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  • 1.
    Atif, Yacine
    et al.
    University of Skövde, School of Informatics. University of Skövde, The Informatics Research Centre.
    Gamalielsson, Jonas
    University of Skövde, School of Informatics. University of Skövde, The Informatics Research Centre.
    Lundell, Björn
    University of Skövde, School of Informatics. University of Skövde, The Informatics Research Centre.
    Open Source Collaboration Tools and Organisational Learning: On Adopting EtherPad in Small Companies2016In: Proceedings of FLOSSEdu: FLOSS education and computational thinking workshop. Open Source Systems Conference 2016. Gothenburg, Sweden., 2016Conference paper (Refereed)
    Abstract [en]

    Organisations could benefit from the improvements in collaborative learning and increased control gained by the use of open source software. EtherPad enables simultaneous updates on a shared document from remotely located participants. We discuss the adoption life-cycle of this open source tool in the context of a strategic intervention, with a focus on a learning agenda to guide the installation and configuration processes, and to reduce the learning curve involved in the adoption experience.

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  • 2.
    Butler, Simon
    et al.
    University of Skövde, School of Informatics. University of Skövde, Informatics Research Environment.
    Gamalielsson, Jonas
    University of Skövde, School of Informatics. University of Skövde, Informatics Research Environment.
    Lundell, Björn
    University of Skövde, School of Informatics. University of Skövde, Informatics Research Environment.
    Brax, Christoffer
    Combitech AB, Linköping, Sweden.
    Mattsson, Anders
    Husqvarna AB, Huskvarna, Sweden.
    Gustavsson, Tomas
    PrimeKey Solutions AB, Stockholm, Sweden.
    Feist, Jonas
    RedBridge AB, Stockholm, Sweden.
    Kvarnström, Bengt
    Saab AB, Linköping, Sweden.
    Lönroth, Erik
    Scania CV AB, Södertälje, Sweden.
    Considerations and challenges for the adoption of open source components in software-intensive businesses2022In: Journal of Systems and Software, ISSN 0164-1212, E-ISSN 1873-1228, Vol. 186, article id 111152Article in journal (Refereed)
    Abstract [en]

    Component-Based Software Development is a conventional way of working for software-intensive businesses and OpenSource Software (OSS) components are frequently considered by businesses for adoption and inclusion in softwareproducts. Previous research has found a variety of practices used to support the adoption of OSS components, in-cluding formally specified processes and less formal, developer-led approaches, and that the practices used continue todevelop. Evolutionary pressures identified include the proliferation of available OSS components and increases in thepace of software development as businesses move towards continuous integration and delivery. We investigate workpractices used in six software-intensive businesses in the primary and secondary software sectors to understand currentapproaches to OSS component adoption and the challenges businesses face establishing effective work practices to eval-uate OSS components. We find businesses have established processes for evaluating OSS components and communitiesthat support more complex and nuanced considerations of the cost and risks of component adoption alongside matterssuch as licence compliance and functional requirements. We also found that the increasing pace and volume of softwaredevelopment within some businesses provides pressure to continue to evolve software evaluation processes.

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  • 3.
    Butler, Simon
    et al.
    University of Skövde, School of Informatics. University of Skövde, Informatics Research Environment.
    Gamalielsson, Jonas
    University of Skövde, School of Informatics. University of Skövde, Informatics Research Environment.
    Lundell, Björn
    University of Skövde, School of Informatics. University of Skövde, Informatics Research Environment.
    Brax, Christoffer
    Combitech AB, Linköping, Sweden.
    Mattsson, Anders
    Husqvarna AB, Huskvarna, Sweden.
    Gustavsson, Tomas
    PrimeKey Solutions AB, Solna, Sweden.
    Feist, Jonas
    RedBridge AB, Stockholm, Sweden.
    Kvarnström, Bengt
    Saab AB, Linköping, Sweden.
    Lönroth, Erik
    Scania CV AB, Södertälje, Sweden.
    On business adoption and use of reproducible builds for open and closed source software2023In: Software quality journal, ISSN 0963-9314, E-ISSN 1573-1367, Vol. 31, no 3, p. 687-719Article in journal (Refereed)
    Abstract [en]

    Reproducible builds (R-Bs) are software engineering practices that reliably create bit-for-bit identical binary executable files from specified source code. R-Bs are applied in someopen source software (OSS) projects and distributions to allow verification that the distrib-uted binary has been built from the released source code. The use of R-Bs has been advo-cated in software maintenance and R-Bs are applied in the development of some OSS secu-rity applications. Nonetheless, industry application of R-Bs appears limited, and we seekto understand whether awareness is low or if significant technical and business reasonsprevent wider adoption. Through interviews with software practitioners and business man-agers, this study explores the utility of applying R-Bs in businesses in the primary and sec-ondary software sectors and the business and technical reasons supporting their adoption.We find businesses use R-Bs in the safety-critical and security domains, and R-Bs are valu-able for traceability and support collaborative software development. We also found thatR-Bs are valued as engineering processes and are seen as a badge of software quality, butwithout a tangible value proposition. There are good engineering reasons to use R-Bs inindustrial software development, and the principle of establishing correspondence betweensource code and binary offers opportunities for the development of further applications.

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  • 4.
    Butler, Simon
    et al.
    University of Skövde, School of Informatics. University of Skövde, Informatics Research Environment.
    Gamalielsson, Jonas
    University of Skövde, School of Informatics. University of Skövde, Informatics Research Environment.
    Lundell, Björn
    University of Skövde, School of Informatics. University of Skövde, Informatics Research Environment.
    Brax, Christoffer
    Combitech AB, Linköping, Sweden.
    Mattsson, Anders
    Husqvarna AB, Huskvarna, Sweden.
    Gustavsson, Tomas
    PrimeKey Solutions AB, Stockholm, Sweden.
    Feist, Jonas
    RedBridge AB, Stockholm, Sweden.
    Lönroth, Erik
    Scania IT AB, Södertälje, Sweden.
    Maintaining interoperability in open source software: A case study of the Apache PDFBox project2020In: Journal of Systems and Software, ISSN 0164-1212, E-ISSN 1873-1228, Vol. 159, article id 110452Article in journal (Refereed)
    Abstract [en]

    Software interoperability is commonly achieved through the implementation of standards for communication protocols or data representation formats. Standards documents are often complex, difficult to interpret, and may contain errors and inconsistencies, which can lead to differing interpretations and implementations that inhibit interoperability. Through a case study of two years of activity in the Apache PDFBox project we examine day-to-day decisions made concerning implementation of the PDF specifications and standards in a community open source software (OSS) project. Thematic analysis is used to identify semantic themes describing the context of observed decisions concerning interoperability. Fundamental decision types are identified including emulation of the behaviour of dominant implementations and the extent to which to implement the PDF standards. Many factors influencing the decisions are related to the sustainability of the project itself, while other influences result from decisions made by external actors, including the developers of dependencies of PDFBox. This article contributes a fine grained perspective of decision-making about software interoperability by contributors to a community OSS project. The study identifies how decisions made support the continuing technical relevance of the software, and factors that motivate and constrain project activity. 

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  • 5.
    Butler, Simon
    et al.
    University of Skövde, School of Informatics. University of Skövde, Informatics Research Environment.
    Gamalielsson, Jonas
    University of Skövde, School of Informatics. University of Skövde, Informatics Research Environment.
    Lundell, Björn
    University of Skövde, School of Informatics. University of Skövde, Informatics Research Environment.
    Brax, Christoffer
    Combitech AB, Linköping, Sweden.
    Persson, Tomas
    Digitalist Sweden AB, Stockholm, Sweden.
    Mattsson, Anders
    Husqvarna AB, Huskvarna, Sweden.
    Gustavsson, Tomas
    PrimeKey Solutions AB, Solna Sweden.
    Feist, Jonas
    RedBridge AB, Stockholm, Sweden.
    Öberg, Jonas
    Scania CV AB, Södertälje, Sweden.
    An Exploration of Openness in Hardware and Software Through Implementation of a RISC-V Based Desktop Computer2022In: OpenSym '22: Proceedings of the 18th International Symposium on Open Collaboration / [ed] Gregorio Robles; Amel Charleux; Igor Steinmacher; Javier Arroyo; Antonio Balderas; Gemma Catolino; Alexandre Decan; Francisco Martín-Rico; Amit Kumar Verma, New York, NY, USA: Association for Computing Machinery (ACM), 2022, article id 4Conference paper (Refereed)
    Abstract [en]

    Open hardware and open source software platforms bring benefits to both implementers and users in the form of system adaptability and maintainability, and through the avoidance of lock-in, for example. Development of the \riscv\ Instruction Set Architecture and processors during the last ten years has made the implementation of a desktop computer using open hardware, including open processors, and open source software an approaching possibility. We use the SiFive Unmatched development board and Ubuntu Linux, and the recorded experiences of system builders using the Unmatched board to explore the extent to which it is possible to create an open desktop computer. The work identifies current limitations to implementing an open computer system, which lie mainly at the interface between the operating system and hardware components. Potential solutions to the challenges uncovered are proposed, including greater consideration of openness during the early stages of product design. A further contribution is made by an account of the synergies arising from open collaboration in a private-collective innovation process.

