{"entity": "journal", "iuid": "c7eaedee44bf44398d6d28fee69c0d7f", "timestamp": "2026-07-18T02:18:59.409Z", "links": {"self": {"href": "https://publications.scilifelab.se/journal/F1000Res.json"}, "display": {"href": "https://publications.scilifelab.se/journal/F1000Res"}}, "title": "F1000Res", "issn": "2046-1402", "issn-l": "2046-1402", "publications_count": 15, "publications": [{"entity": "publication", "iuid": "43ff9ae2ee304005b3b75d388520674e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/43ff9ae2ee304005b3b75d388520674e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/43ff9ae2ee304005b3b75d388520674e"}}, "title": "From Recruitment to Retirement: Research Infrastructure Staff Views on the Diversification of Scientific Career Paths at Universities in Sweden in 2024.", "authors": [{"family": "Schroeder", "given": "Kristen", "initials": "K", "orcid": "0000-0002-6271-4530", "researcher": {"href": "https://publications.scilifelab.se/researcher/79f3c1b13a9844be86fdce0b7f425fb3.json"}}, {"family": "Fern\u00e1ndez-Rodr\u00edguez", "given": "Julia", "initials": "J"}, {"family": "Jenmalm-Jensen", "given": "Annika", "initials": "A"}, {"family": "Lundgren-Gawell", "given": "Josefin", "initials": "J"}, {"family": "Sandin", "given": "Sara", "initials": "S"}, {"family": "Stadler", "given": "Charlotte", "initials": "C", "orcid": "0000-0002-6781-1938", "researcher": {"href": "https://publications.scilifelab.se/researcher/2db3b27c7d7143cbacc8c1dd8ac90a31.json"}}, {"family": "Lindvall", "given": "Jessica M", "initials": "JM", "orcid": "0000-0002-5042-8481", "researcher": {"href": "https://publications.scilifelab.se/researcher/78debae1bc714b11a97ecf9e9656f1eb.json"}}], "type": "journal article", "published": "2025-07-04", "journal": {"title": "F1000Res", "issn": "2046-1402", "issn-l": "2046-1402", "volume": "14", "issue": null, "pages": "652"}, "abstract": "There is an ongoing need to develop diverse career paths that support the vital contributions of staff scientists, research engineers, scientific officers, and other knowledge professionals in scientific discovery. Research infrastructures and core facilities have a particular need to support sustainable and diverse careers, as they either employ - if being a legal entity - or daily manage research professionals in a broad variety of roles to enable resources, services, and innovation.\r\n\r\nIn 2019, a survey of the facility staff at SciLifeLab, a large national research infrastructure in Sweden, led to a recommendation for universities to develop career paths for their staff scientists. Five years later, we have conducted a survey and workshop to determine current views of infrastructure staff on career path diversity in Sweden.\r\n\r\nOur results indicate there is a strong need for clarity and communication about planning and implementation of career path structures at Swedish universities, as well as opportunities to foster excellence in infrastructure staff. While the workshop participants ranked Sweden as a stable and attractive place to work and reported continuous development of their technical and service skills, the lack of recognition of this expertise presents a barrier to a sustainable career.\r\n\r\nWe conclude that there is a need to continue advocating for increased clarity and diversity in career paths for staff scientists in Sweden, and raise the views presented by infrastructure staff on the challenges and opportunities unique to their roles.", "doi": "10.12688/f1000research.164794.1", "pmid": "40904623", "labels": {"Integrated Microscopy Technologies Gothenburg": "Technology development"}, "xrefs": [{"db": "pmc", "key": "PMC12402762"}], "notes": [], "created": "2025-11-05T14:09:53.317Z", "modified": "2025-11-05T14:10:39.124Z"}, {"entity": "publication", "iuid": "78334cbf714c404dbcaf69b205a46838", "links": {"self": {"href": "https://publications.scilifelab.se/publication/78334cbf714c404dbcaf69b205a46838.json"}, "display": {"href": "https://publications.scilifelab.se/publication/78334cbf714c404dbcaf69b205a46838"}}, "title": "A research data management (RDM) community for ELIXIR.", "authors": [{"family": "D'Anna", "given": "Flora", "initials": "F", "orcid": "0000-0003-4665-6673", "researcher": {"href": "https://publications.scilifelab.se/researcher/acbe32273ec04832a89d6a00852e5ff7.json"}}, {"family": "Jareborg", "given": "Niclas", "initials": "N", "orcid": "0000-0002-4520-044X", "researcher": {"href": "https://publications.scilifelab.se/researcher/09533c4bd4174ecab9ba866d22a1e585.json"}}, {"family": "Jetten", "given": "Mijke", "initials": "M", "orcid": "0000-0001-9114-2896", "researcher": {"href": "https://publications.scilifelab.se/researcher/fd5a15802004447db1e05eed9ee84fd6.json"}}, {"family": "Ahokas", "given": "Minna", "initials": "M", "orcid": "0000-0003-2313-0011", "researcher": {"href": "https://publications.scilifelab.se/researcher/3c44832cc5bb487ca373cea9d4330775.json"}}, {"family": "Alper", "given": "Pinar", "initials": "P"}, {"family": "Andrews", "given": "Robert", "initials": "R"}, {"family": "B\u00f6sl", "given": "Korbinian", "initials": "K"}, {"family": "D'Altri", "given": "Teresa", "initials": "T"}, {"family": "Faria", "given": "Daniel", "initials": "D"}, {"family": "Fatima", "given": "Nazeefa", "initials": "N"}, {"family": "Fuchs", "given": "Siiri", "initials": "S"}, {"family": "Garrard", "given": "Clare", "initials": "C", "orcid": "0000-0001-6561-073X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a1ec04331b345c8a4cfc17523f6011b.json"}}, {"family": "Gu", "given": "Wei", "initials": "W"}, {"family": "Heil", "given": "Katharina F", "initials": "KF", "orcid": "0000-0003-3341-3736", "researcher": {"href": "https://publications.scilifelab.se/researcher/e3b2cbf1f0ed49faaf5dfd158da1a35e.json"}}, {"family": "Kallberg", "given": "Yvonne", "initials": "Y"}, {"family": "Licciulli", "given": "Flavio", "initials": "F", "orcid": "0000-0002-1861-8947", "researcher": {"href": "https://publications.scilifelab.se/researcher/5d440682d4304980bbb126f04f142976.json"}}, {"family": "L\u00fcbke", "given": "Nils-Christian", "initials": "NC"}, {"family": "Melo", "given": "Ana M P", "initials": "AMP", "orcid": "0000-0003-0695-3817", "researcher": {"href": "https://publications.scilifelab.se/researcher/3969d70d08d54df6ad8329b3e904db90.json"}}, {"family": "Mi\u010deti\u0107", "given": "Ivan", "initials": "I"}, {"family": "Oliveira", "given": "Jorge", "initials": "J", "orcid": "0000-0001-6425-2176", "researcher": {"href": "https://publications.scilifelab.se/researcher/7ae125171bd144c2b8dd33aa0c04a3fa.json"}}, {"family": "Oulas", "given": "Anastasis", "initials": "A"}, {"family": "Palagi", "given": "Patricia