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  • 1.
    Abdulla, Parosh
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datorteknik.
    Aronis, Stavros
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datalogi.
    Jonsson, Bengt
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datorteknik.
    Sagonas, Konstantinos
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datalogi.
    Optimal dynamic partial order reduction2014Ingår i: Proc. 41st ACM SIGPLAN-SIGACT Symposium on Principles of Programming Languages, New York: ACM Press, 2014, s. 373-384Konferensbidrag (Refereegranskat)
    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 universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datorteknik.
    Aronis, Stavros
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datalogi.
    Jonsson, Bengt
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datalogi.
    Sagonas, Konstantinos
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datalogi.
    Source Sets: A Foundation for Optimal Dynamic Partial Order Reduction2017Ingår i: Journal of the ACM, ISSN 0004-5411, E-ISSN 1557-735X, Vol. 64, nr 4, artikel-id 25Artikel i tidskrift (Refereegranskat)
    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 universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datorteknik.
    Aronis, Stavros
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datalogi.
    Atig, Mohamed Faouzi
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datorteknik.
    Jonsson, Bengt
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datorteknik.
    Leonardsson, Carl
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datorteknik.
    Sagonas, Konstantinos
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datalogi.
    Stateless model checking for TSO and PSO2015Ingår i: Tools and Algorithms for the Construction and Analysis of Systems: TACAS 2015, Springer Berlin/Heidelberg, 2015, s. 353-367Konferensbidrag (Refereegranskat)
  • 4.
    Abdulla, Parosh Aziz
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datorteknik.
    Atig, Mohamed Faouzi
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datorteknik.
    Chen, Yu-Fang
    Academia Sinica.
    Leonardsson, Carl
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datorteknik.
    Rezine, Ahmed
    Linköping University.
    MEMORAX, a Precise and Sound Tool for Automatic Fence Insertion under TSO2013Ingår i: Tools and Algorithms for the Construction and Analysis of Systems, Springer Berlin/Heidelberg, 2013, s. 530-536Konferensbidrag (Refereegranskat)
    Ladda ner fulltext (pdf)
    memorax2013.pdf
  • 5. Abel, John H.
    et al.
    Drawert, Brian
    Hellander, Andreas
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för beräkningsvetenskap. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Tillämpad beräkningsvetenskap.
    Petzold, Linda R.
    GillesPy: A Python package for stochastic model building and simulation2016Ingår i: IEEE Life Sciences Letters, E-ISSN 2332-7685, Vol. 2, s. 35-38Artikel i tidskrift (Refereegranskat)
  • 6.
    Al Khatib, Sultan M.
    et al.
    Al Balqa Appl Univ BAU, Prince Abdullah Bin Ghazi Fac Informat & Commun Te, Dept Software Engn, Al Salt 19117, Jordan..
    Alkharabsheh, Khalid
    Al Balqa Appl Univ BAU, Prince Abdullah Bin Ghazi Fac Informat & Commun Te, Dept Software Engn, Al Salt 19117, Jordan..
    Alawadi, Sadi
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för beräkningsvetenskap. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Tillämpad beräkningsvetenskap. Halmstad Univ, Ctr Appl Intelligent Syst Res, Sch Informat Technol, S-30118 Halmstad, Sweden.
    Selection of human evaluators for design smell detection using dragonfly optimization algorithm: An empirical study2023Ingår i: Information and Software Technology, ISSN 0950-5849, E-ISSN 1873-6025, Vol. 155, artikel-id 107120Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Context: Design smell detection is considered an efficient activity that decreases maintainability expenses and improves software quality. Human context plays an essential role in this domain.Objective: In this paper, we propose a search-based approach to optimize the selection of human evaluators for design smell detection.Method: For this purpose, Dragonfly Algorithm (DA) is employed to identify the optimal or near-optimal human evaluator's profiles. An online survey is designed and asks the evaluators to evaluate a sample of classes for the presence of god class design smell. The Kappa-Fleiss test has been used to validate the proposed approach. Results: The results show that the dragonfly optimization algorithm can be utilized effectively to decrease the efforts (time, cost ) of design smell detection concerning the identification of the number and the optimal or near-optimal profile of human experts required for the evaluation process.Conclusions: A Search-based approach can be effectively used for improving a god-class design smell detection. Consequently, this leads to minimizing the maintenance cost.

    Ladda ner fulltext (pdf)
    fulltext
  • 7. Alhoush, George
    et al.
    Edvardsson, Emil
    Peak shaving optimisation in school kitchens: A machine learning approach2022Självständigt arbete på grundnivå (kandidatexamen), 10 poäng / 15 hpStudentuppsats (Examensarbete)
    Abstract [en]

    With the increasing electrification of todays society the electrical grid is experiencing increasing pressure from demand. One factor that affects the stability of the grid are the time intervals at which power demand is at its highest which is referred to as peak demand. This project was conducted in order to reduce the peak demand through a process called peak shaving in order to relieve some of this pressure through the use of batteries and renewable energy. By doing so, the user of such systems could reduce the installation cost of their electrical infrastructure as well as the electrical billing. Peak shaving in this project was implemented using machine learning algorithms that predicted the daily power consumption in school kitchens with help of their food menus, which were then fed to an algorithm to steer a battery according to the results. All of these project findings are compared to another system installed by a company to decide whether the algorithm has the right accuracy and performance. The results of the simulations were promising as the algorithm was able to detect the vast majority of the peaks and perform peak shaving intelligently. Based on the graphs and values presented in this report, it can be concluded that the algorithm is ready to be implemented in the real world with the potential to contribute to a long-term sustainable electrical grid while saving money for the user. 

    Ladda ner fulltext (pdf)
    fulltext
  • 8.
    Alkharabsheh, Khalid
    et al.
    Al Balqa Appl Univ BAU, Prince Abdullah Bin Ghazi Fac Informat & Commun T, Dept Software Engn, As Salt 197111, Jordan..
    Alawadi, Sadi
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för beräkningsvetenskap.
    Crespo, Yania
    Univ Valladolid, Escuela Ingn Informat, Dept Informat, Campus Miguel Delibes, Valladolid 47011, Spain..
    Manso, M. Esperanza
    Univ Valladolid, Escuela Ingn Informat, Dept Informat, Campus Miguel Delibes, Valladolid 47011, Spain..
    Gonzalez, Jose A. Taboada
    Univ Santiago de Compostela, Ctr Singular Invest Tecnoloxias Informac, CiTIUS, Santiago De Compostela 15782, Spain..
    Analysing Agreement Among Different Evaluators in God Class and Feature Envy Detection2021Ingår i: IEEE Access, E-ISSN 2169-3536, Vol. 9, s. 145191-145211Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The automatic detection of Design Smells has evolved in parallel to the evolution of automatic refactoring tools. There was a huge rise in research activity regarding Design Smell detection from 2010 to the present. However, it should be noted that the adoption of Design Smell detection in real software development practice is not comparable to the adoption of automatic refactoring tools. On the basis of the assumption that it is the objectiveness of a refactoring operation as opposed to the subjectivity in definition and identification of Design Smells that makes the difference, in this paper, the lack of agreement between different evaluators when detecting Design Smells is empirically studied. To do so, a series of experiments and studies were designed and conducted to analyse the concordance in Design Smell detection of different persons and tools, including a comparison between them. This work focuses on two well known Design Smells: God Class and Feature Envy. Concordance analysis is based on the Kappa statistic for inter-rater agreement (particularly Kappa-Fleiss). The results obtained show that there is no agreement in detection in general, and, in those cases where a certain agreement appears, it is considered to be a fair or poor degree of agreement, according to a Kappa-Fleiss interpretation scale. This seems to confirm that there is a subjective component which makes the raters evaluate the presence of Design Smells differently. The study also raises the question of a lack of training and experience regarding Design Smells.