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  • 6.
    Butler, Simon
    et al.
    University of Skövde, School of Informatics. University of Skövde, Informatics Research Environment.
    Gamalielsson, Jonas
    University of Skövde, School of Informatics. University of Skövde, Informatics Research Environment.
    Lundell, Björn
    University of Skövde, School of Informatics. University of Skövde, Informatics Research Environment.
    Brax, Christoffer
    Combitech AB, Linköping, Sweden.
    Sjöberg, Johan
    Findwise AB, Göteborg, Sweden.
    Mattsson, Anders
    Husqvarna AB, Huskvarna, Sweden.
    Gustavsson, Thomas
    PrimeKey Solutions AB, Stockholm, Sweden.
    Feist, Jonas
    RedBridge AB, Stockholm, Sweden.
    Lönroth, Erik
    Scania IT AB, Södertälje, Sweden.
    On Company Contributions to Community Open Source Software Projects2021In: IEEE Transactions on Software Engineering, ISSN 0098-5589, E-ISSN 1939-3520, Vol. 47, no 7, p. 1381-1401Article in journal (Refereed)
    Abstract [en]

    The majority of contributions to community open source software (OSS) projects are made by practitioners acting on behalf of companies and other organisations. Previous research has addressed the motivations of both individuals and companies to engage with OSS projects. However, limited research has been undertaken that examines and explains the practical mechanisms or work practices used by companies and their developers to pursue their commercial and technical objectives when engaging with OSS projects. This research investigates the variety of work practices used in public communication channels by company contributors to engage with and contribute to eight community OSS projects. Through interviews with contributors to the eight projects we draw on their experiences and insights to explore the motivations to use particular methods of contribution. We find that companies utilise work practices for contributing to community projects which are congruent with the circumstances and their capabilities that support their short- and long-term needs. We also find that companies contribute to community OSS projects in ways that may not always be apparent from public sources, such as employing core project developers, making donations, and joining project steering committees in order to advance strategic interests. The factors influencing contributor work practices can be complex and are often dynamic arising from considerations such as company and project structure, as well as technical concerns and commercial strategies. The business context in which software created by the OSS project is deployed is also found to influence contributor work practices.

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  • 7.
    Butler, Simon
    et al.
    University of Skövde, School of Informatics. University of Skövde, The Informatics Research Centre.
    Gamalielsson, Jonas
    University of Skövde, School of Informatics. University of Skövde, The Informatics Research Centre.
    Lundell, Björn
    University of Skövde, School of Informatics. University of Skövde, The Informatics Research Centre.
    Jonsson, Per
    Combitech AB.
    Sjöberg, Johan
    Findwise AB.
    Mattsson, Anders
    Husqvarna AB.
    Rickö, Niklas
    JAK.
    Gustavsson, Tomas
    PrimeKey Solutions AB.
    Feist, Jonas
    RedBridge AB.
    Landemoo, Stefan
    Saab AB.
    Lönroth, Erik
    Scania IT AB.
    An Investigation of Work Practices Used by Companies Making Contributions to Established OSS Projects2018In: ICSE-SEIP '18 Proceedings of the 40th International Conference on Software Engineering: Software Engineering in Practice, New York: Association for Computing Machinery (ACM), 2018, p. 201-210Conference paper (Refereed)
    Abstract [en]

    Professionals contribute to open source software (OSS) projects aspart of their employment. Previous research has addressed motivationsof individuals and the ways they engage with OSS projects.However, there is a lack of research which examines and explainswork practices used by companies in their engagement with projects.Work practices used by companies to contribute to five establishedOSS projects are investigated through examination of the actions ofemployees in public communication channels and draw on our experienceswhen analysing engagement with the same projects. Wefind that companies utilise work practices for contributing whichare congruent with the circumstances and their capabilities thatsupport their short and long term needs. We find that companiescontribute to OSS projects in different ways, such as employing coreproject developers, making donations, and joining project steeringcommittees in order to advance strategic interests.

  • 8.
    Crowston, Kevin
    et al.
    Syracuse University, Syracuse, NY, USA.
    Hammouda, ImedUniversity of Gothenburg, Sweden.Lundell, BjörnUniversity of Skövde, School of Informatics. University of Skövde, The Informatics Research Centre.Robles, GregorioGSyC, Universidad Rey Juan Carlos, Madrid, Spain.Gamalielsson, JonasUniversity of Skövde, School of Informatics. University of Skövde, The Informatics Research Centre.Lindman, JuhoChalmers, Gothenburg, Sweden ; University of Gothenburg, Gothenburg, Sweden.
    Open Source Systems: Integrating Communities: 12th IFIP WG 2.13 International Conference, OSS 2016, Gothenburg, Sweden, May 30 - June 2, 2016, Proceedings2016Collection (editor) (Refereed)
    Abstract [en]

    This book constitutes the refereed proceedings of the 12th International IFIP WG 2.13 International Conference on Open Source Systems, OSS 2016, held in Gothenburg, Sweden, in May/June 2016. The 13 revised full papers presented were carefully reviewed and selected from 38 submissions. The papers cover a wide range of topics related to free, libre, and open source software, including: organizational aspects of communities; organizational adoption; participation of women; software maintenance and evolution; open standards and open data; collaboration; hybrid communities; code reviews; and certification.

  • 9.
    Feller, Joseph
    et al.
    University College Cork, Ireland.
    Gamalielsson, JonasUniversity of Skövde, School of Informatics. University of Skövde, The Informatics Research Centre.Hill, Benjamin MakoUniversity of Washington, USA.Robles, GregorioUniversidad Rey Juan Carlos, Spain.
    Proceedings of the Doctoral Consortium at the 15th International Symposium on Open Collaboration2019Conference proceedings (editor) (Refereed)
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  • 10.
    Fischer, Thomas
    et al.
    University of Skövde, School of Informatics. University of Skövde, Informatics Research Environment.
    Lundell, Björn
    University of Skövde, School of Informatics. University of Skövde, Informatics Research Environment.
    Gamalielsson, Jonas
    University of Skövde, School of Informatics. University of Skövde, Informatics Research Environment.
    Achieving Conformance to Document Standards: Can PDF Files Conform to the PDF/A-1b Specification?2021In: International Journal of Standardization Research, ISSN 2470-8542, Vol. 19, no 1, p. 1-32Article in journal (Refereed)
    Abstract [en]

    In the context of long-term archival of digital assets, file formats that are standardized and designed for longevity such as PDF/A are preferred. However, due to the complexity of and ambiguities in PDF standards, it is far from trivial to either create standard-conformant files or check the conformance of any given file. This study investigates the challenges when checking real-world PDF files from public sector organizations meant for long-term archival for PDF/A conformance. Results show that only a small set of PDF files claims to conform to the PDF/A-1b specification variant and even fewer files pass conformance checks by various conformance checking tools. Challenges for conformance checking tools include both ambiguities in the standards’ technical specifications and limitations in the implementation.

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  • 11.
    Fischer, Thomas
    et al.
    University of Skövde, School of Informatics. University of Skövde, Informatics Research Environment.
    Lundell, Björn
    University of Skövde, School of Informatics. University of Skövde, Informatics Research Environment.
    Gamalielsson, Jonas
    University of Skövde, School of Informatics. University of Skövde, Informatics Research Environment.
    On challenges for achieving conformance of files to document standards: The case of PDF/A-1b2021In: Joint Proceedings EURAS 2021: Standardisation and Innovation SIIT 2021 The Past, Present and Future of ICT Standardisation / [ed] Kai Jakobs, Aachen: Verlag Mainz , 2021, Vol. 16, p. 171-190Conference paper (Refereed)
    Abstract [en]

    File formats that are standardized and designed for longevity, such as PDF/A, are preferred in the context of long-term archival of digital assets. However, it is far from trivial to either create standard-conformant files or check the conformance of any given file due to the complexity and ambiguities in PDF standards. This study aims to investigate challenges when checking PDF/A conformance for real-world PDF files from public sector organizations that are intended for long-term-archival. Findings show that only a small proportion of the PDF files claim to conform to the PDF/A-1b specification and even fewer files pass conformance checks performed through the use of various conformance checking tools. Challenges for conformance checking tools include both ambiguities in the technical specifications of standards and limitations in the implementation of software.