M", "initials": "PM", "orcid": "0000-0001-9062-6303", "researcher": {"href": "https://publications.scilifelab.se/researcher/855d6f5c9a994ae49495522dfaf36281.json"}}, {"family": "Poterlowicz", "given": "Krzysztof", "initials": "K", "orcid": "0000-0001-6173-5674", "researcher": {"href": "https://publications.scilifelab.se/researcher/cf64fbc090b346629ce19439d4800cc5.json"}}, {"family": "Perez-Sitja", "given": "Xenia", "initials": "X", "orcid": "0000-0002-7166-0183", "researcher": {"href": "https://publications.scilifelab.se/researcher/21055c6a0f614459ab2db0e7b9515e31.json"}}, {"family": "Ruch", "given": "Patrick", "initials": "P"}, {"family": "Sansone", "given": "Susanna-Assunta", "initials": "SA"}, {"family": "Schnitzer", "given": "Helena", "initials": "H", "orcid": "0000-0002-6382-9452", "researcher": {"href": "https://publications.scilifelab.se/researcher/ae646aba885d4f96b2f9379b38344b2b.json"}}, {"family": "van Gelder", "given": "Celia", "initials": "C", "orcid": "0000-0002-0223-2329", "researcher": {"href": "https://publications.scilifelab.se/researcher/2533ac3cd3274486b5609ac643dc436b.json"}}, {"family": "Vergoulis", "given": "Thanasis", "initials": "T"}, {"family": "Wibberg", "given": "Daniel", "initials": "D", "orcid": "0000-0002-1331-4311", "researcher": {"href": "https://publications.scilifelab.se/researcher/771c66b20cb448e481140f476c6244ca.json"}}, {"family": "Wittig", "given": "Ulrike", "initials": "U", "orcid": "0000-0002-9077-5664", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a09cda9b5ad48b4a1743606ae9757e8.json"}}, {"family": "Lesko\u0161ek", "given": "Brane", "initials": "B"}, {"family": "Vondrasek", "given": "Jiri", "initials": "J"}, {"family": "Andrabi", "given": "Munazah", "initials": "M", "orcid": "0000-0002-7718-5109", "researcher": {"href": "https://publications.scilifelab.se/researcher/c12008356fa545e3ad6ba97482517901.json"}}], "type": "journal article", "published": "2024-09-30", "journal": {"title": "F1000Res", "issn": "2046-1402", "volume": "13", "issn-l": "2046-1402"}, "abstract": "Research data management (RDM) is central to the implementation of the FAIR (Findable Accessible, Interoperable, Reusable) and Open Science principles. Recognising the importance of RDM, ELIXIR Platforms and Nodes have invested in RDM and launched various projects and initiatives to ensure good data management practices for scientific excellence. These projects have resulted in a rich set of tools and resources highly valuable for FAIR data management. However, these resources remain scattered across projects and ELIXIR structures, making their dissemination and application challenging. Therefore, it becomes imminent to coordinate these efforts for sustainable and harmonised RDM practices with dedicated forums for RDM professionals to exchange knowledge and share resources. The proposed ELIXIR RDM Community will bring together RDM experts to develop ELIXIR's vision and coordinate its activities, taking advantage of the available assets. It aims to coordinate RDM best practices and illustrate how to use the existing ELIXIR RDM services. The Community will be built around three integral pillars, namely, a network of RDM professionals, RDM knowledge management and RDM training expertise and resources. It will also engage with external stakeholders to leverage benefits and provide a forum to RDM professionals for regular knowledge exchange, capacity building and development of harmonised RDM practices, keeping in line with the overall scope of the RDM Community. In the short term, the Community aims to build upon the existing resources and ensure that the content of these remain up to date and fit for purpose. In the long run, the Community will aim to strengthen the skills and knowledge of its RDM professionals to support the emerging needs of the scientific community. The Community will also devise an effective strategy to engage with other ELIXIR structures and international stakeholders to influence and align with developments and solutions in the RDM field.", "doi": "10.12688/f1000research.146301.2", "pmid": "39410979", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC11474151"}, {"db": "pii", "key": "ELIXIR-230"}], "notes": [], "created": "2024-10-28T13:06:58.490Z", "modified": "2024-10-28T13:07:04.538Z"}, {"entity": "publication", "iuid": "e4efffe1a3fe4bafa6f2e4b256ee3a7d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e4efffe1a3fe4bafa6f2e4b256ee3a7d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e4efffe1a3fe4bafa6f2e4b256ee3a7d"}}, "title": "Facilitating accessible, rapid, and appropriate processing of ancient metagenomic data with AMDirT", "authors": [{"family": "Borry", "given": "Maxime", "initials": "M", "orcid": "0000-0001-9140-7559", "researcher": {"href": "https://publications.scilifelab.se/researcher/f37c9a36c2c34d4ea4f8756e4a16dba0.json"}}, {"family": "Forsythe", "given": "Adrian", "initials": "A"}, {"family": "Andrades Valtue\u00f1a", "given": "Aida", "initials": "A"}, {"family": "H\u00fcbner", "given": "Alexander", "initials": "A"}, {"family": "Ibrahim", "given": "Anan", "initials": "A", "orcid": "0000-0003-3719-901X", "researcher": {"href": "https://publications.scilifelab.se/researcher/686fb778845345b9aac5b1527cbc9276.json"}}, {"family": "Quagliariello", "given": "Andrea", "initials": "A"}, {"family": "White", "given": "Anna E", "initials": "AE", "orcid": "0000-0001-6922-7885", "researcher": {"href": "https://publications.scilifelab.se/researcher/affa464cff694825a20a6a8fcfee2787.json"}}, {"family": "Kocher", "given": "Arthur", "initials": "A"}, {"family": "V\u00e5gene\u202c", "given": "\u00c5shild J", "initials": "\u00c5J"}, {"family": "Bartholdy", "given": "Bj\u00f8rn Peare", "initials": "BP"}, {"family": "Spur\u012bte", "given": "Di\u0101na", "initials": "D"}, {"family": "Ponce-Soto", "given": "Gabriel Yaxal", "initials": "GY"}, {"family": "Neumann", "given": "Gunnar", "initials": "G"}, {"family": "Huang", "given": "I Ting", "initials": "IT"}, {"family": "Light", "given": "Ian", "initials": "I"}, {"family": "Velsko", "given": "Irina M", "initials": "IM"}, {"family": "Jackson", "given": "Iseult", "initials": "I", "orcid": "0000-0001-6572-8244", "researcher": {"href": "https://publications.scilifelab.se/researcher/5796a1b209134dbaa3684e6c818946c5.json"}}, {"family": "Frangenberg", "given": "Jasmin", "initials": "J", "orcid": "0009-0004-5961-4709", "researcher": {"href": "https://publications.scilifelab.se/researcher/b5c33d573584490cb13929c3e76b6353.json"}}, {"family": "Serrano", "given": "Javier