    Ladda ner fulltext (pdf)
    FULLTEXT01
  • 9.
    Alkharabsheh, Khalid
    et al.
    Al Balqa Appl Univ BAU, Prince Abdullah bin Ghazi Fac Informat & Commun T, Dept Software Engn, Salt, Jordan.
    Alawadi, Sadi
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för beräkningsvetenskap. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Tillämpad beräkningsvetenskap. Halmstad Univ, Sch Informat Technol, Ctr Appl Intelligent Syst Res, S-30118 Halmstad, Sweden.
    Ignaim, Karam
    Al Balqa Appl Univ BAU, Prince Abdullah bin Ghazi Fac Informat & Commun T, Dept Software Engn, Salt, Jordan.
    Zanoon, Nabeel
    Al Balqa Appl Univ BAU, Appl Sci Dept, Aqaba Coll, Salt, Jordan.
    Crespo, Yania
    Univ Valladolid, Escuela Ingn Informat, Dept Informat, Campus Miguel Delibes,Paseo Belen 15, Valladolid 47011, Spain.
    Manso, Esperanza
    Al Balqa Appl Univ BAU, Prince Abdullah bin Ghazi Fac Informat & Commun T, Dept Software Engn, Salt, Jordan.;Univ Valladolid, Escuela Ingn Informat, Dept Informat, Campus Miguel Delibes,Paseo Belen 15, Valladolid 47011, Spain.
    Taboada, Jose A.
    Univ Santiago Compostela, Ctr Singular Invest Tecnol Intelixent, CiTIUS, Santiago De Compostela 15782, Spain.
    Prioritization of god class design smell: A multi-criteria based approach2022Ingår i: JOURNAL OF KING SAUD UNIVERSITY-COMPUTER AND INFORMATION SCIENCES, ISSN 1319-1578, Vol. 34, nr 10, s. 9332-9342Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Context: Design smell Prioritization is a significant activity that tunes the process of software quality enhancement and raises its life cycle.

    Objective: A multi-criteria merge strategy for Design Smell prioritization is described. The strategy is exemplified with the case of God Class Design Smell.

    Method: An empirical adjustment of the strategy is performed using a dataset of 24 open source projects. Empirical evaluation was conducted in order to check how is the top ranked God Classes obtained by the proposed technique compared against the top ranked God class according to the opinion of developers involved in each of the projects in the dataset.

    Results: Results of the evaluation show the strategy should be improved. Analysis of the differences between projects where respondents answer correlates with the strategy and those projects where there is no correlation should be done.

    Ladda ner fulltext (pdf)
    fulltext
  • 10.
    Alkharabsheh, Khalid
    et al.
    Al Balqa Appl Univ BAU, Prince Abdullah Bin Ghazi Fac Informat & Commun T, Dept Software Engn, Salt, Jordan..
    Alawadi, Sadi
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för beräkningsvetenskap.
    Kebande, Victor R.
    Blekinge Inst Technol, Dept Comp Sci DIDA, S-37179 Karlskrona, Sweden..
    Crespo, Yania
    Univ Valladolid, Dept Informat, Escuela Ingn Informat, Campus Miguel Delibes, Paseo Belen 15, Valladolid 47011, Spain..
    Fernández-Delgado, Manuel
    Univ Santiago de Compostela, Ctr Singular Invest Tecnoloxias Intelixentes, CiTIUS, Santiago De Compostela 15782, Spain..
    Taboada, José Á.
    Univ Santiago de Compostela, Ctr Singular Invest Tecnoloxias Intelixentes, CiTIUS, Santiago De Compostela 15782, Spain..
    A comparison of machine learning algorithms on design smell detection using balanced and imbalanced dataset: A study of God class2022Ingår i: Information and Software Technology, ISSN 0950-5849, E-ISSN 1873-6025, Vol. 143, artikel-id 106736Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Context: Design smell detection has proven to be a significant activity that has an aim of not only enhancing the software quality but also increasing its life cycle.

    Objective: This work investigates whether machine learning approaches can effectively be leveraged for software design smell detection. Additionally, this paper provides a comparatively study, focused on using balanced datasets, where it checks if avoiding dataset balancing can be of any influence on the accuracy and behavior during design smell detection.

    Method: A set of experiments have been conducted-using 28 Machine Learning classifiers aimed at detecting God classes. This experiment was conducted using a dataset formed from 12,587 classes of 24 software systems, in which 1,958 classes were manually validated.

    Results: Ultimately, most classifiers obtained high performances,-with Cat Boost showing a higher performance. Also, it is evident from the experiments conducted that data balancing does not have any significant influence on the accuracy of detection. This reinforces the application of machine learning in real scenarios where the data is usually imbalanced by the inherent nature of design smells.

    Conclusions: Machine learning approaches can effectively be used as a leverage for God class detection. While in this paper we have employed SMOTE technique for data balancing, it is worth noting that there exist other methods of data balancing and with other design smells. Furthermore, it is also important to note that application of those other methods may improve the results, in our experiments SMOTE did not improve God class detection.

    The results are not fully generalizable because only one design smell is studied with projects developed in a single programming language, and only one balancing technique is used to compare with the imbalanced case. But these results are promising for the application in real design smells detection scenarios as mentioned above and the focus on other measures, such as Kappa, ROC, and MCC, have been used in the assessment of the classifier behavior.

    Ladda ner fulltext (pdf)
    fulltext
  • 11.
    Araujo, Hugo
    et al.
    Univ Fed Pernambuco, Recife, PE, Brazil.
    Carvalho, Gustavo
    Univ Fed Pernambuco, Recife, PE, Brazil.
    Mohaqeqi, Morteza
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datorteknik.
    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 implementation2018Ingår i: Science of Computer Programming, ISSN 0167-6423, E-ISSN 1872-7964, Vol. 162, s. 35-54Artikel i tidskrift (Refereegranskat)
    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.

    Ladda ner fulltext (pdf)
    fulltext
  • 12.
    Aronis, Stavros
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datalogi.
    Papaspyrou, Nikolaos
    Roukounaki, Katerina
    Sagonas, Konstantinos
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datalogi.
    Tsiouris, Yiannis
    Venetis, Ioannis E.
    A scalability benchmark suite for Erlang/OTP2012Ingår i: Proc. 11th ACM SIGPLAN Workshop on Erlang, New York: ACM Press, 2012, s. 33-42Konferensbidrag (Refereegranskat)
    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.

  • 13.
    Aronis, Stavros
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datalogi.
    Sagonas, Konstantinos
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datalogi.
    The shared-memory interferences of Erlang/OTP built-ins2017Ingår i: 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, s. 43-54Konferensbidrag (Refereegranskat)
    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.

    Ladda ner fulltext (pdf)
    fulltext
  • 14.
    Aronis, Stavros
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datalogi.
    Sagonas, Konstantinos
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datalogi.
    Lystig Fritchie, Scott
    VMware, Cambridge, MA, USA.
    Testing And Verifying Chain Repair Methods For CORFU Using Stateless Model Checking2017Konferensbidrag (Refereegranskat)
    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.