  • 12.
    Fischer, Thomas
    et al.
    University of Skövde, School of Informatics. University of Skövde, Informatics Research Environment.
    Lundell, Björn
    University of Skövde, School of Informatics. University of Skövde, Informatics Research Environment.
    Gamalielsson, Jonas
    University of Skövde, School of Informatics. University of Skövde, Informatics Research Environment.
    On challenges for achieving conformance to document standards: Can PDF files conform to the PDF/A-1b specification?2020In: Proceedings 25th EURAS Annual Standardisation Conference: Standards for Digital Transformation: Blockchain and Innovation / [ed] Kai Jakobs; Dong-hyu Kim, Aachen: Verlagshaus Mainz , 2020, p. 21-40Conference paper (Refereed)
    Abstract [en]

    In the context of long-term archival of digital assets, file formats that are standardized and designed for longevity such as PDF/A are preferred. However, due to the complexity and ambiguities in PDF standards, it is far from trivial to either create standard-conformant files or check the conformance of any given file. This study aims at investigating the challenges when checking real-world PDF files from public sector organizations meant for long-term archival for PDF/A conformance. Results show that only a small set of PDF files claims to conform to the PDF/A-1b specification variant and even fewer files pass conformance checks by various conformance checking tools. Challenges for conformance checking tools include both ambiguities in the standards’ technical specifications and limitations in the implementation.

  • 13.
    Fischer, Thomas
    et al.
    University of Skövde, School of Informatics. University of Skövde, Informatics Research Environment.
    Lundell, Björn
    University of Skövde, School of Informatics. University of Skövde, Informatics Research Environment.
    Gamalielsson, Jonas
    University of Skövde, School of Informatics. University of Skövde, Informatics Research Environment.
    On PDF/A Conformance and Font Usage in PDF Documents Provided by Public Sector Organizations2023In: International Journal of Standardization Research, ISSN 2470-8542, Vol. 20, no 1, p. 1-19Article in journal (Refereed)
    Abstract [en]

    The use of appropriate fonts and file formats for long-term maintenance of digital assets is a challenge for organizations in the public sector. The article reports from a study which investigated the PDF/A conformance and font usage in PDF files provided by Swedish public sector organizations (PSOs). This article presents an analysis of the PDF files’ properties and font usage including a categorization of fonts’ licenses. This study is motivated by the PDF/A-1 standard’s requirement that ‘only fonts that are legally embeddable in a file for unlimited, universal rendering shall be used.’ Analyzing PDF sets from three PSOs, the finding shows that the proportion of files that claim or succeed at conforming to PDF/A greatly varies among the sets despite similar backgrounds. Although the most popular way to make use of fonts is by embedding a subset of the font data, for some fonts expected to be ‘always available,’ a considerable proportion of PDF files does not include any font data. This puts the onus of locating this data on the PDF reader which is problematic for long-term archival

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  • 14.
    Francke, Helena
    et al.
    Swedish School of Library and Information Science, University of Borås, Sweden.
    Gamalielsson, Jonas
    University of Skövde, School of Informatics. University of Skövde, The Informatics Research Centre.
    Lundell, Björn
    University of Skövde, School of Informatics. University of Skövde, The Informatics Research Centre.
    Institutional repositories as infrastructures for long-term preservation2017In: Information research, E-ISSN 1368-1613, Vol. 22, no 2, article id 757Article in journal (Refereed)
    Abstract [en]

    Introduction. The study describes the conditions for long-term preservation of the content of the institutional repositories of Swedish higher education institutions based on an investigation of how deposited files are managed with regards to file format and how representatives of the repositories describe the functions of the repositories.

    Method. The findings are based on answers to a questionnaire completed by thirty-four institutional repository representatives (97% response rate).

    Analysis. Questionnaire answers were analysed through descriptive statistics and qualitative coding. The concept of information infrastructures was used to analytically discuss repository work.

    Results. Visibility and access to content were considered to be the most important functions of the repositories, but long-term preservation was also considered important for publications and student theses. Whereas a majority of repositories had some form of guidelines for which file formats were accepted, very few considered whether or not file formats constitute open standards. This can have consequences for the long-term sustainability and access of the content deposited in the repositories.

    Conclusion. The study contributes to the discussion about the sustainability of research publications and data in the repositories by pointing to the potential difficulties involved for long-term preservation and access when there is little focus on and awareness of open file formats.

  • 15.
    Gamalielson, Jonas
    University of Skövde, School of Humanities and Informatics.
    Developing Semantic Pathway Alignment Algorithms for Systems Biology2006Report (Other academic)
    Abstract [en]

    Systems biology is an emerging multi-disciplinary field in which the behaviour of complex biological systems is studied by considering the interaction of all cellular and molecular constituents rather than using a "traditional" reductionist approach where constituents are studied individually. Systems are often studied over time with the ultimate goal of developing models which can be used to predict and understand complex biological processes, such as human diseases. To support systems biology, a large number of biological pathways are being derived for many different organisms, and these are stored in various databases. There is a lack of and need for algorithms for analysis of biological pathways. Here, a thesis is proposed where three related methods are developed for semantic analysis of biological pathways utilising the Gene Ontology. It is believed that the methods will be useful to biologists in order to assess the biological plausibility of derived pathways, compare different pathways for semantic similarities, and to derive hypothetical pathways that are semantically similar to documented biological pathways. To our knowledge, all methods are novel, and will therefore extend the bioinformatics toolbox that biologists can use to make new biological discoveries.

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  • 16.
    Gamalielson, Jonas
    University of Skövde, School of Humanities and Informatics.
    Methods for Assessing the Interestingness of Rules Induced from Microarray Gene Expression Data2003Report (Other academic)
    Abstract [en]

    Microarray technology makes it possible to simultaneously measure the expression of thousands of genes. Gene expression data can be analysed in many different ways to produce putative knowledge on for example co-regulated genes, differentially expressed genes and how genes interact with each other. One way to derive gene interactions is to use rule induction algorithms such as association rule discovery algorithms or decision trees. The application of such algorithms to gene expression data sets typically generates a large set of rules serving as hypotheses of how genes interact. It is necessary to apply different measures to assess the interestingness of the rule hypotheses. There are well known domain independent objective measures, but there is a lack of domain specific interestingness measures tailored for microarray gene expression data. Without domain specific interestingness measures it is impossible to know if the hypotheses are interesting from a biological perspective, without resorting to time consuming manual evaluation of every single rule. The aim and contribution of this work is to develop a method for assessing the interestingness of rules induced from microarray gene expression data using a combination of objective and domain specific measures.

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  • 17.
    Gamalielson, Jonas
    et al.
    University of Skövde, School of Humanities and Informatics.
    Olsson, Björn
    University of Skövde, School of Humanities and Informatics.
    On the Robustness of Algorithms for Clustering of Gene Expression Data2003Report (Other academic)
    Abstract [en]

    The progress in microarray technology is evident and huge amounts of gene expression data are currently being produced. A complicating matter is that there are various sources of uncertainty in microarray experiments, as well as in the analysis of expression data. This problem has generated an increased interest in the validation of methods for analysis of expression data. Clustering algorithms have been found particularly useful for the study of coexpressed genes, and this paper therefore concerns the robustness of partitional clustering algorithms. These algorithms use a predefined number of clusters and assign each gene to exactly one cluster. The effect of repeated clustering using identical algorithm parameters and input data is investigated for the self-organizing map (SOM) and the $k$-means algorithm. The susceptibility to measurement noise is also studied. A reproducibility measure is proposed and used to assess the results from the performed clustering experiments. Well-known publicly available datasets are used. Results show that clusterings are not necessarily reproducible even when identical algorithm parameters are used, and that the problems are aggravated when measurement noise is introduced.

