivable project, situational method engineering (SME) acknowledges that most projects typically have individual characteristics and situations. Thus, finding the most effective methodology for a particular project needs specific tailoring to that situation. Such a tailored software development methodology needs to take into account all the bits and pieces needed for an organization to develop software, including the software process, the input and output work products, the people involved, the languages used to describe requirements, design, code, and eventually also measures of success or failure.

    The authors have structured the book into three parts. Part I deals with all the basic concepts, terminology and overall ideas underpinning situational method engineering. As a summary of this part, they present a formal meta-model that enables readers to create their own quality methods and supporting tools. In Part II, they explain how to implement SME in practice, i.e., how to find method components and put them together and how to evaluate the resulting method. For illustration, they also include several industry case studies of customized or constructed processes, highlighting the impact that high-quality engineered methods can have on the success of an industrial software development. Finally, Part III summarizes some of the more recent and forward-looking ideas.

    This book presents the first summary of the state of the art for SME. For academics, it provides a comprehensive conceptual framework and discusses new research areas. For lecturers, thanks to its step-by-step explanations from basics to the customization and quality assessment of constructed methods, it serves as a solid basis for comprehensive courses on the topic. For industry methodologists, it offers a reference guide on features and technologies to consider when developing in-house software development methods or customising and adopting off-the-shelf ones.

  • 40.
    Holm, Marcus
    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.
    Tillenius, Martin
    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.
    Black-Schaffer, David
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computer Systems.
    A simple model for tuning tasks2011In: Proc. 4th Swedish Workshop on Multi-Core Computing, Linköping, Sweden: Linköping University , 2011, p. 45-49Conference paper (Other academic)
  • 41.
    Hommerberg, Måns
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology.
    Enriching Circuit Switched Mobile Phone Calls with Cooperative Web Applications2011Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    The thesis investigates the possibility to enrich standard mobile phone calls with cooperative web applications. Originating from the research field know as Computer Supported Cooperative Work (CSCW) this thesis report introduces and describes the implementation of several applications which can be used by the calling parties together during a phone call. Additionally, the report describes a proof-of-concept prototype for the Android platform, and discusses the performance of cooperative web application running on mobile devices in terms of network and CPU use.

    The conclusions of the thesis describe a prototype application addressing and implementing the requirements as described by the theory of computer supported collaborated work. The performance of the running application showed to be satisfactory, both regarding to network

    demand and processor use.

  • 42. 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)
  • 43.
    Håkansson, John
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Mathematics and Computer Science, Department of Information Technology. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Mathematics and Computer Science, Department of Information Technology, Computer Systems. Datorteknik.
    Jonsson, Bengt
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Mathematics and Computer Science, Department of Information Technology. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Mathematics and Computer Science, Department of Information Technology, Computer Systems. Datorteknik.
    Lundqvist, Ola
    Generating on-line test oracles from temporal logic specifications2003In: International Journal of Software Tools for Technology Transfer, ISSN 1433-2779, Vol. 4, no 4, p. 456-471Article in journal (Refereed)
  • 44.
    Högström, Kjell
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Numerical Analysis.
    Thuné, Michael
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Numerical Analysis.
    Portability and data structures in scientific computing: Object-oriented design of utility routines in Fortran1992In: Parallel Computing: From Theory to Sound Practice, Amsterdam, The Netherlands: IOS Press , 1992, p. 585-588Conference paper (Refereed)
  • 45. Islam, Shareeful
    et al.
    Stoica, Anca-Juliana
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    Software risk management modeling using goal-driven approach from early requirements engineering2012In: Risk Assessment and Management / [ed] Zhang, Zhiyong, Cheyenne, WY: Publishing Services LLC , 2012, p. 385-401Chapter in book (Refereed)
  • 46. 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)
  • 47.
    Jayawardena, Mahen
    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.
    An e-Science Approach to Genetic Analysis of Quantitative Traits2010Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Many important traits in plants, animals and humans are quantitative, and most such traits are generally believed to be affected by multiple genetic loci. Standard computational tools for mapping of quantitative traits (i.e. for finding Quantitative Trait Loci, QTL, in the genome) use linear regression models for relating the observed phenotypes to the genetic composition of individuals in an experimental population. Using these tools to simultaneously search for multiple QTL is computationally demanding. The main reason for this is the complex optimization landscape for the multidimensional global optimization problems that must be solved. This thesis describes parallel algorithms, implementations and tools for simultaneous mapping of several QTL. These new computational tools enable genetic analysis exploiting new classes of multidimensional statistical models, potentially resulting in interesting results in genetics.