    Ladda ner fulltext (pdf)
    fulltext
  • 15.
    Asada, Akira
    et al.
    Osaka Inst Technol, Fac Informat Sci & Technol, Osaka, Japan.
    Hayashi, Masaki
    Uppsala universitet, Humanistisk-samhällsvetenskapliga vetenskapsområdet, Historisk-filosofiska fakulteten, Institutionen för speldesign.
    Hirayama, Makoto J.
    Osaka Inst Technol, Fac Informat Sci & Technol, Osaka, Japan.
    TV production tool to make art programmes based on a simple scenario2019Ingår i: 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, artikel-id 1104921Konferensbidrag (Refereegranskat)
    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.

  • 16.
    Asadian, Hooman
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datorteknik. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för datorteknik.
    Fiterau-Brostean, Paul
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datorteknik. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för datorteknik.
    Jonsson, Bengt
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datorteknik. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för datorteknik.
    Sagonas, Konstantinos
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datalogi.
    Applying Symbolic Execution to Test Implementations of a Network Protocol Against its Specification2022Ingår i: 2022 IEEE 15TH INTERNATIONAL CONFERENCE ON SOFTWARE TESTING, VERIFICATION AND VALIDATION (ICST 2022), Institute of Electrical and Electronics Engineers (IEEE), 2022, s. 70-81Konferensbidrag (Refereegranskat)
    Abstract [en]

    Implementations of network protocols must conform to their specifications in order to avoid security vulnerabilities and interoperability issues. We describe our experiences using symbolic execution to thoroughly test several implementations of a network security protocol against its specification. We employ a methodology in which we first extract requirements from the protocol's RFC and turn them into formulas. These formulas are then utilized by symbolically executing the protocol implementation to explore code paths that can be traversed on packet sequences that violate a requirement. When this exploration exposes a bug, corresponding input values are produced and turned into test cases that can validate the bug in the original implementation. Since we let symbolic execution be guided by requirements, it can naturally produce a wide variety of requirement-violating input sequences, which is difficult to achieve with existing techniques for protocol testing. We applied this methodology to test four different implementations of MILS against the protocol's RFC. We were able to quickly expose a known CVE in an older version of OpenSSL, and to discover numerous previously unknown vulnerabilities and nonconformance issues in DTI.S implementations, which have by now been confirmed and fixed by their implementors.

  • 17.
    Ausmees, Kristiina
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för beräkningsvetenskap.
    Methodology and Infrastructure for Statistical Computing in Genomics: Applications for Ancient DNA2022Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
    Abstract [en]

    This thesis concerns the development and evaluation of computational methods for analysis of genetic data. A particular focus is on ancient DNA recovered from archaeological finds, the analysis of which has contributed to novel insights into human evolutionary and demographic history, while also introducing new challenges and the demand for specialized methods.

    A main topic is that of imputation, or the inference of missing genotypes based on observed sequence data. We present results from a systematic evaluation of a common imputation pipeline on empirical ancient samples, and show that imputed data can constitute a realistic option for population-genetic analyses. We also develop a tool for genotype imputation that is based on the full probabilistic Li and Stephens model for haplotype frequencies and show that it can yield improved accuracy on particularly challenging data.  

    Another central subject in genomics and population genetics is that of data characterization methods that allow for visualization and exploratory analysis of complex information. We discuss challenges associated with performing dimensionality reduction of genetic data, demonstrating how the use of principal component analysis is sensitive to incomplete information and performing an evaluation of methods to handle unobserved genotypes. We also discuss the use of deep learning models as an alternative to traditional methods of data characterization in genomics and propose a framework based on convolutional autoencoders that we exemplify on the applications of dimensionality reduction and genetic clustering.

    In genomics, as in other fields of research, increasing sizes of data sets are placing larger demands on efficient data management and compute infrastructures. The final part of this thesis addresses the use of cloud resources for facilitating data analysis in scientific applications. We present two different cloud-based solutions, and exemplify them on applications from genomics.

    Delarbeten
    1. An empirical evaluation of genotype imputation of ancient DNA
    Öppna denna publikation i ny flik eller fönster >>An empirical evaluation of genotype imputation of ancient DNA
    2022 (Engelska)Ingår i: G3: Genes, Genomes, Genetics, E-ISSN 2160-1836, Vol. 12, nr 6, artikel-id jkac089Artikel i tidskrift (Refereegranskat) Published
    Abstract [en]

    With capabilities of sequencing ancient DNA to high coverage often limited by sample quality or cost, imputation of missing genotypes presents a possibility to increase the power of inference as well as cost-effectiveness for the analysis of ancient data. However, the high degree of uncertainty often associated with ancient DNA poses several methodological challenges, and performance of imputation methods in this context has not been fully explored. To gain further insights, we performed a systematic evaluation of imputation of ancient data using Beagle v4.0 and reference data from phase 3 of the 1000 Genomes project, investigating the effects of coverage, phased reference, and study sample size. Making use of five ancient individuals with high-coverage data available, we evaluated imputed data for accuracy, reference bias, and genetic affinities as captured by principal component analysis. We obtained genotype concordance levels of over 99% for data with 1× coverage, and similar levels of accuracy and reference bias at levels as low as 0.75×. Our findings suggest that using imputed data can be a realistic option for various population genetic analyses even for data in coverage ranges below 1×. We also show that a large and varied phased reference panel as well as the inclusion of low- to moderate-coverage ancient individuals in the study sample can increase imputation performance, particularly for rare alleles. In-depth analysis of imputed data with respect to genetic variants and allele frequencies gave further insight into the nature of errors arising during imputation, and can provide practical guidelines for postprocessing and validation prior to downstream analysis.

    Ort, förlag, år, upplaga, sidor
    Oxford University Press, 2022
    Nationell ämneskategori
    Beräkningsmatematik Genetik
    Forskningsämne
    Beräkningsvetenskap
    Identifikatorer
    urn:nbn:se:uu:diva-396336 (URN)10.1093/g3journal/jkac089 (DOI)000791204600001 ()35482488 (PubMedID)
    Projekt
    eSSENCE
    Forskningsfinansiär
    Forskningsrådet Formas, 2020-00712
    Tillgänglig från: 2019-11-04 Skapad: 2019-11-04 Senast uppdaterad: 2024-01-17Bibliografiskt granskad
    2. Achieving improved accuracy for imputation of ancient DNA
    Öppna denna publikation i ny flik eller fönster >>Achieving improved accuracy for imputation of ancient DNA
    2023 (Engelska)Ingår i: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811, Vol. 39, nr 1, artikel-id btac738Artikel i tidskrift (Refereegranskat) Published
    Abstract [en]

    Motivation

    Genotype imputation has the potential to increase the amount of information that can be gained from the often limited biological material available in ancient samples. As many widely used tools have been developed with modern data in mind, their design is not necessarily reflective of the requirements in studies of ancient DNA. Here, we investigate if an imputation method based on the full probabilistic Li and Stephens model of haplotype frequencies might be beneficial for the particular challenges posed by ancient data.

    Results

    We present an implementation called prophaser and compare imputation performance to two alternative pipelines that have been used in the ancient DNA community based on the Beagle software. Considering empirical ancient data downsampled to lower coverages as well as present-day samples with artificially thinned genotypes, we show that the proposed method is advantageous at lower coverages, where it yields improved accuracy and ability to capture rare variation. The software prophaser is optimized for running in a massively parallel manner and achieved reasonable runtimes on the experiments performed when executed on a GPU.

    Ort, förlag, år, upplaga, sidor
    Oxford University Press, 2023
    Nyckelord
    Bioinformatics, Computational biology, Genotype imputation, Ancient DNA
    Nationell ämneskategori
    Bioinformatik (beräkningsbiologi) Beräkningsmatematik Genetik
    Forskningsämne
    Bioinformatik; Beräkningsvetenskap
    Identifikatorer
    urn:nbn:se:uu:diva-470292 (URN)10.1093/bioinformatics/btac738 (DOI)000892594400001 ()36377787 (PubMedID)
    Projekt
    eSSENCE - An eScience Collaboration
    Forskningsfinansiär
    Forskningsrådet Formas, 2017-00453
    Tillgänglig från: 2022-03-22 Skapad: 2022-03-22 Senast uppdaterad: 2023-03-02Bibliografiskt granskad
    3. Evaluation of methods handling missing data in PCA on genotype data: Applications for ancient DNA
    Öppna denna publikation i ny flik eller fönster >>Evaluation of methods handling missing data in PCA on genotype data: Applications for ancient DNA
    2019 (Engelska)Rapport (Övrigt vetenskapligt)
    Serie
    Technical report / Department of Information Technology, Uppsala University, ISSN 1404-3203 ; 2019-009
    Nationell ämneskategori
    Beräkningsmatematik Genetik
    Identifikatorer
    urn:nbn:se:uu:diva-396346 (URN)
    Projekt
    eSSENCE
    Tillgänglig från: 2019-11-04 Skapad: 2019-11-04 Senast uppdaterad: 2024-05-28Bibliografiskt granskad
    4. A deep learning framework for characterization of genotype data
    Öppna denna publikation i ny flik eller fönster >>A deep learning framework for characterization of genotype data
    2022 (Engelska)Ingår i: G3: Genes, Genomes, Genetics, E-ISSN 2160-1836, Vol. 12, nr 3, artikel-id jkac020Artikel i tidskrift (Refereegranskat) Published
    Abstract [en]

    Dimensionality reduction is a data transformation technique widely used in various fields of genomics research. The application of dimensionality reduction to genotype data is known to capture genetic similarity between individuals, and is used for visualization of genetic variation, identification of population structure as well as ancestry mapping. Among frequently used methods are principal component analysis, which is a linear transform that often misses more fine-scale structures, and neighbor-graph based methods which focus on local relationships rather than large-scale patterns. Deep learning models are a type of nonlinear machine learning method in which the features used in data transformation are decided by the model in a data-driven manner, rather than by the researcher, and have been shown to present a promising alternative to traditional statistical methods for various applications in omics research. In this study, we propose a deep learning model based on a convolutional autoencoder architecture for dimensionality reduction of genotype data. Using a highly diverse cohort of human samples, we demonstrate that the model can identify population clusters and provide richer visual information in comparison to principal component analysis, while preserving global geometry to a higher extent than t-SNE and UMAP, yielding results that are comparable to an alternative deep learning approach based on variational autoencoders. We also discuss the use of the methodology for more general characterization of genotype data, showing that it preserves spatial properties in the form of decay of linkage disequilibrium with distance along the genome and demonstrating its use as a genetic clustering method, comparing results to the ADMIXTURE software frequently used in population genetic studies.

    Ort, förlag, år, upplaga, sidor
    Oxford University Press (OUP), 2022
    Nyckelord
    deep learning, convolutional autoencoder, dimensionality reduction, genetic clustering, population genetics
    Nationell ämneskategori
    Bioinformatik (beräkningsbiologi) Beräkningsmatematik Genetik
    Forskningsämne
    Beräkningsvetenskap
    Identifikatorer
    urn:nbn:se:uu:diva-470290 (URN)10.1093/g3journal/jkac020 (DOI)000776673300018 ()35078229 (PubMedID)
    Projekt
    eSSENCE - An eScience Collaboration
    Forskningsfinansiär
    Forskningsrådet Formas, 2017-00453Forskningsrådet Formas, 2020-00712
    Tillgänglig från: 2022-03-22 Skapad: 2022-03-22 Senast uppdaterad: 2024-01-17Bibliografiskt granskad
    5. BAMSI: a multi-cloud service for scalable distributed filtering of massive genome data
    Öppna denna publikation i ny flik eller fönster >>BAMSI: a multi-cloud service for scalable distributed filtering of massive genome data
    Visa övriga...
    2018 (Engelska)Ingår i: BMC Bioinformatics, E-ISSN 1471-2105, Vol. 19, s. 240:1-11, artikel-id 240Artikel i tidskrift (Refereegranskat) Published
    Nationell ämneskategori
    Programvaruteknik Genetik
    Identifikatorer
    urn:nbn:se:uu:diva-360033 (URN)10.1186/s12859-018-2241-z (DOI)000436517200001 ()29940842 (PubMedID)
    Projekt
    eSSENCE
    Tillgänglig från: 2018-06-26 Skapad: 2018-09-09 Senast uppdaterad: 2024-01-17Bibliografiskt granskad
    6. SWEEP: Accelerating scientific research through scalable serverless workflows
    Öppna denna publikation i ny flik eller fönster >>SWEEP: Accelerating scientific research through scalable serverless workflows
    Visa övriga...
    2019 (Engelska)Ingår i: Companion Proc. 12th International Conference on Utility and Cloud Computing, New York: ACM Press, 2019, s. 43-50Konferensbidrag, Publicerat paper (Refereegranskat)
    Ort, förlag, år, upplaga, sidor
    New York: ACM Press, 2019
    Nationell ämneskategori
    Programvaruteknik
    Identifikatorer
    urn:nbn:se:uu:diva-396405 (URN)10.1145/3368235.3368839 (DOI)978-1-4503-7044-8 (ISBN)
    Konferens
    UCC 2019
    Projekt
    eSSENCE
    Tillgänglig från: 2019-12-02 Skapad: 2019-11-04 Senast uppdaterad: 2022-03-28Bibliografiskt granskad
    Ladda ner fulltext (pdf)
    UUThesis-K,Ausmees_2022
    Ladda ner (jpg)
    presentationsbild
  • 18.
    Ausmees, Kristiina
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för beräkningsvetenskap. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Tillämpad beräkningsvetenskap.
    John, Aji
    Toor, Salman Z.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för beräkningsvetenskap. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Tillämpad beräkningsvetenskap.
    Hellander, Andreas
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för beräkningsvetenskap. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Tillämpad beräkningsvetenskap.
    Nettelblad, Carl
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för beräkningsvetenskap. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Tillämpad beräkningsvetenskap.
    BAMSI: a multi-cloud service for scalable distributed filtering of massive genome data2018Ingår i: BMC Bioinformatics, E-ISSN 1471-2105, Vol. 19, s. 240:1-11, artikel-id 240Artikel i tidskrift (Refereegranskat)
  • 19.
    Axelsson, Veronica
    Högskolan på Gotland, Institutionen för speldesign, teknik och lärande.
    What technique is most appropriate for 3D modeling a chair for a movie production?2013Självständigt arbete på grundnivå (kandidatexamen), 10 poäng / 15 hpStudentuppsats (Examensarbete)
    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.