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  • 18.
    Gamalielsson, Jonas
    University of Skövde, School of Humanities and Informatics. University of Skövde, The Systems Biology Research Centre.
    Developing Semantic Pathway Comparison Methods for Systems Biology2009Doctoral thesis, monograph (Other academic)
    Abstract [en]

    Systems biology is an emerging multi-disciplinary field in which the behaviour of complex biological systems is studied by considering the interaction of many cellular and molecular constituents rather than using a “traditional” reductionist approach where constituents are studied individually. Systems are often studied over time with the ultimate goal of developing models which can be used to understand and predict complex biological processes, such as human diseases. To support systems biology, a large number of biological pathways are being derived for many different organisms, and these are stored in various databases. This pathway collection presents an opportunity to compare and contrast pathways, and to utilise the knowledge they represent. This thesis presents some of the first algorithms that are designed to explore this opportunity. It is argued that the methods will be useful to biologists in order to assess the biological plausibility of derived pathways, compare different biological pathways for semantic similarities, and to derive putative pathways that are semantically similar to documented biological pathways. The methods will therefore extend the systems biology toolbox that biologists can use to make new biological discoveries.

  • 19.
    Gamalielsson, Jonas
    University of Skövde, School of Humanities and Informatics.
    Thesis Methods: Assessing the Biological Plausibility of Regulatory Hypotheses2005Report (Other academic)
    Abstract [en]

    Many algorithms that derive gene regulatory networks from microarray gene expression data have been proposed in the literature. The performance of such an algorithm is often measured by how well a genetic network can recreate the gene expression data that the network was derived from. However, this kind of performance does not necessarily mean that the regulatory hypotheses in the network are biologically plausible. We have therefore proposed a Gene Ontology based method for assessing the biological plausibility of regulatory hypotheses at the gene product level using prior biological knowledge in the form of Gene Ontology (GO) annotation of gene products and regulatory pathway databases (Gamalielsson et al. 2005). Templates were designed to encode general knowledge, derived by generalizing from known interactions to typical properties of interacting gene product pairs. By matching regulatory hypotheses to templates, the plausible hypotheses can be separated from inplausible ones. This document elaborates on how the present method can be improved and extended.

    Download full text (pdf)
    FULLTEXT01
  • 20.
    Gamalielsson, Jonas
    et al.
    University of Skövde, School of Humanities and Informatics. University of Skövde, The Informatics Research Centre.
    Grahn, Alexander
    University of Skövde, School of Humanities and Informatics. University of Skövde, The Informatics Research Centre.
    Lundell, Björn
    University of Skövde, School of Humanities and Informatics. University of Skövde, The Informatics Research Centre.
    Learning through analysis of coding practices in FLOSS projects2012In: Proceedings of FLOSSEdu 2012: FLOSS Education - Long-term Sustainability / [ed] Gregorio Robles, Jesús González Barahona, Wouter Tebbens, Imed Hammouda, Tampere: Tampere University of Technology, 2012, p. 13-19Conference paper (Refereed)
  • 21.
    Gamalielsson, Jonas
    et al.
    University of Skövde, School of Informatics. University of Skövde, The Informatics Research Centre.
    Jakobsson, Fredrik
    University of Skövde, School of Informatics. University of Skövde, The Informatics Research Centre.
    Lundell, Björn
    University of Skövde, School of Informatics. University of Skövde, The Informatics Research Centre.
    Feist, Jonas
    RedBridge AB, Kista, Sweden.
    Gustavsson, Tomas
    PrimeKey Solutions AB, Solna, Sweden.
    Landqvist, Fredric
    Findwise AB, Göteborg, Sweden.
    On the availability and effectiveness of open source software for digital signing of PDF documents2015In: Open Source Systems: Adoption and Impact: 11th IFIP WG 2.13 International Conference, OSS 2015, Florence, Italy, May 16-17, 2015, Proceedings / [ed] Ernesto Damiani, Fulvio Frati, Dirk Riehle & Anthony I. Wasserman, Cham: Springer, 2015, p. 71-80Conference paper (Refereed)
    Abstract [en]

    Digital signatures are important in order to ensure the integrity and authenticity of information communicated over the Internet involving different stakeholders within and beyond the borders of different nations. The topic has gained increased interest in the European context and there is legislation and project initiatives aiming to facilitate use and standardisation of digital signatures. Open standards and open source implementations of open standards are important means for the interoperability and long-term maintenance of software systems implementing digital signatures. In this paper we report from a study aiming to establish the availability and effectiveness of software provided under an open source license for digital signing and validation of PDF documents. Specifically, we characterise the use of digital signatures in Swedish Governmental agencies, report on the interoperability of open source and proprietary licensed software for digital signatures in PDF documents, and establish the effectiveness of software provided under an open source license for validation of digital signatures in PDF documents.

  • 22.
    Gamalielsson, Jonas
    et al.
    University of Skövde, School of Humanities and Informatics. University of Skövde, The Informatics Research Centre.
    Lundell, Björn
    University of Skövde, School of Humanities and Informatics. University of Skövde, The Informatics Research Centre.
    Experiences from implementing PDF in open source: challenges and opportunities for standardisation processes2013In: Proceedings of the 8th IEEE Conference on Standardization and Innovation in Information Technology (SIIT 2013) / [ed] Kai Jakobs, Piscataway: IEEE Press, 2013, p. 39-49Conference paper (Refereed)
  • 23.
    Gamalielsson, Jonas
    et al.
    University of Skövde, School of Informatics. University of Skövde, Informatics Research Environment.
    Lundell, Björn
    University of Skövde, School of Informatics. University of Skövde, Informatics Research Environment.
    Exploring Influences Between ICT Standards and Their Implementations in Open Source Software Projects: The Case of H.2642021In: Joint Proceedings EURAS 2021: Standardisation and Innovation SIIT 2021 The Past, Present and Future of ICT Standardisation / [ed] Kai Jakobs, Aachen: Verlag Mainz , 2021, Vol. 16, p. 211-226Conference paper (Refereed)
    Abstract [en]

    Novel results concerning influences between ICT standards and their implementations in open source software (OSS) are presented in this paper. Findings draw from observations and analysis related to the ITU-T H.264 standard and two OSS projects (OpenH264 and x264) that implement the standard. The study reports on a characterisation of organisations that influence and control the H.264 standard, organisations that influence and control OSS projects implementing the H.264 standard, and influences between contributors involved with the H.264 standard and OSS projects that implement the standard. Furthermore, projects for standardisation and implementation of H.264 are contrasted with respect to the mix of contributing organisations, and findings are put in relation to organisational strategies of contributing organisations and previous research.

  • 24.
    Gamalielsson, Jonas
    et al.
    University of Skövde, School of Humanities and Informatics. University of Skövde, The Informatics Research Centre.
    Lundell, Björn
    University of Skövde, School of Humanities and Informatics. University of Skövde, The Informatics Research Centre.
    Long-Term Sustainability of Open Source Software Communities beyond a Fork: A Case Study of LibreOffice2012In: Open Source Systems: Long-Term Sustainability: 8th IFIP WG 2.13 International Conference, OSS 2012, Hammamet, Tunisia, September 10-13, 2012. Proceedings / [ed] Imed Hammouda, Björn Lundell, Tommi Mikkonen, Walt Scacchi, Springer Berlin/Heidelberg, 2012, p. 29-47Conference paper (Refereed)
    Abstract [en]

    Many organisations have requirements for long-term sustainable software systems and associated communities. In this paper we consider long-term sustainability of Open Source software communities in Open Source projects involving a fork. There is currently a lack of studies in the literature that address how specific Open Source software communities are affected by a fork. We report from a case study aiming to investigate the developer community around the LibreOffice project, which is a fork from the OpenOffice.org project. The results strongly suggest a long-term sustainable community and that there are no signs of stagnation in the project 15 months after the fork. Our analysis provides details on the LibreOffice developer community and how it has evolved from the OpenOffice.org community with respect to project activity, long-term involvement of committers, and organisational influence over time. The findings from our analysis of the LibreOffice project make an important contribution towards a deeper understanding of challenges regarding long-term sustainability of Open Source software communities.

  • 25.
    Gamalielsson, Jonas
    et al.
    University of Skövde, School of Informatics. University of Skövde, Informatics Research Environment.
    Lundell, Björn
    University of Skövde, School of Informatics. University of Skövde, Informatics Research Environment.
    On Engagement With ICT Standards and Their Implementations in Open Source Software Projects: Experiences and Insights From the Multimedia Field2021In: International Journal of Standardization Research (IJSR), ISSN 2470-8542, Vol. 19, no 1, p. 1-28, article id 2Article in journal (Refereed)
    Abstract [en]

    The overarching goal in this paper is to investigate organisational engagement with an ICT standard and open source software (OSS) projects that implement the standard, with a specific focus on the multimedia field, which is relevant in light of the wide deployment of standards and different legal challenges in this field. The first part reports on experiences and insights from engagement with standards in the multimedia field and from implementation of such standards in OSS projects. The second part focuses on the case of the ITU-T H.264 standard and the two OSS projects OpenH264 and x264 that implement the standard, and reports on a characterisation of organisations that engage with and control the H.264 standard, and organisations that engage with and control OSS projects implementing the H.264 standard. Further, projects for standardisation and implementation of H.264 are contrasted with respect to mix of contributing organisations, and findings are related to organisational strategies of contributing organisations and previous research.

    Download full text (pdf)
    fulltext
  • 26.
    Gamalielsson, Jonas
    et al.
    University of Skövde, School of Informatics. University of Skövde, Informatics Research Environment.
    Lundell, Björn
    University of Skövde, School of Informatics. University of Skövde, Informatics Research Environment.
    On influences between ICT standards and their implementations in open source software projects: the case of H.2642020In: Booklet of Papers of the 11th International Conference on Standardisation and Innovation in Information Technology (SIIT 2020): The Past, 20/20 and Future of ICT Standardisation ; should have been held on 2-4 September 2020, at RWTH Aachen University, Aachen, Germany / [ed] Kai Jakobs, Aachen: Verlagshaus Mainz , 2020, p. 1-12Conference paper (Refereed)
    Abstract [en]

    This paper presents novel results concerning influences between ICT standards and their implementations in open source software (OSS). Specifically, findings draw from observations and analysis related to the ITU-T H.264 standard and the two OSS projects OpenH264 and x264 that both implement the standard. The study reports on a characterisation of organisations that influence and control the H.264 standard, organisations that influence and control OSS projects implementing the H.264 standard, and influences between contributors involved with the H.264 standard and OSS projects implementing that standard. Further, projects for standardisation and implementation of H.264 are contrasted with respect to mix of contributing organisations, and findings are related to organisational strategies of contributing organisations and previous research.

  • 27.
    Gamalielsson, Jonas
    et al.
    University of Skövde, School of Informatics. University of Skövde, The Informatics Research Centre.
    Lundell, Björn
    University of Skövde, School of Informatics. University of Skövde, The Informatics Research Centre.
    On Involvement in Open Standards: How Do Organisations Contribute to W3C Standards Through Editorship?2016In: Open Source Systems: Integrating Communities: 12th IFIP WG 2.13 International Conference, OSS 2016, Gothenburg, Sweden, May 30 - June 2, 2016, Proceedings / [ed] Kevin Crowston; Imed Hammouda; Björn Lundell; Gregorio Robles; Jonas Gamalielsson; Juho Lindman, Cham: Springer, 2016, 1, Vol. 472, p. 57-70Chapter in book (Refereed)
    Abstract [en]

    Over the years, a number of open standards have been developed and implemented in software for addressing a number of challenges, such as lock-in, interoperability and longevity of software systems and associated digital artefacts. Understanding organisational involvement and collaboration in standardisation is important for informing any future policy and organisational decisions concerning involvement in standardisation. The overarching goal of the study is to establish how organisations contribute to open standards development through editorship. Specifically, the focus is on open standards development in W3C. Through an analysis of editorship for all W3C recommendations we contribute novel findings concerning organisational involvement and collaboration, and highlight contributions from different types of organisations and countries for headquarter of each organisation. We make three principal contributions. First, we establish an overall characterisation of organisational involvement in W3C standardisation. Second, we report on organisational involvement in W3C standardisation over time. Third, we establish organisational collaboration in W3C standardisation through social network analysis.

  • 28.
    Gamalielsson, Jonas
    et al.
    University of Skövde, School of Informatics. University of Skövde, The Informatics Research Centre.
    Lundell, Björn
    University of Skövde, School of Informatics. University of Skövde, The Informatics Research Centre.
    On licensing and other conditions for contributing to widely used open source projects: an exploratory analysis2017In: OpenSym '17: Proceedings of the 13th International Symposium on Open Collaboration, New York: Association for Computing Machinery (ACM), 2017, p. 9:1-9:14Conference paper (Refereed)
    Abstract [en]

    Open source software (OSS) projects are provided under different open source licenses and some projects use other conditions (in addition to licensing terms) for contributors to adhere to. Licensing terms and conditions may affect community involvement and contributions, and are perceived differently by different stakeholders in different OSS projects. The study reports from an exploratory analysis of licensing terms and other conditions for 200 widely used OSS projects, and an investigation of the relationship between licensing terms and other conditions for contributing. We find that strong copyleft licenses are most common and are used in the majority of the projects. Further, a clear majority of the OSS projects use no specific other condition for contributing in addition to the license terms. However, a clear majority of the OSS projects supported by foundations use other conditions for contributing in addition to the license terms. Finally, use of no specific other conditions in addition to the license terms is more common for projects using strong copyleft licensing compared to projects using non-copyleft licensing.

  • 29.
    Gamalielsson, Jonas
    et al.
    University of Skövde, School of Informatics. University of Skövde, The Informatics Research Centre.
    Lundell, Björn
    University of Skövde, School of Informatics. University of Skövde, The Informatics Research Centre.
    On organisational involvement and collaboration in W3C standards through editorship2017In: Journal of Internet Services and Applications, ISSN 1867-4828, E-ISSN 1869-0238, Vol. 8, no 1, p. 5:1-5:26, article id 5Article in journal (Refereed)
    Abstract [en]

    Over time, a number of open standards have been developed and implemented in software for addressing a number of challenges, such as lock-in, interoperability and longevity of software systems and associated digital artefacts. An understanding of organisational involvement and collaboration in standardisation is important for informing any future policy and organisational decisions concerning involvement in standardisation. The overarching goal of the study is toestablish how organisations contribute to open standards development through editorship. Specifically, the focus is on open standards development in the World Wide Web Consortium (W3C). Through an analysis of editorship for all W3C recommendations we contribute novel findings concerning organisational involvement and collaboration, and highlight contributions from different types of organisations and countries. We make five principal contributions. First, we establish an overall characterisation of organisational involvement in W3C standardisation. Second, we report on organisational involvement in W3C standardisation over time. Third, we establish how different organisations, organisation types, and countries are involved in W3C technologies. Fourth, we report on organisational involvement in relation to standard development time. Fifth, we establish how organisations collaborate in W3C standardisation through social network analysis.

    Download full text (pdf)
    fulltext
  • 30.
    Gamalielsson, Jonas
    et al.
    University of Skövde, School of Humanities and Informatics. University of Skövde, The Informatics Research Centre.
    Lundell, Björn
    University of Skövde, School of Humanities and Informatics. University of Skövde, The Informatics Research Centre.
    Open Source communities for long-term maintenance of digital assets: what is offered for ODF & OOXML?2011In: Proceedings of SOS 2011: Towards Sustainable Open Source / [ed] Imed Hammouda & Björn Lundell, Tampere: Tampere University of Technology, 2011, p. 19-24Conference paper (Refereed)
  • 31.
    Gamalielsson, Jonas
    et al.
    University of Skövde, School of Humanities and Informatics. University of Skövde, The Informatics Research Centre.
    Lundell, Björn
    University of Skövde, School of Humanities and Informatics. University of Skövde, The Informatics Research Centre.
    Open Source Software for Data Curation of Digital Assets: a case study2010In: Proceedings of the 14th International Academic MindTrek Conference: Envisioning Future Media Environments, New York: Association for Computing Machinery (ACM), 2010, p. 61-64Conference paper (Refereed)
    Abstract [en]

    Legacy file formats is an increasing concern for organisations. Therefore it is important for any company to develop sustainable strategies for data curation in order to maintain valuable digital assets. In this paper we report from a case study conducted in a company context aiming to investigate the feasibility of using Open Source approaches for curation of corporate digital assets kept in proprietary legacy file formats to open file formats. We consider different aspects of openness in a corporate strategy for maintaining digital assets. An important aspect concerns activity and company influence in an Open Source tool-chain, another concerns support for data curation of digital assets actually offered by the tool chain. We find that organisational concern over legacy file formats continues to be an issue, and that strong commercial influence on Open Source projects is no guarantee for success.

  • 32.
    Gamalielsson, Jonas
    et al.
    University of Skövde, The Informatics Research Centre. University of Skövde, School of Informatics.
    Lundell, Björn
    University of Skövde, The Informatics Research Centre. University of Skövde, School of Informatics.
    Sustainability of Open Source software communities beyond a fork: How and why has the LibreOffice project evolved?2014In: Journal of Systems and Software, ISSN 0164-1212, E-ISSN 1873-1228, Vol. 89, no 1, p. 128-145Article in journal (Refereed)
    Abstract [en]

    Many organisations are dependent upon long-term sustainable software systems and associated communities. In this paper we consider long-term sustainability of Open Source software communities in Open Source software projects involving a fork. There is currently a lack of studies in the literature that address how specific Open Source software communities are affected by a fork. We report from a study aiming to investigate the developer community around the LibreOffice project, which is a fork from the OpenOffice.org project. In so doing, our analysis also covers the OpenOffice.org project and the related Apache OpenOffice project. The results strongly suggest a long-term sustainable LibreOffice community and that there are no signs of stagnation in the LibreOffice project 33 months after the fork. Our analysis provides details on developer communities for the LibreOffice and Apache OpenOffice projects and specifically concerning how they have evolved from the OpenOffice.org community with respect to project activity, developer commitment, and retention of committers over time. Further, we present results from an analysis of first hand experiences from contributors in the LibreOffice community. Findings from our analysis show that Open Source software communities can outlive Open Source software projects and that LibreOffice is perceived by its community as supportive, diversified, and independent. The study contributes new insights concerning challenges related to long-term sustainability of Open Source software communities.

  • 33.
    Gamalielsson, Jonas
    et al.
    University of Skövde, School of Informatics. University of Skövde, Informatics Research Environment.
    Lundell, Björn
    University of Skövde, School of Informatics. University of Skövde, Informatics Research Environment.
    Brax, Christoffer
    Combitech AB, Sweden.
    Persson, Tomas
    Digitalist Sweden AB, Sweden.
    Mattsson, Anders
    Husqvarna AB, Sweden.
    Gustavsson, Tomas
    PrimeKey Solutions AB, Sweden.
    Feist, Jonas
    RedBridge AB, Sweden.
    On availability of Open Source Software reference implementations for standards issued by different standards setting organisations2023In: Joint Proceedings EURAS & SIIT 2023: (Responsible) Standardisation for Smart Systems / [ed] Kai Jakobs, Aachen: Verlag Mainz , 2023, p. 97-116Conference paper (Refereed)
    Abstract [en]

    Software reference implementations of ICT standards have an important role for verifying that a standard is implementable, supporting interoperability testing among other implementations, and providing feedback to the standard development process. Providing reference implementations and widely used implementations of a standard as Open Source Software also promotes wide deployment in software systems, avoidance of different lock-in effects, interoperability, and longevity of systems and associated digital assets. In this paper results are reported on the availability of reference implementations and widely deployed implementations provided as Open Source Software for standards issued by different standards setting organisations. Specifically, findings draw from observations and analyses related to software implementations for identified standards issued by ETSI, IEC, IEEE, IETF, ISO, ITU-T, OASIS, and W3C.

  • 34.
    Gamalielsson, Jonas
    et al.
    University of Skövde, School of Informatics. University of Skövde, Informatics Research Environment.
    Lundell, Björn
    University of Skövde, School of Informatics. University of Skövde, Informatics Research Environment.
    Butler, Simon
    University of Skövde, School of Informatics. University of Skövde, Informatics Research Environment.
    On engagement with ICT standards and their implementations in open source software projects: The case of H.2652021In: Joint Proceedings EURAS 2021: Standardisation and Innovation SIIT 2021 The Past, Present and Future of ICT Standardisation / [ed] Kai Jakobs, Aachen: Verlag Mainz , 2021, Vol. 16, p. 191-210Conference paper (Refereed)
    Abstract [en]

    In this paper novel results are reported on engagement with ICT standards and their implementations in open source software (OSS). Specifically, findings draw from observations and analyses related to the ITU-T H.265 standard and five OSS projects (x265, libde265, SVT-HEVC, Kvazaar, and Turing codec) implementing the standard. The study reports on a characterisation of organisations that engage with standard development for the H.265 standard and organisations with declarations for H.265 in the ITU-T patent database in relation to standard development for H.265, and how OSS projects implementing H.265 are related to standard development for H.265.

  • 35.
    Gamalielsson, Jonas
    et al.
    University of Skövde, School of Informatics. University of Skövde, Informatics Research Environment.
    Lundell, Björn
    University of Skövde, School of Informatics. University of Skövde, Informatics Research Environment.
    Butler, Simon
    University of Skövde, School of Informatics. University of Skövde, Informatics Research Environment.
    Brax, Christoffer
    Combitech AB, Skövde, Sweden.
    Persson, Tomas
    Digitalist Sweden AB, Stockholm, Sweden.
    Mattsson, Anders
    Husqvarna AB, Huskvarna, Sweden.
    Gustavsson, Tomas
    PrimeKey Solutions AB, Solna, Sweden.
    Feist, Jonas
    RedBridge AB, Stockholm, Sweden.
    Lönroth, Erik
    Scania CV AB, Södertälje, Sweden.
    Towards open government through open source software for web analytics: The case of Matomo2021In: eJournal of eDemocracy & Open Government, E-ISSN 2075-9517, Vol. 13, no 2, p. 133-153Article in journal (Refereed)
    Abstract [en]

    Web analytics technologies provide opportunities for organisations to obtain information about users visiting their websites in order to understand and optimise web usage. Use of such technologies often leads to issues related to data privacy and potential lock-in to specific suppliers and proprietary technologies. Use of open source software (OSS) for web analytics can create conditions for avoiding issues related to data privacy and lock-in, and thereby provides opportunities for a long-term sustainable solution for organisations both in the public and private sectors. This paper characterises use of and engagement with OSS projects for web analytics. Specifically, we contribute a characterisation of use of OSS licensed web analytics technologies in Swedish government authorities, and a characterisation of organisational engagement with the Matomo OSS project for web analytics.

    Download full text (pdf)
    fulltext
  • 36.
    Gamalielsson, Jonas
    et al.
    University of Skövde, School of Informatics. University of Skövde, Informatics Research Environment.
    Lundell, Björn
    University of Skövde, School of Informatics. University of Skövde, Informatics Research Environment.
    Butler, Simon
    University of Skövde, School of Informatics. University of Skövde, Informatics Research Environment.
    Brax, Christoffer
    Combitech AB, Sweden.
    Persson, Tomas
    Digitalist Sweden AB, Sweden.
    Mattsson, Anders
    Husqvarna AB, Sweden.
    Gustavsson, Tomas
    PrimeKey Solutions AB, Sweden.
    Feist, Jonas
    RedBridge AB, Sweden.
    Öberg, Jonas
    Scania CV AB, Sweden.
    On engagement with ICT standards and their implementations in open source software projects: the case of WebRTC2022In: Proceedings 26th EURAS Annual Standardisation Conference: Standards for Digital Transformation: Blockchain and Innovation / [ed] Kai Jakobs; Dong-hyu Kim, Aachen: Verlag Mainz , 2022, p. 143-162Conference paper (Refereed)
    Abstract [en]

    Real-time communication (RTC) technologies for the web provide opportunities for individuals and organisations to work and collaborate remotely, and the need for such technologies has recently increased. Use of RTC technologies and tools for the web involves a number of challenges concerning data privacy and lock-in effects, such as dependency to specific suppliers and proprietary technologies. Use of open standards for RTC and open source software (OSS) implementing such standards can create conditions for avoiding issues related to data privacy and lock-in, and thereby provides opportunities for long-term sustainable solutions. The paper characterises how engagement with standardisation of WebRTC in the context of IETF and W3C is related to engagement with the WebRTC OSS project.

