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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.

  • 2.
    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. University of Skövde, The Systems Biology Research Centre.
    Lundell, Björn
    University of Skövde, School of Informatics. University of Skövde, The Informatics Research Centre.
    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. 

  • 3.
    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.
    Brax, Christoffer
    Combitech AB, Linköping.
    Sjöberg, Johan
    Findwise AB, Göteborg.
    Mattsson, Anders
    Husqvarna AB.
    Gustavsson, Thomas
    PrimeKey Solutions AB, Stockholm.
    Feist, Jonas
    RedBridge AB, Stockholm.
    Lönroth, Erik
    Scania IT AB, Södertälje.
    On Company Contributions to Community Open Source Software Projects2019In: IEEE Transactions on Software Engineering, ISSN 0098-5589, E-ISSN 1939-3520Article 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. CCBY

  • 4.
    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.

  • 5.
    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, Proceedings2016Conference proceedings (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.

  • 6.
    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)
  • 7.
    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, ISSN 1368-1613, 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.

  • 8.
    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.

  • 9.
    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.

  • 10.
    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.

  • 11.
    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.

  • 12.
    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.

  • 13.
    Gamalielsson, Jonas
    et al.
    University of Skövde, School of Humanities and Informatics.
    Grahn, Alexander
    University of Skövde, School of Humanities and Informatics.
    Lundell, Björn
    University of Skövde, School of Humanities and Informatics.
    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)
  • 14.
    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.

  • 15.
    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)
  • 16.
    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.

  • 17.
    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, Springer, 2016, Vol. 472, p. 57-70Conference paper (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.

  • 18.
    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.

  • 19.
    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 0896-4327, 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.

  • 20.
    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)
  • 21.
    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.

  • 22.
    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.

  • 23.
    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.

  • 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.
    Grahn, Alexander
    University of Skövde, School of Humanities and Informatics.
    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)
  • 25.
    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] Hammouda, I., 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.

  • 26.
    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, University of Skövde, Sweden , 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.

  • 27.
    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.

  • 28.
    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.

  • 29.
    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: ICCS 2006: 6th International Conference on Computational Science, 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.

  • 30.
    Gamalielsson, Jonas
    et al.
    University of Skövde, School of Life Sciences.
    Olsson, Björn
    University of Skövde, School of Life Sciences.
    EGOSAP: Evolutionary Gene Ontology based Semantic Alignment of Biological Pathways2007In: Proceedings of the third Moscow Conference on Computational Molecular Biology, Moscow, Russia, 27-30 July 2007, 2007, p. 98-100Conference paper (Refereed)
  • 31.
    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)
  • 32.
    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.

  • 33.
    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)
  • 34.
    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.

  • 35.
    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.

  • 36.
    Gamalielsson, Jonas
    et al.
    University of Skövde, School of Humanities and Informatics.
    Olsson, Björn
    University of Skövde, School of Humanities and Informatics.
    Nilsson, Patric
    University of Skövde, School of Humanities and Informatics.
    A Gene Ontology based Method for 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 therefore propose 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 annotation of gene products and regulatory pathway databases. Templates are 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. In a cross-validation test we verify that the templates reliably identify interactions which have not been used in the template creation process, thereby confirming the generality of the approach. The method also proves useful when applied to an example network reconstruction problem, where a Bayesian approach is used to create hypothetical relations which are evaluated for biological plausibility. The cell cycle pathway and the MAPK signaling pathway for S. cerevisiae and H. sapiens are used in the experiments.

  • 37.
    Katz, Andrew
    et al.
    University of Skövde, School of Informatics. University of Skövde, The Informatics Research Centre. Moorcrofts LLP Solicitors, Buckinghamshire, United Kingdom.
    Lundell, Björn
    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.
    Software, copyright and the learning environment: An analysis of the IT contracts Swedish schools impose on their students and the implications for FOSS2016In: International Free and Open Source Software Law Review, ISSN 1877-6922, Vol. 8, no 1, p. 1-28Article in journal (Refereed)
    Abstract [en]

    Free and open source software (FOSS) is commonly made available to students in schools, but the schools do not necessarily take a holistic approach to their provision of IT (including software) which takes into account the nature of FOSS. In particular, we have identified a number of contracts with which Swedish students who are provided with laptops by their schools are required to comply which set out conditions for the use of the laptops, and associated software and content. Many clauses in these contracts are legally incompatible with certain FOSS licences, or contain misconceptions about FOSS, licensing and culture. This paper explores the relationship between the contracts and FOSS licensing and culture, and suggests a number of resolutions to the contradictions and misconceptions, as well as considering related issues.

  • 38.
    Laurio, Kim
    et al.
    University of Skövde, School of Humanities and Informatics. University of Skövde, The Systems Biology Research Centre.
    Svensson, Thomas
    Biovitrum AB, Göteborg, Sweden.
    Jirstrand, Mats
    Fraunhofer-Chalmers Research Center for Industrial Mathematics, Göteborg, Sweden.
    Nilsson, Patric
    University of Skövde, School of Life Sciences. University of Skövde, The Systems Biology Research Centre.
    Gamalielsson, Jonas
    University of Skövde, School of Humanities and Informatics. University of Skövde, The Systems Biology Research Centre.
    Olsson, Björn
    University of Skövde, School of Humanities and Informatics. University of Skövde, The Systems Biology Research Centre.
    Evolutionary search for improved path diagrams2007In: Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics: 5th European Conference, EvoBIO 2007, Valencia, Spain, April 11-13, 2007. Proceedings / [ed] Elena Marchiori, Jason H. Moore, Jagath C. Rajapakse, Springer Berlin/Heidelberg, 2007, p. 114-121Conference paper (Refereed)
    Abstract [en]

    A path diagram relates observed, pairwise, variable correlations to a functional structure which describes the hypothesized causal relations between the variables. Here we combine path diagrams, heuristics and evolutionary search into a system which seeks to improve existing gene regulatory models. Our evaluation shows that once a correct model has been identified it receives a lower prediction error compared to incorrect models, indicating the overall feasibility of this approach. However, with smaller samples the observed correlations gradually become more misleading, and the evolutionary search increasingly converges on suboptimal models. Future work will incorporate publicly available sources of experimentally verified biological facts to computationally suggest model modifications which might improve the model’s fitness.

  • 39.
    Lubovac, Zelmina
    et al.
    University of Skövde, School of Humanities and Informatics.
    Corne, David
    Gamalielsson, Jonas
    University of Skövde, School of Humanities and Informatics.
    Olsson, Björn
    University of Skövde, School of Humanities and Informatics.
    Weighted Cohesiveness for Identification of Functional Modules and their Interconnectivity2007In: Bioinformatics Research and Development: First International Conference, BIRD ’07, Springer Berlin/Heidelberg, 2007, p. 185-198Conference paper (Refereed)
    Abstract [en]

    Systems biology offers a holistic perspective where individual proteins are viewed as elements in a network of protein-protein interactions (PPI), in which the proteins have contextual functions within functional modules. In order to facilitate the identification and analysis of such modules, we have previously proposed a Gene Ontology-weighted clustering coefficient for identification of modules in PPI networks and a method, named SWEMODE (Semantic WEights for MODule Elucidation), where this measure is used to identify network modules. Here, we introduce novel aspects of the method that are tested and evaluated. One of the aspects that we consider is to use the k-core graph instead of the original protein-protein interaction graph.Also, by taking the spatial aspect into account, by using the GO cellular component annotation when calculating weighted cohesiveness, we are able to improve the results compared to previous work where only two of the GO aspects (molecular function and biological process) were combined. We here evaluate the predicted modules by calculating their overlap with MIPS functional complexes. In addition, we identify the “most frequent” proteins, i.e. the proteins that most frequently participate in overlapping modules. We also investigate the role of these proteins in the interconnectivity between modules. We find that the majority of identified proteins are involved in the assembly and arrangement of cell structures, such as the cell wall and cell envelope.

  • 40.
    Lubovac, Zelmina
    et al.
    University of Skövde, The Systems Biology Research Centre. University of Skövde, School of Life Sciences.
    Gamalielsson, Jonas
    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.
    Combining functional and topological properties to identify core modules in protein interaction networks2006In: Proteins: Structure, Function, and Bioinformatics, ISSN 0887-3585, E-ISSN 1097-0134, Vol. 64, no 4, p. 948-959Article in journal (Refereed)
    Abstract [en]

    Advances in large-scale technologies in proteomics, such as yeast two-hybrid screening and mass spectrometry, have made it possible to generate large Protein Interaction Networks (PINs). Recent methods for identifying dense sub-graphs in such networks have been based solely on graph theoretic properties. Therefore, there is a need for an approach that will allow us to combine domain-specific knowledge with topological properties to generate functionally relevant sub-graphs from large networks. This article describes two alternative network measures for analysis of PINs, which combine functional information with topological properties of the networks. These measures, called weighted clustering coefficient and weighted average nearest-neighbors degree, use weights representing the strengths of interactions between the proteins, calculated according to their semantic similarity, which is based on the Gene Ontology terms of the proteins. We perform a global analysis of the yeast PIN by systematically comparing the weighted measures with their topological counterparts. To show the usefulness of the weighted measures, we develop an algorithm for identification of functional modules, called SWEMODE (Semantic WEights for MODule Elucidation), that identifies dense sub-graphs containing functionally similar proteins. The proposed method is based on the ranking of nodes, i.e., proteins, according to their weighted neighborhood cohesiveness. The highest ranked nodes are considered as seeds for candidate modules. The algorithm then iterates through the neighborhood of each seed protein, to identify densely connected proteins with high functional similarity, according to the chosen parameters. Using a yeast two-hybrid data set of experimentally determined protein-protein interactions, we demonstrate that SWEMODE is able to identify dense clusters containing proteins that are functionally similar. Many of the identified modules correspond to known complexes or subunits of these complexes.

  • 41.
    Lubovac, Zelmina
    et al.
    University of Skövde, School of Humanities and Informatics.
    Gamalielsson, Jonas
    University of Skövde, School of Humanities and Informatics.
    Olsson, Björn
    University of Skövde, School of Humanities and Informatics.
    Lindlöf, Angelica
    University of Skövde, School of Humanities and Informatics.
    Exploring protein networks with a semantic similarity measure across Gene Ontology2005In: Proceedings of the 8th Joint Conference on Information Sciences, Vols 1-3 / [ed] Blair, S., Durham, NC: Joint Conference on Information Sciences , 2005, p. 1203-1208Conference paper (Refereed)
  • 42.
    Lubovac, Zelmina
    et al.
    University of Skövde, School of Humanities and Informatics.
    Olsson, Björn
    University of Skövde, School of Humanities and Informatics.
    Gamalielsson, Jonas
    University of Skövde, School of Humanities and Informatics.
    Combining topological characteristics and domain knowledge reveals functional modules in protein interaction networks2005In: Proceedings of CompBioNets 2005: Algorithms and Computational Methods for Biochemical and Evolutionary Networks / [ed] Marie-France Sagot and Katia S. Guimaraes, 2005, p. 93-106Conference paper (Refereed)
  • 43.
    Lubovac, Zelmina
    et al.
    University of Skövde, School of Humanities and Informatics.
    Olsson, Björn
    University of Skövde, School of Humanities and Informatics.
    Gamalielsson, Jonas
    University of Skövde, School of Humanities and Informatics.
    Weighted Clustering Coefficient for Identifying Modular Formations in Protein-Protein Interaction Networks2006In: Proceedings of World Academy of Science, Engineering and Technology, Vol 14 / [ed] C. Ardil, World Academy of Science, Engineering and Technology , 2006, p. 122-127Conference paper (Refereed)
    Abstract [en]

    This paper describes a novel approach for deriving modules from protein-protein interaction networks, which combines functional information with topological properties of the network. This approach is based on weighted clustering coefficient, which uses weights representing the functional similarities between the proteins. These weights are calculated according to the semantic similarity between the proteins, which is based on their Gene Ontology terms. We recently proposed an algorithm for identification of functional modules, called SWEMODE (Semantic WEights for MODule Elucidation), that identifies dense sub-graphs containing functionally similar proteins. The rational underlying this approach is that each module can be reduced to a set of triangles (protein triplets connected to each other). Here, we propose considering semantic similarity weights of all triangle-forming edges between proteins. We also apply varying semantic similarity thresholds between neighbours of each node that are not neighbours to each other (and hereby do not form a triangle), to derive new potential triangles to include in module-defining procedure. The results show an improvement of pure topological approach, in terms of number of predicted modules that match known complexes.

  • 44.
    Lundell, Björn
    et al.
    University of Skövde, School of Humanities and Informatics. University of Skövde, The Informatics Research Centre.
    Abdurahmanovic, Admir
    PrimeKey Solutions AB, Solna, Sweden.
    Andersson, Stefan
    RedBridge AB, Kista, Sweden.
    Bergström, Erik
    University of Skövde, School of Humanities and Informatics. University of Skövde, The Informatics Research Centre.
    Feist, Jonas
    RedBridge AB, Kista, Sweden.
    Gamalielsson, Jonas
    University of Skövde, School of Humanities and Informatics. University of Skövde, The Informatics Research Centre.
    Gustavsson, Tomas
    PrimeKey Solutions AB, Solna, Sweden.
    Kahlbom, Roger
    Pro4u Open Source AB, Stockholm, Sweden.
    Papaxanthis, Konstantin
    PrimeKey Solutions AB, Solna, Sweden.
    How Can Open Standards Be Effectively Implemented in Open Source?: Challenges and the ORIOS Project2012In: Open Source Systems: Long-Term Sustainability: 8th IFIP WG 2.13 International Conference, OSS 2012, Hammamet, Tunisia, September 10-13, 2012. Proceedings / [ed] Hammouda, I., Lundell, B., Mikkonen, T. & Scacchi, W., Heidelberg, Dordrecht, London, New York: Springer, 2012, p. 383-388Conference paper (Refereed)
    Abstract [en]

    Many organisations are currently restricted in their choice of software because of restrictions imposed by existing systems. Challenges include a lack of interoperability and a risk of technological lock-in, which many small companies seek to address by utiilising Open Standards and Open Source implementations of such standards when developing and deploying systems. This paper presents an overview of how the industrial research project ORIOS (Open Source software Reference Implementations of Open Standards) seeks to address identified challenges. An overarching goal of the project is to improve understanding within organisations of Open Standards, Open Source Reference Implementations, and the ecosystems around them. This will be done by developing a reference model of necessary and desirable features of an Open Standard, and how Open Standards and their implementations can be utilised by small companies in different usage contexts. An action case study approach will be used as a core strategy for evolving a reference model together with Swedish companies.

  • 45.
    Lundell, Björn
    et al.
    University of Skövde, School of Humanities and Informatics. University of Skövde, The Informatics Research Centre.
    Forssten, Bo
    TeliaSonera.
    Gamalielsson, Jonas
    University of Skövde, School of Humanities and Informatics. University of Skövde, The Informatics Research Centre.
    Gustavsson, Henrik
    University of Skövde, School of Humanities and Informatics. University of Skövde, The Informatics Research Centre.
    Karlsson, Robert
    SSAB.
    Lennerholt, Christian
    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.
    Mattsson, Anders
    Combitech.
    Olsson, Erik
    University of Skövde, School of Humanities and Informatics. University of Skövde, The Informatics Research Centre.
    Exploring health within OSS ecosystems2009In: Proceedings of the First International Workshop on Building Sustainable Open Source Communities / [ed] Hammouda, Imed, Aaltonen, Timo, Capiluppi, Andrea., Tampere University of Technology , 2009Conference paper (Refereed)
    Abstract [en]

    Open Source Software (OSS) is software which can be freely used, modified and redistributed, generally produced in a collaborative fashion by global communities of firms and individuals. In this paper we consider OSS ecosystems using an analytical device which we refer to as the OSS Stakeholder triangle. We believe that the OSS Stakeholder triangle constitues a useful means for analysing many aspects of Open Source ecosystems, including interaction between stakeholder roles and the overall health of an ecosystem.

  • 46.
    Lundell, Björn
    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.
    Collaborative research involving small companies: Experiences from co-production of knowledge for research and practice through use of an action case approach2017In: SER&IP '17 Proceedings of the 4th International Workshop on Software Engineering Research and Industrial Practice, IEEE Press, 2017, p. 24-30Conference paper (Refereed)
    Abstract [en]

    In order for the conduct of collaborative research projects and their outcomes to be valuable for both research and practice it is necessary to successfully address a number of sociotechnical challenges in the field of software engineering. Collaborative research involving researchers and practitionersrelated to software systems have utilised a variety of different research approaches. Adoption of an effective research approach for the situation at hand in a research project may significantly contribute to project success. Experiences from collaborative research show that action case can be an appropriate choice of approach for addressing socio-technical challenges in the software domain, which is appealing to both practitioners and researchers. This paper elaborates on a number of challenges for successful conduct of collaborative research projects and reports on experiences from use of action case as a research approach for conduct of collaborative research related to software systems.

  • 47.
    Lundell, Björn
    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.
    D8.8: Monitoring of the Open Source Project implementation2017Report (Other academic)
    Abstract [en]

    Deliverable D8.8 reports on monitoring of the Open Source Project implementations. Based on development efforts for each supplier, this updated deliverable (version 2.1) provides feedback on their use of: an open work practice for development; frequent open releases; and promotion activities aiming towards a sustainable community. In particular, it focuses on establishing sustainable communities, together with an assessment of how this is succeeded. The deliverable presents an evaluation of how each open source project implementation adheres to requirements expressed in deliverable D4.3 and how projects and suppliers have acted upon feedback and recommendations from PREFORMA. In so doing, the deliverable provides an evaluation of the extent to which best practices from community driven open source projects have been adopted with adherence to full transparency for all digital assets. Specifically, the evaluation considers software and associated digital assets provided via links to developed and provided resources (including source code, executables, and test files) and tools (including software configuration management system, mailing lists, and build environment) used in each open source project. An important outcome from this evaluation is a report on adherence to requirements (as specified in D4.3 and clarified in feedback from PREFORMA) and an assessment of how contracted organisations have managed to provide open source software and establish thriving and long-term sustainable open source communities of relevance for memory institutions and other stakeholder groups. Based on these outcomes, recommendations are given for further actions by the suppliers, the PREFORMA Consortium, and any potential adopter of software from the Open Source Portal provided by the PREFORMA Consortium.

  • 48.
    Lundell, Björn
    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.
    On Implementation of Open Standards in Open Source Software: Under What Conditions Can Formal and Open Standards Be Used?2015In: Proceedings 20th EURAS Annual Standardisation Conference: The Role of Standards in Transatlantic Regulation / [ed] K. Bergh-Skriver et al., European Academy for Standardisation , 2015, p. 235-252Conference paper (Refereed)
    Abstract [en]

    The European Commission and several European countries have acknowledged the importance of open standards and have taken various initiatives for addressing specific challenges. Formal standards (e.g. from ISO) are often referred to in software development and procurement. However, there is a lack of knowledge concerning use of formal and open standards in national policy and implications for implementation in software. This paper characterises how requirements for open standards have been adopted in national policy, elaborates on conditions for use of formal standards in scenarios when national policy imposes requirements for use of open standards, and elaborates conditions for implementation of specific open and formal standards in open source software. It is shown that not all formal standards are open standards. Specifically, while some formal standards (e.g. the ISO standard for PNG) are also considered open standards according to the definition adopted in national policies for open standards, it is also clear that other formal standards (e.g. the ISO standard for JPEG 2000) are not considered open standards by the same policies. Use of such formal standards creates barriers for implementation in open source software and inhibits an open and inclusive business friendly ecosystem, something which is of particular importance for small companies that are essential players in an innovative and international society.

  • 49.
    Lundell, Björn
    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.
    On the potential for improved standardisation through use of open source work practices in different standardisation organisations: How can open source-projects contribute to development of IT-standards?2017In: Digitalisation: Challenge and Opportunity for Standardisation: Proceedings of the 22nd EURAS Annual Standardisation Conference / [ed] Kai Jakobs, Knut Blind, Aachen: Verlag Mainz , 2017, p. T137-T155Conference paper (Refereed)
    Abstract [en]

    Open source has had significant impact on how work practices for development and deployment of software and has thereby transformed the way of working in the domain of software. From a review of the literature and current activities amongst policy makers and standardisation organisations it is evident that there is potential for utilising open source work practices for improved standardisation processes in the domain of standards. This paper presents three principle contributions. First, we clarify core concepts and elaborate on work related to how organisations seek to utilise open source software for developing standards. Second, we present opportunities and challenges for how open source work practices can be used for development of IT-standards. Third, for different standardisation organisations we illustrate through a review of existing open source projects implementing standards provided by three different standardisation organisations how those projects have contributed to development and governance of each standard. We find that open source work practices may contribute to improved standardisation processes and thereby constitute an effective strategy for improved standardisation.

  • 50.
    Lundell, Björn
    et al.
    University of Skövde, School of Humanities and Informatics. University of Skövde, The Informatics Research Centre.
    Gamalielsson, Jonas
    University of Skövde, School of Humanities and Informatics. University of Skövde, The Informatics Research Centre.
    Open Standards and Open Source in Swedish schools: On Promotion of Openness and Transparency2013In: Open Source Software: Quality Verification / [ed] Etiel Petrinja, Giancarlo Succi, Nabil El Ioini, Alberto Sillitti, Springer Berlin/Heidelberg, 2013, p. 207-221Conference paper (Refereed)
12 1 - 50 of 64
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