Blar i Bergen Open Research Archive på tidsskrift "F1000 Research"

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    • Bioimage analysis workflows: community resources to navigate through a complex ecosystem [version 1; peer review: 2 approved] 

      Paul-Gilloteaux, Perrine; Tosi, Sébastien; Hériche, Jean-Karim; Gaignard, Alban; Ménager, Hervé; Marée, Raphaël; Baecker, Volker; Klemm, Anna; Kalaš, Matúš; Zhang, Chong; Miura, Kota; Colombelli, Julien (Journal article; Peer reviewed, 2021)
      Workflows are the keystone of bioimage analysis, and the NEUBIAS (Network of European BioImage AnalystS) community is trying to gather the actors of this field and organize the information around them. One of its most ...

    • Case Report: Polyvinylpyrrolidone deposition disease from repeated injection of opioid substitution drugs: Report of a case with a fatal outcome 

      Stalund, Ida Viken; Riise, Gro Nygard; Leh, Friedemann; Bjånes, Tormod Karlsen; Riise, Lars; Svarstad, Einar; Leh, Sabine (Journal article; Peer reviewed, 2021)
      Background: Intravenous injection of oral opioid substitution drugs (OSD) is widespread among injecting drug users. Several OSDs contain the polymer polyvinylpyrrolidone (PVP) as an excipient. Parenterally administered PVP ...

    • EDAM-bioimaging: the ontology of bioimage informatics operations, topics, data, and formats (update 2020) 

      Kalaš, Matúš; Plantard, Laure; Lindblad, Joakim; Jones, Martin; Sladoje, Nataša; Kirschmann, Moritz A.; Chessel, Anatole; Scholz, Leandro; Rössler, Fabianne; Nicolás Sáenz, Laura; Gómez de Mariscal, Estibaliz; Bogovic, John; Dufour, Alexandre; Heiligenstein, Xavier; Waithe, Dominic; Domart, Marie-Charlotte; Karreman, Matthia; Van de Plas, Raf; Haase, Robert; Hörl, David; Paavolainen, Lassi; Vrhovac Madunić, Ivana; Karaica, Dean; Muñoz-Barrutia, Arrate; Sampaio, Paula; Sage, Daniel; Munck, Sebastian; Golani, Ofra; Moore, Josh; Levet, Florian; Ison, Jon; Gaignard, Alban; Ménager, Hervé; Zhang, Chong; Miura, Kota; Colombelli, Julien; Paul-Gilloteaux, Perrine (Others, 2020)
      EDAM is a well-established ontology of operations, topics, types of data, and data formats that are used in bioinformatics and its neighbouring fields [1,2] . EDAM-bioimaging is an extension of EDAM dedicated to bioimage ...

    • EDAM: the bioscientific data analysis ontology (update 2021) [version 1; not peer reviewed] 

      Black, Melissa; Lamothe, Lucie; Eldakroury, Hager; Kierkegaard, Mads; Priya, Ankita; Machinda, Anne; Singh Khanduja, Uttam; Patoliya, Drashti; Rathi, Rashika; Che Nico, Tawah Peggy; Umutesi, Gloria; Blankenburg, Claudia; Op, Anita; Chieke, Precious; Babatunde, Omodolapo; Laurie, Steve; Neumann, Steffen; Schwämmle, Veit; Kuzmin, Ivan; Hunter, Chris; Karr, Jonathan; Ison, Jon; Gaignard, Alban; Brancotte, Bryan; Ménager, Hervé; Kalaš, Matúš (Others, 2021)
      EDAM [1] is a domain ontology of data analysis and data management in bio- and other sciences, and science-based applications. It comprises concepts related to analysis, modelling, optimisation, and data life-cycle. ...

    • EDAM: the ontology of bioinformatics operations, topics, data, and formats (update 2020) 

      Kalaš, Matúš; Ménager, Hervé; Gaignard, Alban; Schwämmle, Veit; Ison, Jon (Others, 2020)
      Project website: http://edamontology.org Source code: https://github.com/edamontology/edamontology License: CC BY-SA 4.0 EDAM is an ontology of well-established, familiar concepts that are prevalent within bioinformatics, ...

    • Norwegian e-Infrastructure for Life Sciences (NeLS) 

      Tekle, Kidane M; Gundersen, Sveinung; Klepper, Kjetil; Bongo, Lars Ailo; Raknes, Inge Alexander; Li, Xiaxi; Zhang, Wei; Andreetta, Christian; Mulugeta, Teshome Dagne; Kalaš, Matúš; Rye, Morten Beck; Hjerde, Erik; Antony Samy, Jeevan Karloss; Fornous, Ghislain; Azab, Abdulrahman; Våge, Dag Inge; Hovig, Eivind; Willassen, Nils Peder; Drabløs, Finn; Nygård, Ståle; Petersen, Kjell; Jonassen, Inge (Peer reviewed; Journal article, 2018)
      The Norwegian e-Infrastructure for Life Sciences (NeLS) has been developed by ELIXIR Norway to provide its users with a system enabling data storage, sharing, and analysis in a project-oriented fashion. The system is ...

    • Perspectives on automated composition of workflows in the life sciences [version 1; peer review: 2 approved] 

      Lamprecht, Anna-Lena; Palmblad, Magnus; Ison, Jon; Schwämmle, Veit; Al Manir, Mohammad Sadnan; Altintas, Ilkay; Baker, Christopher J. O.; Ben Hadj Amor, Ammar; Capella-Gutierrez, Salvador; Charonyktakis, Paulos; Crusoe, Michael R.; Gil, Yolanda; Goble, Carole; Griffin, Timothy J.; Groth, Paul; Ienasescu, Hans; Jagtap, Pratik; Kalaš, Matúš; Kasalica, Vedran; Khanteymoori, Alireza; Kuhn, Tobias; Mei, Hailiang; Ménager, Hervé; Möller, Steffen; Richardson, Robin A.; Robert, Vincent; Soiland-Reyes, Stian; Stevens, Robert; Szaniszlo, Szoke; Verberne, Suzan; Verhoeven, Aswin; Wolstencroft, Katherine (Journal article; Peer reviewed, 2021)
      Scientific data analyses often combine several computational tools in automated pipelines, or workflows. Thousands of such workflows have been used in the life sciences, though their composition has remained a cumbersome ...

    • Toward understanding scarless skin wound healing and pathological scarring 

      Karppinen, Sanna-Maria; Heljasvaara, Ritva Leena; Gullberg, Donald; Tasanen, Kaisa; Pihlajaniemi, Taina (Peer reviewed; Journal article, 2019)
      The efficient healing of skin wounds is crucial for securing the vital barrier function of the skin, but pathological wound healing and scar formation are major medical problems causing both physiological and psychological ...