    Ladda ner fulltext (pdf)
    What technique is most appropriate for 3D modeling a chair for a movie production - Veronica_Axelsson
  • 20.
    Aziz, Yama
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för datalogi.
    Exploring a keyword driven testing framework: a case study at Scania IT2017Självständigt arbete på avancerad nivå (yrkesexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
    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.

    Ladda ner fulltext (pdf)
    Exploring a keyword driven testing framework
  • 21. Bangerth, Wolfgang
    et al.
    Burstedde, Carsten
    Heister, Timo
    Kronbichler, Martin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för teknisk databehandling. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Numerisk analys.
    Algorithms and data structures for massively parallel generic adaptive finite element codes2011Ingår i: ACM Transactions on Mathematical Software, ISSN 0098-3500, E-ISSN 1557-7295, Vol. 38, nr 2, s. 14:1-28Artikel i tidskrift (Refereegranskat)
  • 22.
    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 universitet, Humanistisk-samhällsvetenskapliga vetenskapsområdet, Historisk-filosofiska fakulteten, Institutionen för speldesign.
    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 Program2016Ingår i: The AI Magazine, ISSN 0738-4602, Vol. 37, nr 2, s. 91-94Artikel i tidskrift (Refereegranskat)
    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.

  • 23.
    Bauer, Paul
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - BMC, Biokemi.
    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 universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - BMC, Biokemi.
    Amrein, Beat Anton
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi.
    Esguerra, Mauricio
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Beräkningsbiologi och bioinformatik.
    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 universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Beräkningsbiologi och bioinformatik.
    Kamerlin, Shina C. Lynn
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Strukturbiologi.
    Q6: A comprehensive toolkit for empirical valence bond and related free energy calculations2018Ingår i: SoftwareX, E-ISSN 2352-7110, Vol. 7, s. 388-395Artikel i tidskrift (Refereegranskat)
    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.

    Ladda ner fulltext (pdf)
    fulltext
  • 24.
    Baxter, Amanda L.
    et al.
    Purdue Univ, Dept Phys & Astron, W Lafayette, IN 47907 USA..
    BenZvi, Segev Y.
    Univ Rochester, Dept Phys & Astron, Rochester, NY USA..
    Bonivento, Walter
    Complesso Univ Monserrato, Ist Nazl Fis Nucl, Sez Cagliari, Ist Nazl, Cagliari, Italy..
    Brazier, Adam
    Cornell Univ, Ctr Adv Comp, Ithaca, NY USA..
    Clark, Michael
    Purdue Univ, Dept Phys & Astron, W Lafayette, IN 47907 USA..
    Coleiro, Alexis
    Univ Paris, AstroParticule & Cosmol, CNRS, Paris, France..
    Collom, David
    Cumbres Observ, Goleta, CA USA..
    Colomer-Molla, Marta
    Univ Paris, AstroParticule & Cosmol, CNRS, Paris, France.;Univ Valencia, CSIC, Inst Fis Corpuscular, Valencia, Spain..
    Cousins, Bryce
    Penn State Univ, Inst Computat & Data Sci, University Pk, PA 16802 USA.;Penn State Univ, Dept Phys, 104 Davey Lab, University Pk, PA 16802 USA..
    Orellana, Aliwen Delgado
    Pontificia Univ Catolica Chile, Inst Fis, Santiago, Region Metropol, Chile..
    Dornic, Damien
    Aix Marseille Univ, CPPM, CNRS IN2P3, Marseille, France..
    Ekimtcov, Vladislav
    Univ Illinois, Natl Ctr Supercomp Applicat, Urbana, IL USA..
    ElSayed, Shereen
    Univ Calif Santa Barbara, Dept Comp Sci, Santa Barbara, CA 93106 USA..
    Rosso, Andrea Gallo
    Laurentian Univ, Dept Phys, Sudbury, ON, Canada..
    Godwin, Patrick
    Penn State Univ, Dept Phys, 104 Davey Lab, University Pk, PA 16802 USA.;Penn State Univ, Inst Gravitat & Cosmos, University Pk, PA 16802 USA..
    Griswold, Spencer
    Univ Rochester, Dept Phys & Astron, Rochester, NY USA..
    Habig, Alec
    Univ Minnesota, Dept Phys & Astron, Duluth, MN 55812 USA..
    Hill, Remington
    Laurentian Univ, Dept Phys, Sudbury, ON, Canada..
    Horiuchi, Shunsaku
    Virginia Tech, Dept Phys, Ctr Neutrino Phys, Blacksburg, VA USA..
    Howell, D. Andrew
    Cumbres Observ, Goleta, CA USA.;Univ Calif Santa Barbara, Dept Comp Sci, Santa Barbara, CA 93106 USA..
    Johnson, Margaret W. G.
    Univ Illinois, Natl Ctr Supercomp Applicat, Urbana, IL USA..
    Kneller, James P.
    NC State Univ, Dept Phys, Raleigh, NC USA..
    Kopec, Abigail
    Purdue Univ, Dept Phys & Astron, W Lafayette, IN 47907 USA.;Univ Calif San Diego, Dept Phys, La Jolla, CA 92093 USA..
    Kopper, Claudio
    Michigan State Univ, Dept Phys & Astron, E Lansing, MI 48824 USA..
    Kulikovskiy, Vladimir
    Ist Nazl Fis Nucl, Sez Genova, Genoa, Italy..
    Lamoureux, Mathieu
    Ist Nazl Fis Nucl, Sez Padova, Dipartimento Fis, Padua, Italy.;Univ Padua, Padua, Italy..
    Lang, Rafael F.
    Purdue Univ, Dept Phys & Astron, W Lafayette, IN 47907 USA..
    Li, Shengchao
    Purdue Univ, Dept Phys & Astron, W Lafayette, IN 47907 USA..
    Lincetto, Massimiliano
    Aix Marseille Univ, CPPM, CNRS IN2P3, Marseille, France..
    Lindstrom, Lindy
    Cumbres Observ, Goleta, CA USA..
    Linvill, Mark W.
    Purdue Univ, Dept Phys & Astron, W Lafayette, IN 47907 USA..
    McCully, Curtis
    Cumbres Observ, Goleta, CA USA..
    Migenda, Jost
    Kings Coll London, Dept Phys, London, England..
    Milisavljevic, Danny
    Purdue Univ, Dept Phys & Astron, W Lafayette, IN 47907 USA..
    Nelson, Spencer
    Univ Washington, DiRAC Inst, Seattle, WA 98195 USA.;Univ Washington, Dept Astron, Seattle, WA 98195 USA..
    Novoseltseva, Rita
    Russian Acad Sci, Inst Nucl Res, Baksan Neutrino Observ, Neytrino, Kabardino Balka, Russia..
    O'Sullivan, Erin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för fysik och astronomi, Högenergifysik.
    Petravick, Donald
    Univ Illinois, Natl Ctr Supercomp Applicat, Urbana, IL USA..
    Pointon, Barry W.
    British Columbia Inst Technol, Dept Phys, Burnaby, BC, Canada.;TRIUMF, Vancouver, BC, Canada..
    Raj, Nirmal
    TRIUMF, Vancouver, BC, Canada..
    Renshaw, Andrew
    Univ Houston, Dept Phys, Houston, TX USA..
    Rumleskie, Janet
    Laurentian Univ, Dept Phys, Sudbury, ON, Canada..
    Sonley, Tom
    SNOLAB, Sudbury, ON, Canada..
    Tapia, Ron
    Penn State Univ, Inst Computat & Data Sci, University Pk, PA 16802 USA.;Penn State Univ, Dept Phys, 104 Davey Lab, University Pk, PA 16802 USA..
    Tseng, Jeffrey C. L.
    Univ Oxford, Dept Phys, Oxford, England..
    Tunnell, Christopher D.
    Rice Univ, Dept Comp Sci, Houston, TX USA.;Rice Univ, Dept Phys & Astron, Houston, TX USA..
    Vannoye, Godefroy
    Aix Marseille Univ, CPPM, CNRS IN2P3, Marseille, France..
    Vigorito, Carlo F.
    Univ Torino, Dept Phys, Turin, Italy.;Ist Nazl Fis Nucl, Turin, Italy..
    Virtue, Clarence J.
    Laurentian Univ, Dept Phys, Sudbury, ON, Canada..
    Weaver, Christopher
    Michigan State Univ, Inst Cyber Enabled Res, E Lansing, MI 48824 USA..
    Weil, Kathryn E.
    Purdue Univ, Dept Phys & Astron, W Lafayette, IN 47907 USA..
    Winslow, Lindley
    MIT, Dept Phys, Cambridge, MA 02139 USA..
    Wolski, Rich
    Univ Calif Santa Barbara, Dept Comp Sci, Santa Barbara, CA 93106 USA..
    Xu, Xun-Jie
    Univ Libre Bruxelles, Serv Phys Theor, Brussels, Belgium..
    Xu, Yiyang
    Rice Univ, Dept Comp Sci, Houston, TX USA..
    Collaborative experience between scientific software projects using Agile Scrum development2022Ingår i: Software, practice & experience, ISSN 0038-0644, E-ISSN 1097-024X, Vol. 52, nr 10, s. 2077-2096Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Developing sustainable software for the scientific community requires expertise in software engineering and domain science. This can be challenging due to the unique needs of scientific software, the insufficient resources for software engineering practices in the scientific community, and the complexity of developing for evolving scientific contexts. While open-source software can partially address these concerns, it can introduce complicating dependencies and delay development. These issues can be reduced if scientists and software developers collaborate. We present a case study wherein scientists from the SuperNova Early Warning System collaborated with software developers from the Scalable Cyberinfrastructure for Multi-Messenger Astrophysics project. The collaboration addressed the difficulties of open-source software development, but presented additional risks to each team. For the scientists, there was a concern of relying on external systems and lacking control in the development process. For the developers, there was a risk in supporting a user-group while maintaining core development. These issues were mitigated by creating a second Agile Scrum framework in parallel with the developers' ongoing Agile Scrum process. This Agile collaboration promoted communication, ensured that the scientists had an active role in development, and allowed the developers to evaluate and implement the scientists' software requirements. The collaboration provided benefits for each group: the scientists actuated their development by using an existing platform, and the developers utilized the scientists' use-case to improve their systems. This case study suggests that scientists and software developers can avoid scientific computing issues by collaborating and that Agile Scrum methods can address emergent concerns.