  • 37.
    Gamalielsson, Jonas
    et al.
    University of Skövde, School of Informatics. University of Skövde, Informatics Research Environment.
    Lundell, Björn
    University of Skövde, School of Informatics. University of Skövde, Informatics Research Environment.
    Butler, Simon
    University of Skövde, School of Informatics. University of Skövde, Informatics Research Environment.
    Brax, Christoffer
    Combitech AB, Sweden.
    Persson, Tomas
    Digitalist Sweden AB, Sweden.
    Mattsson, Anders
    Husqvarna AB, Sweden.
    Gustavsson, Tomas
    PrimeKey Solutions AB, Sweden.
    Feist, Jonas
    Redbridge AB, Sweden.
    Öberg, Jonas
    Scania CV AB, Sweden.
    On Engagement with Open Source Software, Open Source Hardware, and Standard Setting: The Case of White Rabbit2022In: OpenSym '22: Proceedings of the 18th International Symposium on Open Collaboration / [ed] Gregorio Robles; Amel Charleux; Igor Steinmacher; Javier Arroyo; Antonio Balderas; Gemma Catolino; Alexandre Decan; Francisco Martín-Rico; Amit Kumar Verma, Association for Computing Machinery (ACM), 2022Conference paper (Refereed)
  • 38.
    Gamalielsson, Jonas
    et al.
    University of Skövde, School of Informatics. University of Skövde, The Informatics Research Centre.
    Lundell, Björn
    University of Skövde, School of Informatics. University of Skövde, The Informatics Research Centre.
    Feist, Jonas
    RedBridge AB, Kista, Stockholm, Sweden.
    Gustavsson, Tomas
    PrimeKey Solutions AB, Solna, Sweden.
    Landqvist, Fredric
    Findwise AB, Göteborg, Sweden.
    On organisational influences in software standards and their open source implementations2015In: Information and Software Technology, ISSN 0950-5849, E-ISSN 1873-6025, Vol. 67, p. 30-43Article in journal (Refereed)
    Abstract [en]

    Context: It is widely acknowledged that standards implemented in open source software can reduce risks for lock-in, improve interoperability, and promote competition on the market. However, there is limited knowledge concerning the relationship between standards and their implementations in open source software. This paper reports from an investigation of organisational influences in software standards and open source software implementations of software standards. The study focuses on the RDFa standard and its implementation in the Drupal project.

    Objective: The overarching goal of the study is to establish organisational influences in software standards and their implementations in open source software. More specifically, our objective is to establish organisational influences in the RDFa standard and its implementation in the Drupal project.

    Method: By conduct of a case study of the RDFa standard and its implementation in the Drupal project we investigate organisational influences in software standards and their implementations in open source software. Specifically, the case study involved quantitative analyses of issue tracker data for different issue trackers for W3C RDFa and the Drupal implementation of RDFa.

    Results: The case study provides details on how and to what extent organisational influences occur in W3C RDFa and the Drupal implementation of RDFa, by specifically providing a characterisation of issues and results concerning contribution to issue raising and commenting, organisational involvement over time, and individual and organisational collaboration on issues.

    Conclusion: We find that widely deployed standards can benefit from contributions provided by a range of different individuals, organisations, and types of organisations either directly to a standardisation project or indirectly via an open source project implementing the standard. Further, we also find that open processes for standardisation adopted by W3C may also contribute to open source projects implementing specific standards.

  • 39.
    Gamalielsson, Jonas
    et al.
    University of Skövde, School of Humanities and Informatics. University of Skövde, The Informatics Research Centre.
    Lundell, Björn
    University of Skövde, School of Humanities and Informatics. University of Skövde, The Informatics Research Centre.
    Grahn, Alexander
    University of Skövde, School of Humanities and Informatics. University of Skövde, The Informatics Research Centre.
    Andersson, Stefan
    RedBridge AB, Kista, Sweden.
    Feist, Jonas
    RedBridge AB, Kista, Sweden.
    Gustavsson, Tomas
    PrimeKey Solutions AB, Solna, Sweden.
    Strindberg, Henrik
    Findwise AB, Göteborg, Sweden .
    Towards a reference model on how to utilise Open Standards in Open Source projects: experiences based on Drupal2013In: Open Source Software: Quality Verification / [ed] Etiel Petrinja; Giancarlo Succi; Nabil El Ioini; Alberto Sillitti, Springer Berlin/Heidelberg, 2013, p. 257-263Conference paper (Refereed)
    Abstract [en]

    It is known that standards implemented in Open Source software (OSS) can promote a competitive market, reduce the risk for lock-in and improve interoperability, whilst there is limited knowledge concerning the relationship between standards and their implementations in OSS. In this paper we report from an ongoing case study conducted in the context of the ORIOS (Open Source software Reference Implementations of Open Standards) project in which influences between OSS communities and software standard communities are investigated. The study focuses on the Drupal project and three of its implemented standards (RDFa, CMIS, and OpenID).

  • 40.
    Gamalielsson, Jonas
    et al.
    University of Skövde, School of Humanities and Informatics. University of Skövde, The Informatics Research Centre.
    Lundell, Björn
    University of Skövde, School of Humanities and Informatics. University of Skövde, The Informatics Research Centre.
    Lings, Brian
    University of Skövde, School of Humanities and Informatics. University of Skövde, The Informatics Research Centre.
    Responsiveness as a measure for assessing the health of OSS ecosystems2010In: Proceedings of the 2nd International Workshop on Building Sustainable Open Source Communities (OSCOMM 2010) / [ed] Imed Hammouda, Björn Lundell, Tampere: Tampere University of Technology, 2010, p. 1-8Conference paper (Refereed)
    Abstract [en]

    The health of an Open Source ecosystem is an important decision factor when considering the adoption of Open Source software or when monitoring a seeded Open Source project. In this paper we introduce responsiveness as a qualitative measure of the quality of replies within mailing lists, which can be used for assessing ecosystem health. We consider one specific metric of responsiveness in this paper, and that is the response time of follow-up messages in mailing lists. We also describe a way for characterising the nature of communication in messages with short and long response times. The approach is tested in the context of the Nagios project, and we particularly focus on the responsiveness for contributors acting in their professional roles as core developers. Our contribution is a step towards a deeper understanding of voluntary support provided in mailing lists of OSS projects.

  • 41.
    Gamalielsson, Jonas
    et al.
    University of Skövde, School of Humanities and Informatics. University of Skövde, The Informatics Research Centre.
    Lundell, Björn
    University of Skövde, School of Humanities and Informatics. University of Skövde, The Informatics Research Centre.
    Lings, Brian
    University of Skövde, School of Humanities and Informatics. University of Skövde, The Informatics Research Centre.
    Social Network Analysis of the Nagios Community2009In: Proceedings of the Open Source Workshop OSW 2009 / [ed] Björn Lundell, Imed Hammouda, Skövde: University of Skövde , 2009, p. 9-12Conference paper (Refereed)
    Abstract [en]

    The health of an Open Source ecosystem is an important decision factor when considering the adoption of Open Source software. In this paper we assess ecosystem health of the Nagios community using an approach involving analysis of social networks derived from mailing lists. Our investigation focuses on the extent to which core developers act as mediators between participants of the mailing lists.

  • 42.
    Gamalielsson, Jonas
    et al.
    University of Skövde, School of Humanities and Informatics. University of Skövde, The Informatics Research Centre.
    Lundell, Björn
    University of Skövde, School of Humanities and Informatics. University of Skövde, The Informatics Research Centre.
    Lings, Brian
    University of Skövde, School of Humanities and Informatics. University of Skövde, The Informatics Research Centre.
    The Nagios community: An extended quantitative analysis2010In: Open Source Software: New Horizons: 6th International IFIP WG 2.13 Conference on Open Source Systems, OSS 2010, Notre Dame, IN, USA, May 30 – June 2, 2010. Proceedings / [ed] Pär Ågerfalk, Cornelia Boldyreff, Jesús M. González-Barahona, Gregory R. Madey, John Noll, Berlin: Springer, 2010, p. 85-96Conference paper (Refereed)
    Abstract [en]

    The health of an Open Source ecosystem is an important decision factor when considering the adoption of an Open Source software or when monitoring a seeded Open Source project. In this paper we assess the ecosystem health using approaches involving domain analysis and social network analysis of mailing lists for the Nagios project. We elaborate approaches for how involvement of different roles can be analysed through quantitative analysis, specifically focusing on core developers and professional providers. Our contribution is a step towards a deeper understanding of professional involvement in professional Open Source ecoystems.