G", "initials": "JG"}, {"family": "Fumey", "given": "Julien", "initials": "J", "orcid": "0000-0002-6272-5619", "researcher": {"href": "https://publications.scilifelab.se/researcher/29a3d4a77a6c4df593493d28a0377f8e.json"}}, {"family": "\u00d6zdo\u011fan", "given": "Kadir T", "initials": "KT"}, {"family": "Blevins", "given": "Kelly E", "initials": "KE"}, {"family": "Daly", "given": "Kevin G", "initials": "KG"}, {"family": "Lopopolo", "given": "Maria", "initials": "M"}, {"family": "Moraitou", "given": "Markella", "initials": "M"}, {"family": "Michel", "given": "Megan", "initials": "M"}, {"family": "van Os", "given": "Meriam", "initials": "M"}, {"family": "Bravo-Lopez", "given": "Miriam J", "initials": "MJ"}, {"family": "Sarhan", "given": "Mohamed S", "initials": "MS", "orcid": "0000-0003-0904-976X", "researcher": {"href": "https://publications.scilifelab.se/researcher/16a94ba6ed8c40588d340809cdf48e8f.json"}}, {"family": "Dagtas", "given": "Nihan D", "initials": "ND"}, {"family": "Oskolkov", "given": "Nikolay", "initials": "N", "orcid": "0000-0001-5326-8893", "researcher": {"href": "https://publications.scilifelab.se/researcher/1a556bc2e89c457fb1e45cfcd7b567e9.json"}}, {"family": "Smith", "given": "Olivia S", "initials": "OS"}, {"family": "Lebrasseur", "given": "Oph\u00e9lie", "initials": "O"}, {"family": "Rozwalak", "given": "Piotr", "initials": "P"}, {"family": "Eisenhofer", "given": "Raphael", "initials": "R"}, {"family": "Wasef", "given": "Sally", "initials": "S", "orcid": "0000-0002-7207-7395", "researcher": {"href": "https://publications.scilifelab.se/researcher/7097f4b5f9c841908470d2a541dfc0da.json"}}, {"family": "Ramachandran", "given": "Shreya L", "initials": "SL", "orcid": "0000-0001-6760-5053", "researcher": {"href": "https://publications.scilifelab.se/researcher/c95b50b3942e4ac0b2caf2dc30d9db70.json"}}, {"family": "Vanghi", "given": "Valentina", "initials": "V"}, {"family": "Warinner", "given": "Christina", "initials": "C"}, {"family": "Fellows Yates", "given": "James A", "initials": "JA", "orcid": "0000-0001-5585-6277", "researcher": {"href": "https://publications.scilifelab.se/researcher/d9dfb63e40db44e8a1a3ea85028fda09.json"}}], "type": "journal-article", "published": "2023-08-02", "journal": {"title": "F1000Res", "issn": "2046-1402", "volume": "12", "pages": "926", "issn-l": "2046-1402"}, "abstract": null, "doi": "10.12688/f1000research.134798.1", "pmid": null, "labels": {"Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2023-11-22T08:12:52.987Z", "modified": "2025-12-01T07:48:29.014Z"}, {"entity": "publication", "iuid": "6be4e92973934cb69e13cdcf43dbd578", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6be4e92973934cb69e13cdcf43dbd578.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6be4e92973934cb69e13cdcf43dbd578"}}, "title": "Systems Biology in ELIXIR: modelling in the spotlight.", "authors": [{"family": "Martins Dos Santos", "given": "Vitor", "initials": "V"}, {"family": "Anton", "given": "Mihail", "initials": "M", "orcid": "0000-0002-7753-9042", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a28ecc2261e436ea5884ada5e512aed.json"}}, {"family": "Szomolay", "given": "Barbara", "initials": "B"}, {"family": "Ostaszewski", "given": "Marek", "initials": "M"}, {"family": "Arts", "given": "Ilja", "initials": "I"}, {"family": "Benfeitas", "given": "Rui", "initials": "R"}, {"family": "Dominguez Del Angel", "given": "Victoria", "initials": "V", "orcid": "0000-0002-5514-6651", "researcher": {"href": "https://publications.scilifelab.se/researcher/9a708fa6e9a44453b97cfc2089e06bec.json"}}, {"family": "Ferk", "given": "Polonca", "initials": "P"}, {"family": "Fey", "given": "Dirk", "initials": "D"}, {"family": "Goble", "given": "Carole", "initials": "C"}, {"family": "Golebiewski", "given": "Martin", "initials": "M", "orcid": "0000-0002-8683-7084", "researcher": {"href": "https://publications.scilifelab.se/researcher/5159dc6f9fa64c15b83ca6941cefc7b7.json"}}, {"family": "Gruden", "given": "Kristina", "initials": "K"}, {"family": "Heil", "given": "Katharina F", "initials": "KF", "orcid": "0000-0003-3341-3736", "researcher": {"href": "https://publications.scilifelab.se/researcher/e3b2cbf1f0ed49faaf5dfd158da1a35e.json"}}, {"family": "Hermjakob", "given": "Henning", "initials": "H"}, {"family": "Kahlem", "given": "Pascal", "initials": "P", "orcid": "0000-0002-8810-444X", "researcher": {"href": "https://publications.scilifelab.se/researcher/135bc12706264a2abcca62c7eb690f87.json"}}, {"family": "Klapa", "given": "Maria I", "initials": "MI", "orcid": "0000-0002-2047-3185", "researcher": {"href": "https://publications.scilifelab.se/researcher/ad30222c4c554a0881e3ee1d21f5fc87.json"}}, {"family": "Koehorst", "given": "Jasper", "initials": "J"}, {"family": "Kolodkin", "given": "Alexey", "initials": "A", "orcid": "0000-0002-7466-5027", "researcher": {"href": "https://publications.scilifelab.se/researcher/76faac66d6954e6d8d3ee709f1ae2999.json"}}, {"family": "Kutmon", "given": "Martina", "initials": "M", "orcid": "0000-0002-7699-8191", "researcher": {"href": "https://publications.scilifelab.se/researcher/f826bac4e2f04f18a225640a152da567.json"}}, {"family": "Lesko\u0161ek", "given": "Brane", "initials": "B"}, {"family": "Moretti", "given": "S\u00e9bastien", "initials": "S", "orcid": "0000-0003-3947-488X", "researcher": {"href": "https://publications.scilifelab.se/researcher/d303d14d45a14a72bc7f8a9cc16ae964.json"}}, {"family": "M\u00fcller", "given": "Wolfgang", "initials": "W"}, {"family": "Pagni", "given": "Marco", "initials": "M"}, {"family": "Rezen", "given": "Tadeja", "initials": "T"}, {"family": "Rocha", "given": "Miguel", "initials": "M"}, {"family": "Rozman", "given": "Damjana", "initials": "D"}, {"family": "\u0160afr\u00e1nek", "given": "David", "initials": "D", "orcid": "0000-0002-0713-2431", "researcher": {"href": "https://publications.scilifelab.se/researcher/e679c1b8c368494a84b52bae36fefa7f.json"}}, {"family": "Sheriff", "given": "Rahuman S Malik", "initials": "RSM", "orcid": "0000-0003-0705-9809", "researcher": {"href": "https://publications.scilifelab.se/researcher/84d226b68a324e0289c466b6c932a048.json"}}, {"family": "Suarez Diez", "given": "Maria", "initials": "M", "orcid": "0000-0001-5845-146X", "researcher": {"href": "https://publications.scilifelab.se/researcher/023c84ba41c143d28dc00693731abeec.json"}}, {"family": "Van Steen", "given": "Kristel", "initials": "K"}, {"family": "Westerhoff", "given": "Hans