    We first describe how the standard, brute-force algorithm for global optimization in QTL analysis is parallelized and implemented on a grid system. Then, we also present a parallelized version of the more elaborate global optimization algorithm DIRECT and show how this can be efficiently deployed and used on grid systems and other loosely-coupled architectures. The parallel DIRECT scheme is further developed to exploit both coarse-grained parallelism in grid systems or clusters as well as fine-grained, tightly-coupled parallelism in multi-core nodes. The results show that excellent speedup and performance can be archived on grid systems and clusters, even when using a tightly-coupled algorithm such as DIRECT. Finally, we provide two distinctly different front-ends for our code. One is a grid portal providing a graphical front-end suitable for novice users and standard forms of QTL analysis. The other is a prototype of an R-based grid-enabled problem solving environment. Both of these front-ends can, after some further refinement, be utilized by geneticists for performing multidimensional genetic analysis of quantitative traits on a regular basis.

    List of papers
    1. Using parallel computing and grid systems for genetic mapping of quantitative traits
    Open this publication in new window or tab >>Using parallel computing and grid systems for genetic mapping of quantitative traits
    2007 (English)In: Applied Parallel Computing: State of the Art in Scientific Computing, Berlin: Springer-Verlag , 2007, p. 627-636Conference paper, Published paper (Refereed)
    Place, publisher, year, edition, pages
    Berlin: Springer-Verlag, 2007
    Series
    Lecture Notes in Computer Science ; 4699
    National Category
    Bioinformatics (Computational Biology)
    Identifiers
    urn:nbn:se:uu:diva-11546 (URN)10.1007/978-3-540-75755-9_76 (DOI)000250904900076 ()978-3-540-75754-2 (ISBN)
    Available from: 2007-09-26 Created: 2007-09-26 Last updated: 2018-01-12Bibliographically approved
    2. Grid-enabling an efficient algorithm for demanding global optimization problems in genetic analysis
    Open this publication in new window or tab >>Grid-enabling an efficient algorithm for demanding global optimization problems in genetic analysis
    2007 (English)In: Proc. 3rd International Conference on e-Science and Grid Computing, Los Alamitos, CA: IEEE Computer Society, 2007, p. 205-212Conference paper, Published paper (Refereed)
    Place, publisher, year, edition, pages
    Los Alamitos, CA: IEEE Computer Society, 2007
    National Category
    Computer Sciences Computational Mathematics
    Identifiers
    urn:nbn:se:uu:diva-12617 (URN)10.1109/E-SCIENCE.2007.40 (DOI)000253614600025 ()978-0-7695-3064-2 (ISBN)
    Available from: 2008-01-08 Created: 2008-01-08 Last updated: 2018-01-12Bibliographically approved
    3. Efficient optimization algorithms and implementations for genetic analysis of complex traits on a grid system with multicore nodes
    Open this publication in new window or tab >>Efficient optimization algorithms and implementations for genetic analysis of complex traits on a grid system with multicore nodes
    2008 (English)Conference paper, Published paper (Refereed)
    Place, publisher, year, edition, pages
    Trondheim, Norway: Norwegian University of Science and Technology, 2008
    National Category
    Computer Sciences Computational Mathematics
    Identifiers
    urn:nbn:se:uu:diva-111590 (URN)
    Conference
    PARA 2008: State of the Art in Scientific and Parallel Computing
    Projects
    UPMARC
    Available from: 2010-01-12 Created: 2009-12-17 Last updated: 2018-01-12Bibliographically approved
    4. Computational and visualization tools for genetic analysis of complex traits
    Open this publication in new window or tab >>Computational and visualization tools for genetic analysis of complex traits
    2010 (English)Report (Other academic)
    Series
    Technical report / Department of Information Technology, Uppsala University, ISSN 1404-3203 ; 2010-001
    National Category
    Software Engineering Computational Mathematics
    Identifiers
    urn:nbn:se:uu:diva-111593 (URN)
    Projects
    eSSENCE
    Available from: 2010-01-12 Created: 2009-12-17 Last updated: 2018-01-12Bibliographically approved
    5. A Grid-Enabled Problem Solving Environment for QTL Analysis in R
    Open this publication in new window or tab >>A Grid-Enabled Problem Solving Environment for QTL Analysis in R
    Show others...
    2010 (English)In: Proc. 2nd International Conference on Bioinformatics and Computational Biology, Cary, NC: ISCA , 2010, p. 202-209Conference paper, Published paper (Refereed)
    Place, publisher, year, edition, pages
    Cary, NC: ISCA, 2010
    National Category
    Software Engineering Genetics
    Identifiers
    urn:nbn:se:uu:diva-111594 (URN)978-1-880843-76-5 (ISBN)
    Projects
    eSSENCE
    Available from: 2010-01-12 Created: 2009-12-17 Last updated: 2018-01-12Bibliographically approved
  • 48.
    Jayawardena, Mahen
    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.
    Parallel algorithms and implementations for genetic analysis of quantitative traits2007Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