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  • 25.
    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 universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datorteknik. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datavetenskapens didaktik.
    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 environment2017Ingår i: IEEE Software, ISSN 0740-7459, E-ISSN 1937-4194, Vol. 34, nr 1, s. 9-12Artikel i tidskrift (Refereegranskat)
  • 26. Behrmann, Gerd
    et al.
    David, Alexandre
    Larsen, Kim Guldstrand
    Pettersson, Paul
    Yi, Wang
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datorteknik.
    Developing UPPAAL over 15 years2011Ingår i: Software, practice & experience, ISSN 0038-0644, E-ISSN 1097-024X, Vol. 41, nr 2, s. 133-142Artikel i tidskrift (Refereegranskat)
  • 27.
    Bernström, Kristian
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för datalogi.
    Näsman, Anders
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för datalogi.
    Utredning och implementering av en prototyp för integration av Prevas FOCS och ABB 800xA2014Självständigt arbete på avancerad nivå (yrkesexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
    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.

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  • 28. Bjerned, Erik
    et al.
    Persson, Mattias
    Danielsson, Axel
    Shape optimization of coronashield geometry: Simulation techniques for minimizing electricfield with COMSOL 6.02022Självständigt arbete på grundnivå (kandidatexamen), 10 poäng / 15 hpStudentuppsats (Examensarbete)
    Abstract [en]

    This report focuses on the practicality and results of using the COMSOL 6.0 Optimization Module on a HVDC bushing corona shield model provided by Hitachi Energy to minimize electric field. The Optimization Module has several functions and parameters for altering the geometry of a model. Parameter Optimization, Polynomial Boundary and Free Shape Boundary was the primary methods used. The best results in minimizing the electric field was found with the Polynomial Boundary. The optimized shape decreased the maximum electric field by about 15% and when run with constraints to the change in volume the optimization showed similar results. Tests with Parameter Optimization did decrease the electric field but lacked the ability to fine-tune the shape like Polynomial Boundary can. Free Shape Boundaryseemed to have great potential in the documentation but we did not finda successful way of implementing the method. Through testing of different setups for methods and solvers we have concluded that the Optimization Module is both useful and practical for the given model and a clear improvement in electric field was observed in the new shape. Polynomial Boundary is the best option for the given model but more research is needed about Free Shape Boundary.

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  • 29.
    Black-Schaffer, David
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datorteknik.
    Dally, William J.
    Stanford University, Department of Computer Science.
    Block-Parallel Programming for Real-time Embedded Applications2010Ingår i: Proc. 39th International Conference on Parallel Processing, Piscataway, NJ: IEEE , 2010, s. 297-306Konferensbidrag (Refereegranskat)
    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.

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    FULLTEXT01
  • 30.
    Blamey, Ben
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för beräkningsvetenskap. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Tillämpad beräkningsvetenskap.
    Hellander, Andreas
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för beräkningsvetenskap. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Tillämpad beräkningsvetenskap.
    Toor, Salman
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för beräkningsvetenskap. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Tillämpad beräkningsvetenskap.
    Apache Spark Streaming, Kafka and HarmonicIO: A performance benchmark and architecture comparison for enterprise and scientific computing2020Ingår i: Benchmarking, Measuring, and Optimizing, Springer, 2020, s. 335-347Konferensbidrag (Refereegranskat)
  • 31.
    Blom, Johan
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datorteknik. Datorteknik.
    Jonsson, Bengt
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datorteknik. Datorteknik.
    Automated test generation for industrial Erlang applications2003Ingår i: Erlang Workshop 2003: Proceedings of the 2003 ACM SIGPLAN Workshop on Erlang, Uppsala, Sweden, August 29, 2003., 2003, s. 8-14Konferensbidrag (Refereegranskat)
  • 32.
    Boustedt, Jonas
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för teknisk databehandling. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Numerisk analys.
    A student perspective on software development and maintenance2010Rapport (Övrigt vetenskapligt)
    Abstract [en]

    How do Computer Science students view Software Development and Software Maintenance? To answer this question, a Phenomenographic perspective was chosen, and 20 Swedish students at four universities were interviewed.

    The interviews were analyzed to find in which different ways the informants, on collective level, see the phenomena of interest. The resulting outcome spaces show that software development is described in a number of qualitatively different ways reaching from problem solving, design and deliver, design for the future and then a more comprehensive view that includes users, customers, budget and other aspects. Software maintenance is described as correcting bugs, making additions, adapting to new requirements from the surroundings, and something that is a natural part of the job.