  • 43.
    Gamalielsson, Jonas
    et al.
    University of Skövde, School of Humanities and Informatics. University of Skövde, The Informatics Research Centre.
    Lundell, Björn
    University of Skövde, School of Humanities and Informatics. University of Skövde, The Informatics Research Centre.
    Mattsson, Anders
    Combitech AB, Jönköping, Sweden.
    Open Source Software for Model Driven Development: A Case Study2011In: Open Source Systems: Grounding Research: 7th IFIP WG 2.13 International Conference, OSS 2011, Salvador, Brazil, October 6-7, 2011. Proceedings / [ed] Scott A. Hissam, Barbara Russo, Manoel G. de Mendonça Neto, Fabio Kon, Springer, 2011, p. 348-367Conference paper (Refereed)
    Abstract [en]

    Model Driven Development (MDD) is widely used in the embedded systems domain, and many proprietary and Open Source tools exist that support MDD. The potential for sustainability of such tools needs to assessed prior to any organisational adoption. In this paper we report from a case study conducted in a consultancy company context aiming to investigate Open Source tools for MDD. For the company it was interesting to explore the two Open Source modelling tools Topcased and Papyrus for potential adoption. The focus for our case study is on assessing the health of the ecosystems for the two investigated Open Source projects by means of quantitative analysis of publically available data sources about Open Source projects. The health of ecosystems is an important prerequisite for a long term sustainable OSS (Open Source Software) tool-chain in the MDD area, which can aid strategic decision making for potential adoption within a company context. We have established details on the extent to which developers and users are active in two specific OSS ecosystems, and identified organisational influence for both ecosystems. We find that the investigated tools are promising regarding the health of their ecosystems, and a natural next step for the company would be to proceed with a pilot study in order to analyse the effectiveness of the investigated tools in company contexts.

  • 44.
    Gamalielsson, Jonas
    et al.
    University of Skövde, School of Humanities and Informatics.
    Nilsson, Patric
    University of Skövde, School of Humanities and Informatics.
    Olsson, Björn
    University of Skövde, School of Humanities and Informatics.
    A GO-based Method for Assessing the Biological Plausibility of Regulatory Hypotheses2006In: Computational Science - ICCS 2006: 6th International Conference, Reading, UK, May 28-31, 2006, Proceedings, Part II / [ed] Vassil N. Alexandrov; Geert Dick Albada; Peter M. A. Sloot; Jack Dongarra, Springer Berlin/Heidelberg, 2006, p. 879-886Conference paper (Other academic)
    Abstract [en]

    Many algorithms have been proposed for deriving regulatory networks from microarray gene expression data. The performance of such algorithms is often measured by how well the resulting network can recreate the gene expression data that it was derived from. However, this kind of performance does not necessarily mean that the regulatory hypotheses in the network are biologically plausible. We therefore propose a method for assessing the biological plausibility of regulatory hypotheses using prior knowledge in the form of regulatory pathway databases and Gene Ontology-based annotation of gene products. A set of templates is derived by generalising from known interactions to typical properties of interacting gene product pairs. By searching for matches in this set of templates, the plausibility of regulatory hypotheses can be assessed. We evaluate to what degree the collection of templates can separate true from false positive interactions, and we illustrate the practical use of the method by applying it to an example network reconstruction problem.

  • 45.
    Gamalielsson, Jonas
    et al.
    University of Skövde, School of Humanities and Informatics.
    Olsson, Björn
    University of Skövde, School of Humanities and Informatics.
    EGOSAP: Evolutionary Gene Ontology based Semantic Alignment of Biological Pathways2007In: Proceedings of the 3-rd Moscow Conference on Computational Molecular Biology, Moscow, Russia, July 27-31 2007, 2007, p. 98-100Conference paper (Refereed)
  • 46.
    Gamalielsson, Jonas
    et al.
    University of Skövde, Department of Computer Science.
    Olsson, Björn
    University of Skövde, School of Life Sciences.
    Evaluating Protein Structure Prediction Models with Evolutionary Algorithms2005In: Information processing with evolutionary algorithms: from industrial applications to academic speculations / [ed] Manuel Graña, Richard Duro, Alicia d’Anjou and Paul P. Wang, Springer London, 2005, p. 143-158Chapter in book (Refereed)
  • 47.
    Gamalielsson, Jonas
    et al.
    University of Skövde, School of Humanities and Informatics.
    Olsson, Björn
    University of Skövde, The Systems Biology Research Centre. University of Skövde, School of Life Sciences.
    Gene Ontology-based Semantic Alignment of Biological Pathways by Evolutionary Search2008In: Journal of Bioinformatics and Computational Biology, ISSN 0219-7200, E-ISSN 1757-6334, Vol. 6, no 4, p. 825-842Article in journal (Refereed)
    Abstract [en]

    A large number of biological pathways have been elucidated recently, and there is a need for methods to analyze these pathways. One class of methods compares pathways semantically in order to discover parts that are evolutionarily conserved between species or to discover intraspecies similarities. Such methods usually require that the topologies of the pathways being compared are known, i.e. that a query pathway is being aligned to a model pathway. However, sometimes the query only consists of an unordered set of gene products. Previous methods for mapping sets of gene products onto known pathways have not been based on semantic comparison of gene products using ontologies or other abstraction hierarchies. Therefore, we here propose an approach that uses a similarity function defined in Gene Ontology (GO) terms to find semantic alignments when comparing paths in biological pathways where the nodes are gene products. A known pathway graph is used as a model, and an evolutionary algorithm (EA) is used to evolve putative paths from a set of experimentally determined gene products. The method uses a measure of GO term similarity to calculate a match score between gene products, and the fitness value of each candidate path alignment is derived from these match scores. A statistical test is used to assess the significance of evolved alignments. The performance of the method has been tested using regulatory pathways for S. cerevisiae and M. musculus.

    Download full text (pdf)
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  • 48.
    Gamalielsson, Jonas
    et al.
    University of Skövde, School of Humanities and Informatics.
    Olsson, Björn
    University of Skövde, School of Humanities and Informatics.
    GOSAP: Gene Ontology Based Semantic Alignment of Biological Pathways2005Report (Other academic)
    Abstract [en]

    A large number of biological pathways have been assembled in later years, and are being stored in databases. Hence, the need for methods to analyse these pathways has emerged. One class of methods compares pathways, in order to discover parts that are evolutionary conserved between species or to discover intra-species similarites. Most previous work has been focused on methods targeted at metabolic pathways utilising the EC enzyme hierarchy. Here, we propose a Gene Ontology (GO) based approach for finding semantic local alignments when comparing paths in biological pathways where the nodes are gene products. The method takes advantage of all three sub-ontologies, and uses a measure of semantic similarity to calculate a match score between gene products. Our proposed method is applicable to all types of biological pathways, where nodes are gene products, e.g. regulatory pathways, signalling pathways and metabolic enzyme-to-enzyme pathways. It would also be possible to extend the method to work with other types of nodes, as long as there is an ontology or abstraction hierarchy available for categorising the nodes. We demonstrate that the method is useful for studying protein regulatory pathways in S. cerevisiae, as well as metabolic pathways for the same organism.

    Download full text (pdf)
    FULLTEXT01
  • 49.
    Gamalielsson, Jonas
    et al.
    University of Skövde, School of Humanities and Informatics.
    Olsson, Björn
    University of Skövde, School of Humanities and Informatics.
    GOSAP: Gene Ontology based Semantic Alignment of Biological Pathways2008In: International Journal of Bioinformatics Research and Applications, ISSN 1744-5485, E-ISSN 1744-5493, Vol. 4, no 3, p. 274-294Article in journal (Refereed)
  • 50.
    Gamalielsson, Jonas
    et al.
    University of Skövde, School of Humanities and Informatics.
    Olsson, Björn
    University of Skövde, The Systems Biology Research Centre. University of Skövde, School of Humanities and Informatics.
    On the (lack of) robustness of gene expression data clustering2004In: WSEAS Transactions on Biology and Biomedicine, ISSN 1109-9518, E-ISSN 2224-2902, Vol. 1, no 2, p. 198-204Article in journal (Refereed)
    Abstract [en]

    We assess the robustness of partitional clustering algorithms applied to gene expression data. A number of clusterings are made with identical parameter settings and input data using SOM and  k-means algorithms, which both rely on random initialisation and may produce different clusterings with different seeds. We define a reproducibility index and use it to assess the algorithms. The index is based on the number of pairs of genes consistently clustered together in different clusterings. The effect of noise applied to the original data is also studied. Our results show a lack of robustness for both classes of algorithms, with slightly higher reproducibility for SOM than for k-means.

    Download full text (pdf)
    FULLTEXT02
12 1 - 50 of 91
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