V", "initials": "HV", "orcid": "0000-0002-0443-6114", "researcher": {"href": "https://publications.scilifelab.se/researcher/9899f237345c4a489ca21750977783f5.json"}}, {"family": "Wittig", "given": "Ulrike", "initials": "U", "orcid": "0000-0002-9077-5664", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a09cda9b5ad48b4a1743606ae9757e8.json"}}, {"family": "Wolstencroft", "given": "Katherine", "initials": "K", "orcid": "0000-0002-1279-5133", "researcher": {"href": "https://publications.scilifelab.se/researcher/6de31d88de1f486b9853fdad71e0428e.json"}}, {"family": "Zupanic", "given": "Anze", "initials": "A", "orcid": "0000-0003-3303-9086", "researcher": {"href": "https://publications.scilifelab.se/researcher/df0e3f62701448a8a212d49a363fee09.json"}}, {"family": "Evelo", "given": "Chris T", "initials": "CT", "orcid": "0000-0002-5301-3142", "researcher": {"href": "https://publications.scilifelab.se/researcher/5886980760ef4a79b98112a484619c81.json"}}, {"family": "Hancock", "given": "John M", "initials": "JM", "orcid": "0000-0003-2991-2217", "researcher": {"href": "https://publications.scilifelab.se/researcher/23a58deb7c574625bbdf1c7be2128027.json"}}], "type": "journal article", "published": "2022-11-07", "journal": {"title": "F1000Res", "issn": "2046-1402", "volume": "11", "pages": "1265", "issn-l": "2046-1402"}, "abstract": "In this white paper, we describe the founding of a new ELIXIR Community - the Systems Biology Community - and its proposed future contributions to both ELIXIR and the broader community of systems biologists in Europe and worldwide. The Community believes that the infrastructure aspects of systems biology - databases, (modelling) tools and standards development, as well as training and access to cloud infrastructure - are not only appropriate components of the ELIXIR infrastructure, but will prove key components of ELIXIR's future support of advanced biological applications and personalised medicine. By way of a series of meetings, the Community identified seven key areas for its future activities, reflecting both future needs and previous and current activities within ELIXIR Platforms and Communities. These are: overcoming barriers to the wider uptake of systems biology; linking new and existing data to systems biology models; interoperability of systems biology resources; further development and embedding of systems medicine; provisioning of modelling as a service; building and coordinating capacity building and training resources; and supporting industrial embedding of systems biology. A set of objectives for the Community has been identified under four main headline areas: Standardisation and Interoperability, Technology, Capacity Building and Training, and Industrial Embedding. These are grouped into short-term (3-year), mid-term (6-year) and long-term (10-year) objectives.", "doi": "10.12688/f1000research.126734.1", "pmid": "36742342", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9871403"}, {"db": "pii", "key": "ELIXIR-1265"}], "notes": [], "created": "2022-11-25T08:14:57.508Z", "modified": "2023-06-02T10:32:23.545Z"}, {"entity": "publication", "iuid": "c36cf52bd4aa40a8adcb11c537f1ad8e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c36cf52bd4aa40a8adcb11c537f1ad8e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c36cf52bd4aa40a8adcb11c537f1ad8e"}}, "title": "Recommendations for connecting molecular sequence and biodiversity research infrastructures through ELIXIR", "authors": [{"family": "Waterhouse", "given": "Robert M", "initials": "RM"}, {"family": "Adam-Blondon", "given": "Anne Fran\u00e7oise", "initials": "AF"}, {"family": "Agosti", "given": "Donat", "initials": "D"}, {"family": "Baldrian", "given": "Petr", "initials": "P"}, {"family": "Balech", "given": "Bachir", "initials": "B", "orcid": "0000-0002-4419-0729", "researcher": {"href": "https://publications.scilifelab.se/researcher/1d508b8520c9466c9884ccf9b7aa84a8.json"}}, {"family": "Corre", "given": "Erwan", "initials": "E"}, {"family": "Davey", "given": "Robert P", "initials": "RP", "orcid": "0000-0002-5589-7754", "researcher": {"href": "https://publications.scilifelab.se/researcher/1cf570bbd5ba4a22a1eae398748c3087.json"}}, {"family": "Lantz", "given": "Henrik", "initials": "H", "orcid": "0000-0003-2419-0075", "researcher": {"href": "https://publications.scilifelab.se/researcher/85fa15d934214e00bb7818b865c4d754.json"}}, {"family": "Pesole", "given": "Graziano", "initials": "G", "orcid": "0000-0003-3663-0859", "researcher": {"href": "https://publications.scilifelab.se/researcher/5478d454fcd345deaab9863c5476ac2b.json"}}, {"family": "Quast", "given": "Christian", "initials": "C"}, {"family": "Gl\u00f6ckner", "given": "Frank Oliver", "initials": "FO", "orcid": "0000-0001-8528-9023", "researcher": {"href": "https://publications.scilifelab.se/researcher/67f068164c1c40c28b8f46c470c5c0c5.json"}}, {"family": "Raes", "given": "Niels", "initials": "N", "orcid": "0000-0002-4329-4892", "researcher": {"href": "https://publications.scilifelab.se/researcher/29ec7cb00a8945b38b945688b9b15df3.json"}}, {"family": "Sandionigi", "given": "Anna", "initials": "A"}, {"family": "Santamaria", "given": "Monica", "initials": "M", "orcid": "0000-0002-5257-0027", "researcher": {"href": "https://publications.scilifelab.se/researcher/22c839e85d76419e85deb4c9872ef99f.json"}}, {"family": "Addink", "given": "Wouter", "initials": "W"}, {"family": "Vohradsky", "given": "Jiri", "initials": "J"}, {"family": "Nunes-Jorge", "given": "Amandine", "initials": "A"}, {"family": "Willassen", "given": "Nils Peder", "initials": "NP"}, {"family": "Lanfear", "given": "Jerry", "initials": "J", "orcid": "0000-0002-8007-5568", "researcher": {"href": "https://publications.scilifelab.se/researcher/9fbbf24c85954f5c9a30c462324b5879.json"}}], "type": "journal-article", "published": "2021-12-03", "journal": {"title": "F1000Res", "issn": "2046-1402", "volume": "10", "pages": "1238", "issn-l": "2046-1402"}, "abstract": null, "doi": "10.12688/f1000research.73825.1", "pmid": null, "labels": {"Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [], "notes": [], "created": "2021-12-09T09:31:03.057Z", "modified": "2022-01-03T10:02:39.189Z"}, {"entity": "publication", "iuid": "de4d7e55211c439e95a4878e3ab8842e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/de4d7e55211c439e95a4878e3ab8842e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/de4d7e55211c439e95a4878e3ab8842e"}}, "title": "Highlights from the 2016-2020 NEUBIAS training schools for Bioimage Analysts: a success story and key asset for analysts and life scientists.", "authors": [{"family": "Martins", "given": "Gabriel G", "initials": "GG", "orcid": "0000-0002-6506-9776", "researcher": {"href": "https://publications.scilifelab.se/researcher/c04a08e246854401b529158afe9de318.json"}}, {"family": "Cordeli\u00e8res", "given": "Fabrice P", "initials": "FP", "orcid": "0000-0002-5383-5816", "researcher": {"href": "https://publications.scilifelab.se/researcher/cd3da472e85b4b19897bc513e443219f.json"}}, {"family": "Colombelli", "given": "Julien", "initials": "J", "orcid": "0000-0002-2784-4276", "researcher": {"href": "https://publications.scilifelab.se/researcher/e64e92116688467197a2eaadb170eb12.json"}}, {"family": "D'Antuono", "given": "Rocco", "initials": "R", "orcid": "0000-0003-0180-6500", "researcher": {"href": "https://publications.scilifelab.se/researcher/19a219cdf18a48c581c66844eed7f888.json"}}, {"family": "Golani", "given": "Ofra", "initials": "O", "orcid": "0000-0002-9793-236X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e239b26ad266407eb249be51f728f2ef.json"}}, {"family": "Guiet", "given": "Romain", "initials": "R", "orcid": "0000-0001-6715-4897", "researcher": {"href": "https://publications.scilifelab.se/researcher/4e318b0b510843c194d0f1c6b852bceb.json"}}, {"family": "Haase", "given": "Robert", "initials": "R", "orcid": "0000-0001-5949-2327", "researcher": {"href": "https://publications.scilifelab.se/researcher/f99dc020f05f479cafa0aede600157f0.json"}}, {"family": "Klemm", "given": "Anna H", "initials": "AH", "orcid": "0000-0002-3466-1320", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ae78afb2a424b0ab70d49871f361d13.json"}}, {"family": "Louveaux", "given": "Marion", "initials": "M", "orcid": "0000-0002-1794-3748", "researcher": {"href": "https://publications.scilifelab.se/researcher/3901ec2c7f1345f6974d7eae9766a502.json"}}, {"family": "Paul-Gilloteaux", "given": "Perrine", "initials": "P", "orcid": "0000-0002-4822-165X", "researcher": {"href": "https://publications.scilifelab.se/researcher/cc1aedddd2484c60b1e6bcf3aff9262a.json"}}, {"family": "Tinevez", "given": "Jean-Yves", "initials": "JY", "orcid": "0000-0002-0998-4718", "researcher": {"href": "https://publications.scilifelab.se/researcher/ed604822457048af8051bcb4e11da3a6.json"}}, {"family": "Miura", "given": "Kota", "initials": "K", "orcid": "0000-0001-6926-191X", "researcher": {"href": "https://publications.scilifelab.se/researcher/d2924dc08df743e188b5ead9a88449a6.json"}}], "type": "journal article", "published": "2021-04-30", "journal": {"title": "F1000Res", "issn": "2046-1402", "volume": "10", "pages": "334", "issn-l": "2046-1402"}, "abstract": "NEUBIAS, the European Network of Bioimage Analysts, was created in 2016 with the goal of improving the communication and the knowledge transfer among the various stakeholders involved in the acquisition, processing and analysis of biological image data, and to promote the establishment and recognition of the profession of Bioimage Analyst. One of the most successful initiatives of the NEUBIAS programme was its series of 15 training schools, which trained over 400 new Bioimage Analysts, coming from over 40 countries. Here we outline the rationale behind the innovative three-level program of the schools, the curriculum, the trainer recruitment and turnover strategy, the outcomes for the community and the career path of analysts, including some success stories. We discuss the future of the materials created during this programme and some of the new initiatives emanating from the community of NEUBIAS-trained analysts, such as the NEUBIAS Academy. Overall, we elaborate on how this training programme played a key role in collectively leveraging Bioimaging and Life Science research by bringing the latest innovations into structured, frequent and intensive training activities, and on why we believe this should become a model to further develop in Life Sciences.", "doi": "10.12688/f1000research.25485.1", "pmid": "34164115", "labels": {"BioImage Informatics": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC8215561"}], "notes": [], "created": "2021-11-29T12:35:36.781Z", "modified": "2021-11-29T12:35:37.127Z"}, {"entity": "publication", "iuid": "859de35c946e4369a5530fc3194f10d1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/859de35c946e4369a5530fc3194f10d1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/859de35c946e4369a5530fc3194f10d1"}}, "title": "Bioimage analysis workflows: community resources to navigate through a complex ecosystem.", "authors": [{"family": "Paul-Gilloteaux", "given": "Perrine", "initials": "P", "orcid": "0000-0002-4822-165X", "researcher": {"href": "https://publications.scilifelab.se/researcher/cc1aedddd2484c60b1e6bcf3aff9262a.json"}}, {"family": "Tosi", "given": "S\u00e9bastien", "initials": "S", "orcid": "0000-0001-8348-2778", "researcher": {"href": "https://publications.scilifelab.se/researcher/94b7debd554a44b590a5c4bd2b802c82.json"}}, {"family": "H\u00e9rich\u00e9", "given": "Jean-Karim", "initials": "JK"}, {"family": "Gaignard", "given": "Alban", "initials": "A"}, {"family": "M\u00e9nager", "given": "Herv\u00e9", "initials": "H"}, {"family": "Mar\u00e9e", "given": "Rapha\u00ebl", "initials": "R"}, {"family": "Baecker", "given": "Volker", "initials": "V", "orcid": "0000-0002-9129-6403", "researcher": {"href": "https://publications.scilifelab.se/researcher/f5884e3569e5470f8d0a1fe960a85c1c.json"}}, {"family": "Klemm", "given": "Anna", "initials": "A", "orcid": "0000-0002-3466-1320", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ae78afb2a424b0ab70d49871f361d13.json"}}, {"family": "Kala\u0161", "given": "Mat\u00fa\u0161", "initials": "M", "orcid": "0000-0002-1509-4981", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee56816d10554890a6045b9705974854.json"}}, {"family": "Zhang", "given": "Chong", "initials": "C"}, {"family": "Miura", "given": "Kota", "initials": "K"}, {"family": "Colombelli", "given": "Julien", "initials": "J", "orcid": "0000-0002-2784-4276", "researcher": {"href": "https://publications.scilifelab.se/researcher/e64e92116688467197a2eaadb170eb12.json"}}], "type": "journal article", "published": "2021-04-26", "journal": {"title": "F1000Res", "issn": "2046-1402", "volume": "10", "pages": "320", "issn-l": "2046-1402"}, "abstract": "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 recent outputs is the opening of the F1000Research NEUBIAS gateway, whose main objective is to offer a channel of publication for bioimage analysis workflows and associated resources. In this paper we want to express some personal opinions and recommendations related to finding, handling and developing bioimage analysis workflows. The emergence of \"big data\" in bioimaging and resource-intensive analysis algorithms make local data storage and computing solutions a limiting factor. At the same time, the need for data sharing with collaborators and a general shift towards remote work, have created new challenges and avenues for the execution and sharing of bioimage analysis workflows. These challenges are to reproducibly run workflows in remote environments, in particular when their components come from different software packages, but also to document them and link their parameters and results by following the FAIR principles (Findable, Accessible, Interoperable, Reusable) to foster open and reproducible science. In this opinion paper, we focus on giving some directions to the reader to tackle these challenges and navigate through this complex ecosystem, in order to find and use workflows, and to compare workflows addressing the same problem. We also discuss tools to run workflows in the cloud and on High Performance Computing resources, and suggest ways to make these workflows FAIR.", "doi": "10.12688/f1000research.52569.1", "pmid": "34136134", "labels": {"BioImage Informatics": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC8182692"}], "notes": [], "created": "2021-11-29T12:35:24.298Z", "modified": "2021-11-29T12:35:24.493Z"}, {"entity": "publication", "iuid": "6fe3fecb75ee46d289a452ad1fde7083", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6fe3fecb75ee46d289a452ad1fde7083.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6fe3fecb75ee46d289a452ad1fde7083"}}, "title": "CytoBrowser: a browser-based collaborative annotation platform for whole slide images", "authors": [{"family": "Rydell", "given": "Christopher", "initials": "C", "orcid": "0000-0002-3855-8734", "researcher": {"href": "https://publications.scilifelab.se/researcher/cc71008e50024fbc9f8578f861cda329.json"}}, {"family": "Lindblad", "given": "Joakim", "initials": "J", "orcid": "0000-0001-7312-8222", "researcher": {"href": "https://publications.scilifelab.se/researcher/c6b66ce110794e1fb312b82e790646b4.json"}}], "type": "journal-article", "published": "2021-03-22", "journal": {"title": "F1000Res", "issn": "2046-1402", "volume": "10", "pages": "226", "issn-l": "2046-1402"}, "abstract": null, "doi": "10.12688/f1000research.51916.1", "pmid": null, "labels": {"AIDA Data Hub": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [], "notes": [], "created": "2023-05-25T16:04:31.079Z", "modified": "2023-06-19T13:42:03.591Z"}, {"entity": "publication", "iuid": "2c7a1f9990c442bd9f733bc52293c119", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2c7a1f9990c442bd9f733bc52293c119.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2c7a1f9990c442bd9f733bc52293c119"}}, "title": "Chanjo: Clincal grade sequence coverage analysis", "authors": [{"family": "Andeer", "given": "Robin", "initials": "R"}, {"family": "Magnusson", "given": "M\u00e5ns", "initials": "M", "orcid": "0000-0002-0001-1047", "researcher": {"href": "https://publications.scilifelab.se/researcher/8e75a676a1bf4bfb80cf5ea579b44df0.json"}}, {"family": "Wedell", "given": "Anna", "initials": "A"}, {"family": "Stranneheim", "given": "Henrik", "initials": "H"}], "type": "journal-article", "published": "2020-06-16", "journal": {"title": "F1000Res", "issn": "2046-1402", "volume": "9", "issue": null, "pages": "615", "issn-l": "2046-1402"}, "abstract": null, "doi": "10.12688/f1000research.23605.1", "pmid": null, "labels": {"Clinical Genomics Stockholm": "Technology development", "Clinical Genomics": "Technology development"}, "xrefs": [], "notes": [], "created": "2020-11-22T16:12:00.707Z", "modified": "2021-11-10T12:38:31.323Z"}, {"entity": "publication", "iuid": "2327daa01a69409ebeaa040fe7f5fbd3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2327daa01a69409ebeaa040fe7f5fbd3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2327daa01a69409ebeaa040fe7f5fbd3"}}, "title": "Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants.", "authors": [{"family": "Garcia", "given": "Maxime", "initials": "M", "orcid": "0000-0003-2827-9261", "researcher": {"href": "https://publications.scilifelab.se/researcher/8cf9b1b223f04296adcb6bd091c548de.json"}}, {"family": "Juhos", "given": "Szilveszter", "initials": "S"}, {"family": "Larsson", "given": "Malin", "initials": "M"}, {"family": "Olason", "given": "Pall I", "initials": "PI"}, {"family": "Martin", "given": "Marcel", "initials": "M", "orcid": "0000-0002-0680-200X", "researcher": {"href": "https://publications.scilifelab.se/researcher/132afd4fea2e4e86bdf43708c8f49907.json"}}, {"family": "Eisfeldt", "given": "Jesper", "initials": "J", "orcid": "0000-0003-3716-4917", "researcher": {"href": "https://publications.scilifelab.se/researcher/32a701ee07674785b48b047665e18ee6.json"}}, {"family": "DiLorenzo", "given": "Sebastian", "initials": "S"}, {"family": "Sandgren", "given": "Johanna", "initials": "J"}, {"family": "D\u00edaz De St\u00e5hl", "given": "Teresita", "initials": "T"}, {"family": "Ewels", "given": "Philip", "initials": "P", "orcid": "0000-0003-4101-2502", "researcher": {"href": "https://publications.scilifelab.se/researcher/9d0fd82fe18b41539a761c55075f31d6.json"}}, {"family": "Wirta", "given": "Valtteri", "initials": "V", "orcid": "0000-0003-3811-5439", "researcher": {"href": "https://publications.scilifelab.se/researcher/cba024b2e3c347f6b981922d984ad2d6.json"}}, {"family": "Nist\u00e9r", "given": "Monica", "initials": "M", "orcid": "0000-0002-1261-3790", "researcher": {"href": "https://publications.scilifelab.se/researcher/e1dc80e61f574293a190f2f3ef464988.json"}}, {"family": "K\u00e4ller", "given": "Max", "initials": "M", "orcid": "0000-0001-6813-3051", "researcher": {"href": "https://publications.scilifelab.se/researcher/536ad902a272482aba853c078557e240.json"}}, {"family": "Nystedt", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0001-7809-7664", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0af5a168baa4b00a6fab8d3447ebfb4.json"}}], "type": "journal article", "published": "2020-01-29", "journal": {"volume": "9", "issn": "2046-1402", "issue": null, "pages": "63", "title": "F1000Res", "issn-l": "2046-1402"}, "abstract": "Whole-genome sequencing (WGS) is a fundamental technology for research to advance precision medicine, but the limited availability of portable and user-friendly workflows for WGS analyses poses a major challenge for many research groups and hampers scientific progress. Here we present Sarek, an open-source workflow to detect germline variants and somatic mutations based on sequencing data from WGS, whole-exome sequencing (WES), or gene panels. Sarek features (i) easy installation, (ii) robust portability across different computer environments, (iii) comprehensive documentation, (iv) transparent and easy-to-read code, and (v) extensive quality metrics reporting. Sarek is implemented in the Nextflow workflow language and supports both Docker and Singularity containers as well as Conda environments, making it ideal for easy deployment on any POSIX-compatible computers and cloud compute environments. Sarek follows the GATK best-practice recommendations for read alignment and pre-processing, and includes a wide range of software for the identification and annotation of germline and somatic single-nucleotide variants, insertion and deletion variants, structural variants, tumour sample purity, and variations in ploidy and copy number. Sarek offers easy, efficient, and reproducible WGS analyses, and can readily be used both as a production workflow at sequencing facilities and as a powerful stand-alone tool for individual research groups. The Sarek source code, documentation and installation instructions are freely available at https://github.com/nf-core/sarek and at https://nf-co.re/sarek/.", "doi": "10.12688/f1000research.16665.2", "pmid": "32269765", "labels": {"Bioinformatics Support, Infrastructure and Training": "Technology development", "Bioinformatics Long-term Support WABI": "Technology development", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "Clinical Genomics Stockholm": "Collaborative", "Bioinformatics Support and Infrastructure": "Technology development", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Technology development", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC7111497"}], "notes": [], "created": "2020-04-23T08:58:58.026Z", "modified": "2024-01-16T13:48:43.022Z"}, {"entity": "publication", "iuid": "4021e997cb6a4cc2b45dd15b6222ab2a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4021e997cb6a4cc2b45dd15b6222ab2a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4021e997cb6a4cc2b45dd15b6222ab2a"}}, "title": "Ten steps to get started in Genome Assembly and Annotation", "authors": [{"family": "Dominguez Del Angel", "given": "Victoria", "initials": "V"}, {"family": "Hjerde", "given": "Erik", "initials": "E"}, {"family": "Sterck", "given": "Lieven", "initials": "L"}, {"family": "Capella-Gutierrez", "given": "Salvadors", "initials": "S"}, {"family": "Notredame", "given": "Cederic", "initials": "C"}, {"family": "Vinnere Pettersson", "given": "Olga", "initials": "O"}, {"family": "Amselem", "given": "Joelle", "initials": "J"}, {"family": "Bouri", "given": "Laurent", "initials": "L"}, {"family": "Bocs", "given": "Stephanie", "initials": "S"}, {"family": "Klopp", "given": "Christophe", "initials": "C"}, {"family": "Gibrat", "given": "Jean Francois", "initials": "JF"}, {"family": "Vlasova", "given": "Anna", "initials": "A"}, {"family": "Leskosek", "given": "Brane L", "initials": "BL"}, {"family": "Soler", "given": "Lucile", "initials": "L"}, {"family": "Binzer-Panchal", "given": "Mahesh", "initials": "M"}, {"family": "Lantz", "given": "Henrik", "initials": "H"}], "type": "journal-article", "published": "2018-02-05", "journal": {"volume": "7", "issn": "2046-1402", "issue": null, "pages": "148", "title": "F1000Res", "issn-l": "2046-1402"}, "abstract": null, "doi": "10.12688/f1000research.13598.1", "pmid": "29568489", "labels": {"National Genomics Infrastructure": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Technology development", "Bioinformatics Support and Infrastructure": "Technology development", "NGI Uppsala (Uppsala Genome Center)": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Technology development"}, "xrefs": [], "notes": [], "created": "2018-02-09T10:16:05.868Z", "modified": "2024-01-16T13:48:46.950Z"}, {"entity": "publication", "iuid": "41693810bf914d9095a1db79a7f44a49", "links": {"self": {"href": "https://publications.scilifelab.se/publication/41693810bf914d9095a1db79a7f44a49.json"}, "display": {"href": "https://publications.scilifelab.se/publication/41693810bf914d9095a1db79a7f44a49"}}, "title": "Four simple recommendations to encourage best practices in research software", "authors": [{"family": "Jim\u00e9nez", "given": "Rafael C", "initials": "RC"}, {"family": "Kuzak", "given": "Mateusz", "initials": "M"}, {"family": "Alhamdoosh", "given": "Monther", "initials": "M"}, {"family": "Barker", "given": "Michelle", "initials": "M"}, {"family": "Batut", "given": "B\u00e9r\u00e9nice", "initials": "B"}, {"family": "Borg", "given": "Mikael", "initials": "M"}, {"family": "Capella-Gutierrez", "given": "Salvador", "initials": "S"}, {"family": "Chue Hong", "given": "Neil", "initials": "N"}, {"family": "Cook", "given": "Martin", "initials": "M"}, {"family": "Corpas", "given": "Manuel", "initials": "M"}, {"family": "Flannery", "given": "Madison", "initials": "M"}, {"family": "Garcia", "given": "Leyla", "initials": "L"}, {"family": "Gelp\u00ed", "given": "Josep Ll", "initials": "JL"}, {"family": "Gladman", "given": "Simon", "initials": "S"}, {"family": "Goble", "given": "Carole", "initials": "C"}, {"family": "Gonz\u00e1lez Ferreiro", "given": "Montserrat", "initials": "M"}, {"family": "Gonzalez-Beltran", "given": "Alejandra", "initials": "A"}, {"family": "Griffin", "given": "Philippa C", "initials": "PC"}, {"family": "Gr\u00fcning", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Hagberg", "given": "Jonas", "initials": "J"}, {"family": "Holub", "given": "Petr", "initials": "P"}, {"family": "Hooft", "given": "Rob", "initials": "R"}, {"family": "Ison", "given": "Jon", "initials": "J"}, {"family": "Katz", "given": "Daniel S", "initials": "DS"}, {"family": "Lesko\u0161ek", "given": "Brane", "initials": "B"}, {"family": "L\u00f3pez G\u00f3mez", "given": "Federico", "initials": "F"}, {"family": "Oliveira", "given": "Luis J", "initials": "LJ"}, {"family": "Mellor", "given": "David", "initials": "D"}, {"family": "Mosbergen", "given": "Rowland", "initials": "R"}, {"family": "Mulder", "given": "Nicola", "initials": "N"}, {"family": "Perez-Riverol", "given": "Yasset", "initials": "Y"}, {"family": "Pergl", "given": "Robert", "initials": "R"}, {"family": "Pichler", "given": "Horst", "initials": "H"}, {"family": "Pope", "given": "Bernard", "initials": "B"}, {"family": "Sanz", "given": "Ferran", "initials": "F"}, {"family": "Schneider", "given": "Maria V", "initials": "MV"}, {"family": "Stodden", "given": "Victoria", "initials": "V"}, {"family": "Suchecki", "given": "Rados\u0142aw", "initials": "R"}, {"family": "Svobodov\u00e1 