Browsing University of Bergen Library by Journals "F1000 Research"

Now showing items 1-8 of 8

    • 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 ...

    • Crystal structure of Pseudomonas aeruginosa FabB C161A, a template for structure-based design for new antibiotics 

      Yadrykhinsky, Vladyslav; Georgiou, Charis; Brenk, Ruth (Journal article; Peer reviewed, 2022)
      Background: FabB (3-oxoacyl-[acyl-carrier-protein] synthase 1) is part of the fatty acid synthesis II pathway found in bacteria and a potential target for antibiotics. The enzyme catalyses the Claisen condensation of ...

    • 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, ...

    • The ELIXIR Biodiversity Community: Understanding short- and long-term changes in biodiversity 

      Waterhouse, Robert M.; Adam-Blondon, Anne-Françoise; Balech, Bachir; Barta, Endre; Ying Shi Chua, Physilia; Di Cola, Valeria; Heil, Katharina F.; Hughes, Graham M.; Jermiin, Lars S.; Kalaš, Matúš; Lanfear, Jerry; Pafilis, Evangelos; Palagi, Patricia M.; Papageorgiou, Aristotelis C.; Paupério, Joana; Psomopoulos, Fotis; Raes, Niels; Burgin, Josephine; Gabaldón, Toni (Journal article; Peer reviewed, 2024)
      Biodiversity loss is now recognised as one of the major challenges for humankind to address over the next few decades. Unless major actions are taken, the sixth mass extinction will lead to catastrophic effects on the ...

    • 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 ...