    Many important traits in plants, animals and humans are quantitative, and most such traits are generally believed to be regulated by multiple genetic loci. Standard computational tools for analysis of quantitative traits use linear regression models for relating the observed phenotypes to the genetic composition of individuals in a population. However, using these tools to simultaneously search for multiple genetic loci is very computationally demanding. The main reason for this is the complex nature of the optimization landscape for the multidimensional global optimization problems that must be solved. This thesis describes parallel algorithms and implementation techniques for such optimization problems. The new computational tools will eventually enable genetic analysis exploiting new classes of multidimensional statistical models, potentially resulting in interesting results in genetics.

    We first describe how the algorithm used for global optimization in the standard, serial software is parallelized and implemented on a grid system. Then, we also describe a parallelized version of the more elaborate global optimization algorithm DIRECT and show how this can be deployed on grid systems and other loosely-coupled architectures. The parallel DIRECT scheme is further developed to exploit both coarse-grained parallelism in grid or clusters as well as fine-grained, tightly-coupled parallelism in multi-core nodes. The results show that excellent speedup and performance can be archived on grid systems and clusters, even when using a tightly-coupled algorithms such as DIRECT. Finally, a pilot implementation of a grid portal providing a graphical front-end for our code is implemented. After some further development, this portal can be utilized by geneticists for performing multidimensional genetic analysis of quantitative traits on a regular basis.

  • 49.
    Jayawardena, Mahen
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Nettelblad, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Toor, Salman
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Östberg, Per-Olov
    Elmroth, Erik
    Holmgren, Sverker
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    A Grid-Enabled Problem Solving Environment for QTL Analysis in R2010In: Proc. 2nd International Conference on Bioinformatics and Computational Biology, Cary, NC: ISCA , 2010, p. 202-209Conference paper (Refereed)
  • 50.
    Jayawardena, Mahen
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Toor, Salman
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Holmgren, Sverker
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    A grid portal for genetic analysis of complex traits2009In: Proc. 32nd International Convention on Information and Communication Technology, Electronics and Microelectronics: Volume I, Rijeka, Croatia: MIPRO , 2009, p. 281-284Conference paper (Refereed)
1234 1 - 50 of 173
CiteExportLink to result list
Permanent link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf