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  • 1. Aberer, André
    et al.
    Stamatakis, Alexis
    Ronquist, Fredrik
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    An efficient independence sampler for updating branches in Bayesian Markov chain Monte Carlo sampling of phylogenetic trees2016In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 65, no 1, p. 161-176Article in journal (Refereed)
  • 2.
    Englund, Markus
    et al.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Heikkinen, Mikko
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Sundström, Lisa
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Involving Collection Staff in the DINA Software Development – An Agile Approach2018In: Biodiversity Information Science and Standards, Vol. 2Article in journal (Refereed)
    Abstract [en]

    In order to ensure long-term commitment to the DINA project (DIgital information system for NAtural history data, https://dina-project.net), it is essential to continuously deliver features of high value to the user community. This is also what agile software development methods try to achieve by emphasizing early delivery, rapid response to changes and close collaboration with users (see for example the Manifesto for Agile Software Development at http://agilemanifesto.org). We will give a brief overview on how current development of the DINA collection management system core is guided by agile principles. The mammal collection at the Swedish Museum of Natural History will be used as an example. Developing a cross-disciplinary collection management system is a complex task that poses many challenges: Which features should we focus on? What kinds of data should the system ultimately support? How can the system be flexible but still easy to use? Since we cannot do everything at once, we work towards a minimum viable product (MVP) that contains just enough features at a time to bring value for selected target users. In the mammal collection case, the MVP is the simplest product that is able to replace the functions of the current system used for managing the collection. As we begin to work with other collections, new MVPs are defined and used to guide further development. Thus, the set of features available will increase with each MVP, benefiting both new and current users. Another big challenge is migration of legacy data, which is labor intensive and involves standardizing data that are not compatible with the new system. To address these issues, we aim to build a flexible data model that allows less structured data to coexist with more complex, highly structured data. Migration should thus not require extensive data standardization, transformation and cleaning. The plan is to instead offer tools for transforming and cleaning the data after they have been imported. With the data in place, it will be easier for the user to provide feedback and suggest new features.

  • 3. Glöckler, Falko
    et al.
    Englund, Markus
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    DINA Bits - Small Services Growing in the DINA System2018In: Biodiversity Information Science and Standards, Vol. 2Article in journal (Refereed)
    Abstract [en]

    The DINA system (€œDIgital information system for NAtural history data€, https://dina-project.net) consists of several web-based services that fulfill specific tasks. Most of the existing services are covering single core features in the collection management system and can be used either as integrated components in the DINA environment, or as stand-alone services. In this presentation single services will be highlighted as they represent technically interesting approaches and practical solutions for daily challenges in collection management, data curation and migration workflows. The focus will be on the following topics: (1) a generic reporting and label printing service, (2) practical decisions on taxonomic references in collection data and (3) the generic management and referencing of related research data and metadata: Reporting as presented in this context is defined as an extraction and subsequent compilation of information from the collection management system rather than just summarizing statistics. With this quite broad understanding of the term the DINA Reports & Labels Service (Museum für Naturkunde Berlin 2018) can assist in several different collection workflows such as generating labels, barcodes, specimen lists, vouchers, paper loan forms etc. As it is based on customizable HTML templates, it can be even used for creating customized web forms for any kind of interaction (e.g. annotations). Many collection management systems try to cope with taxonomic issues, because in practice taxonomy is used not only for determinations, but also for organizing the collections and categorizing storage units (e.g. €Coleoptera hall). Addressing taxonomic challenges in a collection management system can slow down development and add complexity for the users. The DINA system uncouples these issues in a simple taxonomic service for the sole assignment of names to specimens, for example determinations. This draws a clear line between collection management and taxonomic research, of which the latter can be supported in a separate service. While the digitization of collection data and workflows proceeds, linking related data is essential for data management and enrichment. In many institutions research data is disconnected from the collection specimen data because the type and structure cannot be easily included in the collection management databases. With the DINA Generic Data Module (Museum für Naturkunde Berlin 2017) a service exists that allows for attaching any relational data structures to the DINA system. It can also be used as a standalone service that accommodates structured data within a DINA compliant interface for data management.

  • 4.
    Heikkinen, Mikko
    et al.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Glöckler, Falko
    Englund, Markus
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Plenary Discussion - Future of Collection Management Systems2018In: Biodiversity Information Science and Standards, Vol. 2Article in journal (Refereed)
    Abstract [en]

    The DINA Symposium (DIgital information system for NAtural history data€, https://dina-project.net) ends with a plenary session involving the audience to discuss the interplay of collection management and software tools. The discussion will touch different areas and issues such as: (1) Collection management using modern technology: How should and could collections be managed using current technology?€“ What is the ultimate objective of using a new collection management system? How should traditional management processes be changed? (2) Development and community Why are there so many collection management systems? Why is it so difficult to create one system that fits everyone's requirements? How could the community of developers and collection staff be built around DINA project in the future? (3) Features and tools How to identify needs that are common to all collections? What are the new tools and technologies that could facilitate collection management? How could those tools be implemented as DINA compliant services? (4) Data What data must be captured about collections and specimens? What criteria need to be applied in order to distinguish essential and nice-to-have information? How should established data standards (e.g. Darwin Core & ABCD (Access to Biological Collection Data)) be used to share data from rich and diverse data models? In addition to the plenary discussion around these questions, we will agree on a streamlined format for continuing the discussion in order to write a white paper on these questions. The results and outcome of the session will constitute the basis of the paper and will be subsequently refined.

  • 5.
    Hsiang, Allison
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Elder, Leanne (Contributor)
    Yale University.
    Sibert, Elizabeth (Contributor)
    Harvard University.
    Kahanamoku, Sara (Contributor)
    University of California, Berkeley.
    Burke, Janet (Contributor)
    Yale University.
    Kelly, Abigail (Contributor)
    Smithsonian Tropical Research Institute.
    Liu, Yusu (Contributor)
    Massachusetts Institute of Technology.
    Hull, Pincelli (Contributor)
    Yale University.
    AutoMorph: Accelerating morphometrics with automated 2D and 3D image processing and shape extraction2017In: Methods in Ecology and Evolution, E-ISSN 2041-210XArticle in journal (Refereed)
    Abstract [en]
    1. Large-scale, comparative studies of morphological variation are rare due to the time-intensive nature of shape quantification. This data gap is important to address, as intraspecific and interspecific morphological variation underpins and reflects ecological and evolutionary processes.

    2. Here, we detail a novel software package, AutoMorph, for high-throughput object and shape extraction. AutoMorph can batch image many types of organisms (e.g. foraminifera, molluscs and fish teeth), allowing for rapid generation of assemblage- scale morphological data.

    3. We used AutoMorph to image and generate 2D and 3D morphological data for >100,000 marine microfossils in about a year. Our collaborators have used AutoMorph to process >12,000 patellogastropod shells and >50,000 fish teeth.

    4. AutoMorph allows users to rapidly produce large amounts of morphological data, facilitating community-scale evolutionary and ecological studies. To hasten the adoption of automated approaches, we have made AutoMorph freely available and open source. AutoMorph runs on all UNIX-like systems; future versions will run across all platforms. 

  • 6. Höhna, Sebastian
    et al.
    Landis, Michael J.
    Heath, Tracy A.
    Boussau, Bastien
    Lartillot, Nicolas
    Moore, Brian R.
    Huelsenbeck, John P.
    Ronquist, Fredrik
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    RevBayes: Bayesian phylogenetic inference using graphical models and an interactive model-specification language2016In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 65, no 4, p. 726-736Article in journal (Refereed)
  • 7. Lundén, Daniel
    et al.
    Çaylak, Gizem
    Ronquist, Fredrik
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Broman, David
    Automatic alignment in higher-order programming languages2023In: Programming Languages and Systems: 32nd European Symposium on Programming, ESOP 2023 Held as Part of the European Joint Conferences on Theory and Practice of Software, ETAPS 2023 Paris, France, April 22–27, 2023 Proceedings / [ed] Wies, Thomas, 2023, Vol. 13990, p. 535-563Conference paper (Refereed)
  • 8. Macklin, James
    et al.
    Englund, Markus
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Glöckler, Falko
    Heikkinen, Mikko
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Hoffmann, Jana
    Newton, Glen Keith
    Ronquist, Fredrik
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    General introduction to DINA2018In: Biodiversity Information Science and Standards, Vol. 2Article in journal (Refereed)
    Abstract [en]

    The DINA Consortium (€œDIgital information system for NAtural history data€, https://dina-project.net, Fig. 1 was formed in order to provide a framework for like-minded large natural history collection-holding institutions to collaborate through a distributed Open Source development model to produce a flexible and sustainable collection management system. Target collections include zoological, botanical, mycological, geological and paleontological collections, living collections, biodiversity inventories, observation records, and molecular data. The DINA system is architected as a loosely-coupled set of several web-based modules. The conceptual basis for this modular ecosystem is a compilation of comprehensive guidelines for Web application programming interfaces (APIs) to guarantee the interoperability of its components. Thus, all DINA components can be modified or even replaced by other components without crashing the rest of the system as long as they are DINA compliant. Furthermore, the modularity enables the institutions to host only the components they need. DINA focuses on an Open Source software philosophy and on community-driven open development, so the contributors share their development resources and expertise outside of their own institutions. One of the overarching reasons to develop a new collection management system is the need to better model complex relationships between collection objects (typically specimens) involving their derivatives, preparations and storage. We will discuss enhancements made in the DINA data model to better represent these relationships and the influence it has on the management of these objects, and on the sharing of information. Technical detail of various components of the DINA system will be shown in other talks in this symposium followed by a discussion session.

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