    Finally, conclusions from the results and additional observations are discussed in terms of their implications for teaching, and some suggestions for practical use are given.

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  • 33. Broy, Manfred
    et al.
    Jonsson, BengtUppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datorteknik. datorteknik.Katoen, Joost-PieterLeucker, MartinUppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datorteknik. datorteknik.Pretschner, Alexander
    Model-Based Testing of Reactive Systems: Advanced Lectures2005Samlingsverk (redaktörskap) (Övrigt vetenskapligt)
  • 34.
    Bäcklund, Emil
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi.
    Survailability planning App2012Självständigt arbete på avancerad nivå (yrkesexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
  • 35.
    Bäärnhielm, Arvid
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Tekniska sektionen, Institutionen för teknikvetenskaper.
    Utveckling av applikation till plattformen Android2015Självständigt arbete på grundnivå (kandidatexamen), 10 poäng / 15 hpStudentuppsats (Examensarbete)
    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.

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  • 36. Caulfield, Emmet
    et al.
    Hellander, Andreas
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för teknisk databehandling. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Tillämpad beräkningsvetenskap.
    CellMC: a multiplatform model compiler for the Cell Broadband Engine and x862010Ingår i: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811, Vol. 26, s. 426-428Artikel i tidskrift (Refereegranskat)
  • 37.
    Clear, Tony
    et al.
    Auckland Univ Technol, Sch Engn Comp & Math Sci, Private Bag, Auckland, New Zealand.
    Beecham, Sarah
    Univ Limerick, Lero Irish Software Res Ctr, Limerick, Ireland.
    Barr, John
    Ithaca Coll, Ithaca, NY USA.
    Daniels, Mats
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datorteknik. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datavetenskapens didaktik.
    McDermott, Roger
    Robert Gordon Univ, Dept Comp Sci, Aberdeen, Scotland.
    Oudshoorn, Michael
    Wentworth Inst Technol, Dept Comp Sci & Comp Networking, Boston, MA USA.
    Savickaite, Airina
    Vilnius Univ, Dept Comp Sci & Engn, Vilnius, Lithuania.
    Noll, John
    Univ Limerick, Lero Irish Software Res Ctr, Limerick, Irelan.
    Challenges and recommendations for the design and conduct of global software engineering courses: A systematic review2016Ingår i: Proceedings of The 2015 Iticse Conference on Working Group Reports (Iticse-Wgp'15) / [ed] ACM, New York: ACM Press, 2016, s. 1-39Konferensbidrag (Refereegranskat)
    Abstract [en]

    Context: Global Software Engineering (GSE) has become the predominant form of software development for global companies and has given rise to a demand for students trained in GSE. In response, universities are developing courses and curricula around GSE and researchers have begun to disseminate studies of these new approaches.

    Problem: GSE differs from most other computer science fields, however, in that practice is inseparable from theory. As a result, educators looking to create GSE courses face a daunting task: integrating global practice into the local classroom.

    Aim: This study aims to ameliorate the very difficult task of teaching GSE by delineating the challenges and providing some recommendations for overcoming them.

    Method: To meet our aims we pose two research questions ("When teaching GSE to students in Higher Education, what are the (a) challenges, and (b) recommendations for addressing them") and then conduct a systematic literature review (SLR) to determine the answers to these questions. Our SLR follows a carefully designed and validated protocol.

    Results: We found 82 papers that addressed our research questions. Our findings indicate that in addition to the challenges posed by GSE in general, particular problems arise in educational situations. The majority of these challenges fall into the "global distance" category, though teamwork challenges and people issues (such as trust) also commonly arise. Organizational differences between institutions, differing skill sets between students in different locations, and varying cultural work norms, for example, all operate within educational settings in quite different ways than in professional development teams. Integrating cultural training, conducting teamwork exercises to build trust, and instructor monitoring of team communication are all examples of techniques that have been used successfully by educators according to our review.

    Conclusion: Despite the severity of the challenges in GSE education, many institutions have successfully developed courses and curricula targeting GSE. Indeed, for each of the challenges we have identified in the literature there are numerous recommendations for overcoming them. Instructors can use the recommendations given in this study as a starting point to running successful GSE courses.

  • 38.
    Coulier, Adrien
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för beräkningsvetenskap. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Tillämpad beräkningsvetenskap.
    Hellander, Andreas
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för beräkningsvetenskap. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Tillämpad beräkningsvetenskap.
    Orchestral: a lightweight framework for parallel simulations of cell–cell communication2018Ingår i: Proc. 14th International Conference on e-Science, Los Alamitos, CA: IEEE Computer Society, 2018, s. 168-176Konferensbidrag (Refereegranskat)
  • 39. Dahlin, Carl
    et al.
    Evelius, Axel
    The Undisputable Truth: En undersökning om möjligheten och praktikaliteten i attidentifiera filer som liknar envägskrypterade filer.2023Självständigt arbete på grundnivå (kandidatexamen), 10 poäng / 15 hpStudentuppsats (Examensarbete)
    Abstract [sv]

    Med den stora utvecklingen inom teknologi ämnad för förfalskning av dokument och filer ökarbehovet av att kunna verifiera äktheten och integriteten hos digitala filer. Företaget "TheUndisputable Truth" har introducerat en metod för att lösa detta problem genom att användahashkoder i en blockchain. Istället för att spara hela dokument online, sparas en pseudounikhashkod av filen. Hashkoden är en kryptografiskt genererad representation av filen sompraktiskt taget endast kan skapas från originalfilen och är extremt svår att återskapa utan att hatillgång till filen. En minimal ändring i filen genererar en helt annan hashkod, vilket gör detomöjligt att avgöra filernas likhet utifrån hashkoderna.Projektet syftade till att utveckla en metod som bevarar säkerheten hos hashkoderna samtidigtsom den kan detektera och redovisa små avvikelser i innehåll mellan en fil och en krypteradversion av en fil med mycket liknande innehåll i systemet, med frågeställningen huruvida det varpraktiskt och möjligt. För att uppnå detta undersöktes användningen av felkorrigeringstekniker,specifikt Hammingkoder och Reed Solomon.Initialt undersöktes applikationer av felkorrigering på texter. Hammingkoder är till sin naturbegränsade till att detektera och lokalisera ett fel, men visade att felkorrigering var applicerbart.Reed Solomon kunde hantera ett fel per två extrapunkter av information. Dock uppstod problemom en felaktighet försköt texten, vilket resulterade i att allt efter felet betraktades som felaktigt,då Reed Solomon-algoritmen är designad för meddelanden av bestämd längd. För att lösadetta delades texten upp i segment som avgränsades av ett nyckeltecken och ordnades efterbitarnas innehåll, vilket resulterade i att förskjutningsfel begränsades till små segment av texten.Detta bedömdes att tillfredsställa kraven på algoritmen.När det gäller bilder undersöktes möjligheten att hantera beskurna bilder med hjälp av en metodsom inom projektet kallades Reed Solomon snapping. Metoden grundades i att sparasegmenterade bitar och testa en något större bit än de sparade bitarna, för att sedan användaReed Solomon för att fastställa positionen för beskärningen om den fanns med. Dock leddedenna metod till enorm datalagring och betydande tidsåtgång, vilket gjorde det orealistiskt attuppnå projektets mål med den befintliga teknologin. Möjligtvis är det applicerbart på andraområden, till exempel identifiering av huruvida ett kapitel ingår i en bok.Frågeställningen bedömdes besvaras jakande för texter, då algoritmen klarade målet förprojektet. Däremot kunde detta inte sägas för bilder, som kräver vidare forskning.

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  • 40.
    Daurer, Benedikt J.
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Hantke, Max F.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Nettelblad, Carl
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för beräkningsvetenskap. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Tillämpad beräkningsvetenskap. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Maia, Filipe R. N. C.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Hummingbird: monitoring and analyzing flash X-ray imaging experiments in real time2016Ingår i: Journal of applied crystallography, ISSN 0021-8898, E-ISSN 1600-5767, Vol. 49, s. 1042-1047Artikel i tidskrift (Refereegranskat)
  • 41. Drawert, Brian
    et al.
    Engblom, Stefan
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för beräkningsvetenskap. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Tillämpad beräkningsvetenskap.
    Hellander, Andreas
    URDME: a modular framework for stochastic simulation of reaction-transport processes in complex geometries2012Ingår i: BMC Systems Biology, E-ISSN 1752-0509, Vol. 6, s. 76:1-17Artikel i tidskrift (Refereegranskat)
  • 42. Drawert, Brian
    et al.
    Hellander, Andreas
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för beräkningsvetenskap. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Tillämpad beräkningsvetenskap.
    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 universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för beräkningsvetenskap. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Numerisk analys.
    Krintz, Chandra
    Petzold, Linda R.
    Stochastic Simulation Service: Bridging the gap between the computational expert and the biologist2016Ingår i: PloS Computational Biology, ISSN 1553-734X, E-ISSN 1553-7358, Vol. 12, nr 12, artikel-id e1005220Artikel i tidskrift (Refereegranskat)
  • 43. Drawert, Brian
    et al.
    Trogdon, Michael
    Toor, Salman
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för beräkningsvetenskap. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Tillämpad beräkningsvetenskap.
    Petzold, Linda
    Hellander, Andreas
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för beräkningsvetenskap. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Tillämpad beräkningsvetenskap.
    MOLNs: A cloud platform for interactive, reproducible, and scalable spatial stochastic computational experiments in systems biology using PyURDME2016Ingår i: SIAM Journal on Scientific Computing, ISSN 1064-8275, E-ISSN 1095-7197, Vol. 38, s. C179-C202Artikel i tidskrift (Refereegranskat)
  • 44.
    Edvinsson, Marcus
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Bildanalys och människa-datorinteraktion.
    Implementing the circularly polarized light method for determining wall thickness of cellulosic fibres2012Självständigt arbete på avancerad nivå (yrkesexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
    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.

    Ladda ner fulltext (pdf)
    fulltext
  • 45. Elmroth, Erik
    et al.
    Holmgren, Sverker
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för teknisk databehandling. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Tillämpad beräkningsvetenskap.
    Lindemann, Jonas
    Toor, Salman
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för teknisk databehandling. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Tillämpad beräkningsvetenskap.
    Östberg, Per-Olov
    Empowering a flexible application portal with a SOA-based grid job management framework2008Konferensbidrag (Refereegranskat)
  • 46. Emanuelsson, Daniel
    et al.
    Rimhagen, Elsa
    Mobile application for showing that behind the blocks within block programming there is code2022Självständigt arbete på grundnivå (kandidatexamen), 10 poäng / 15 hpStudentuppsats (Examensarbete)
    Abstract [en]

    Scratch is a block programming language which introduces beginners to programming. Instead of code the user has access to a set of blocks with text and icons, explaining how the block will affect the program that is written. The connection between one block and the corresponding code can be hard to understand for the beginner. The goal of this project is therefore to develop a user-friendly, flashcard-based mobile application to show the target group of 8- to 16-year-olds that behind every block there is code. The application is developed in TypeScript, using React Native as framework and the developer tool Expo for setting up and publishing of the application. The final application consists of 6 different screens; a starting screen, an information screen, a menu, a submenu, an "under development"-screen and a flashcard view. The user can navigate between the screens and by choosing a specific block the flashcard view displays a flashcard with the block and the corresponding translation in Python. The goal of the project is fulfilled, and with a testing group it is also confirmed that the application is user-friendly. Although the goal is achieved, the conclusion that the step between block programming and syntax is hard can be drawn, with difficulties in translating the blocks appearing along the way.

    Ladda ner fulltext (pdf)
    fulltext
  • 47.
    Engquist, Björn
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för teknisk databehandling. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Numerisk analys.
    Smedsaas, Tom
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för teknisk databehandling. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Numerisk analys.
    Automatic analysis in PDE software1984Ingår i: PDE Software: Modules, Interfaces and Systems, Amsterdam, The Netherlands: Elsevier Science , 1984, s. 399-409Konferensbidrag (Refereegranskat)
  • 48.
    Engquist, Björn
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för teknisk databehandling. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Numerisk analys.
    Smedsaas, Tom
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för teknisk databehandling. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Numerisk analys.
    Automatic computer code generation for hyperbolic and parabolic differential equations1980Ingår i: SIAM Journal on Scientific and Statistical Computing, ISSN 0196-5204, Vol. 1, s. 249-259Artikel i tidskrift (Refereegranskat)
  • 49.
    Eriksson, Lars-Henrik
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för datalogi. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datalogi.
    Verification and generation of geographical data using domain theory2005Ingår i: TRain Workshop at the 3rd IEEE International Conference on Software Engineering and Formal Methods (SEFM’05), 2005, 2005Konferensbidrag (Övrigt vetenskapligt)
    Ladda ner fulltext (pdf)
    Extended abstract
  • 50.
    Ghosal, Sandip
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för datorteknik. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Datorteknik.
    Shyamasundar, R. K.
    Indian Inst Technol, Dept Comp Sci & Engn, Mumbai, India.
    Preventing Privacy-Violating Information Flows in JavaScript Applications Using Dynamic Labelling2022Ingår i: Information Systems Security: 18th International Conference, ICISS 2022, Tirupati, India, December 16–20, 2022, Proceedings / [ed] Venkata Ramana Badarla, Surya Nepal & Rudrapatna K. Shyamasundar, Springer Nature, 2022, s. 202-219Konferensbidrag (Refereegranskat)
    Abstract [en]

    Web browser-based applications deal with humongous user information using applications of web scripts. In particular, JavaScript applications access information through built-in browser APIs that dynamically load remote scripts and execute with the same privilege as that of the applications - usually referred to as mashup model. Unfortunately, this allows malicious JavaScripts to manipulate the given browser functionalities leading to various web attacks violating users' privacy. Moreover, with the rapid growth of e-commerce sectors, malicious scripts pose a significant challenge to digital transactions. In this paper, we propose an approach that prevents various web-based attacks such as code injection, cross-site scripting (XSS). The approach adopts a Dynamic Labelling algorithm that generates information flow security policies automatically for local variables in JavaScript based on the given policies for sensitive variables. Unlike existing solutions that are too conservative primarily due to the generic flow policies leading to false-alarms, our solution leads to realizing conditions as to when a script accepts the parameters returned by a dynamic script; thus enabling us to build an automatic platform for preventing information flows to malicious scripts without explicit characterization by programmers or users.

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