Va\u0159ekov\u00e1", "given": "Radka", "initials": "R"}, {"family": "Talvik", "given": "Harry Anton", "initials": "HA"}, {"family": "Todorov", "given": "Ilian", "initials": "I"}, {"family": "Treloar", "given": "Andrew", "initials": "A"}, {"family": "Tyagi", "given": "Sonika", "initials": "S"}, {"family": "van Gompel", "given": "Maarten", "initials": "M"}, {"family": "Vaughan", "given": "Daniel", "initials": "D"}, {"family": "Via", "given": "Allegra", "initials": "A"}, {"family": "Wang", "given": "Xiaochuan", "initials": "X"}, {"family": "Watson-Haigh", "given": "Nathan S", "initials": "NS"}, {"family": "Crouch", "given": "Steve", "initials": "S"}], "type": "journal-article", "published": "2017-06-13", "journal": {"volume": "6", "issn": "2046-1402", "issue": null, "pages": "876", "title": "F1000Res", "issn-l": "2046-1402"}, "abstract": null, "doi": "10.12688/f1000research.11407.1", "pmid": "28751965", "labels": {"Bioinformatics Support, Infrastructure and Training": "Technology development", "Bioinformatics Support and Infrastructure": "Technology development", "Bioinformatics (NBIS)": "Technology development"}, "xrefs": [], "notes": [], "created": "2017-11-03T13:16:15.160Z", "modified": "2020-01-21T13:53:21.698Z"}, {"entity": "publication", "iuid": "fefb54b862b242c7a4164b64ca3b488b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fefb54b862b242c7a4164b64ca3b488b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fefb54b862b242c7a4164b64ca3b488b"}}, "title": "A community proposal to integrate proteomics activities in ELIXIR", "authors": [{"family": "Vizca\u00edno", "given": "Juan Antonio", "initials": "JA"}, {"family": "Walzer", "given": "Mathias", "initials": "M"}, {"family": "Jim\u00e9nez", "given": "Rafael C", "initials": "RC"}, {"family": "Bittremieux", "given": "Wout", "initials": "W"}, {"family": "Bouyssi\u00e9", "given": "David", "initials": "D"}, {"family": "Carapito", "given": "Christine", "initials": "C"}, {"family": "Corrales", "given": "Fernando", "initials": "F"}, {"family": "Ferro", "given": "Myriam", "initials": "M"}, {"family": "Heck", "given": "Albert J R", "initials": "AJR"}, {"family": "Horvatovich", "given": "Peter", "initials": "P"}, {"family": "Hubalek", "given": "Martin", "initials": "M"}, {"family": "Lane", "given": "Lydie", "initials": "L"}, {"family": "Laukens", "given": "Kris", "initials": "K"}, {"family": "Levander", "given": "Fredrik", "initials": "F"}, {"family": "Lisacek", "given": "Frederique", "initials": "F"}, {"family": "Novak", "given": "Petr", "initials": "P"}, {"family": "Palmblad", "given": "Magnus", "initials": "M"}, {"family": "Piovesan", "given": "Damiano", "initials": "D"}, {"family": "P\u00fchler", "given": "Alfred", "initials": "A"}, {"family": "Schw\u00e4mmle", "given": "Veit", "initials": "V"}, {"family": "Valkenborg", "given": "Dirk", "initials": "D"}, {"family": "van Rijswijk", "given": "Merlijn", "initials": "M"}, {"family": "Vondrasek", "given": "Jiri", "initials": "J"}, {"family": "Eisenacher", "given": "Martin", "initials": "M"}, {"family": "Martens", "given": "Lennart", "initials": "L"}, {"family": "Kohlbacher", "given": "Oliver", "initials": "O"}], "type": "journal-article", "published": "2017-06-13", "journal": {"volume": "6", "issn": "2046-1402", "issue": null, "pages": "875", "title": "F1000Res", "issn-l": "2046-1402"}, "abstract": null, "doi": "10.12688/f1000research.11751.1", "pmid": "28713550", "labels": {"Bioinformatics Support, Infrastructure and Training": "Technology development", "Bioinformatics Support and Infrastructure": "Technology development", "Bioinformatics (NBIS)": "Technology development"}, "xrefs": [], "notes": [], "created": "2017-11-03T13:16:14.669Z", "modified": "2020-01-21T13:53:21.691Z"}, {"entity": "publication", "iuid": "cb72c2b5a1184d3591fc1e7dc95f3813", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cb72c2b5a1184d3591fc1e7dc95f3813.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cb72c2b5a1184d3591fc1e7dc95f3813"}}, "title": "TIDDIT, an efficient and comprehensive structural variant caller for massive parallel sequencing data.", "authors": [{"family": "Eisfeldt", "given": "Jesper", "initials": "J"}, {"family": "Vezzi", "given": "Francesco", "initials": "F"}, {"family": "Olason", "given": "Pall", "initials": "P"}, {"family": "Nilsson", "given": "Daniel", "initials": "D"}, {"family": "Lindstrand", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2017-05-10", "journal": {"volume": "6", "issn": "2046-1402", "issue": null, "pages": "664", "title": "F1000Res", "issn-l": "2046-1402"}, "abstract": "Reliable detection of large structural variation ( > 1000 bp) is important in both rare and common genetic disorders. Whole genome sequencing (WGS) is a technology that may be used to identify a large proportion of the genomic structural variants (SVs) in an individual in a single experiment. Even though SV callers have been extensively used in research to detect mutations, the potential usage of SV callers within routine clinical diagnostics is still limited. One well known, but not well-addressed problem is the large number of benign variants and reference errors present in the human genome that further complicates analysis. Even though there is a wide range of SV-callers available, the number of callers that allow detection of the entire spectra of SV at a low computational cost is still relatively limited.", "doi": "10.12688/f1000research.11168.2", "pmid": "28781756", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Clinical Genomics Stockholm": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC5521161"}], "notes": [], "created": "2017-10-04T15:14:48.609Z", "modified": "2024-01-16T13:48:47.976Z"}, {"entity": "publication", "iuid": "8a8e6eb7f7f94c1fb129b51ef32d3405", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8a8e6eb7f7f94c1fb129b51ef32d3405.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8a8e6eb7f7f94c1fb129b51ef32d3405"}}, "title": "Cluster Flow: A user-friendly bioinformatics workflow tool.", "authors": [{"family": "Ewels", "given": "Philip", "initials": "P", "orcid": "0000-0003-4101-2502", "researcher": {"href": "https://publications.scilifelab.se/researcher/9d0fd82fe18b41539a761c55075f31d6.json"}}, {"family": "Krueger", "given": "Felix", "initials": "F"}, {"family": "K\u00e4ller", "given": "Max", "initials": "M", "orcid": "0000-0001-6813-3051", "researcher": {"href": "https://publications.scilifelab.se/researcher/536ad902a272482aba853c078557e240.json"}}, {"family": "Andrews", "given": "Simon", "initials": "S"}], "type": "journal article", "published": "2016-12-06", "journal": {"volume": "5", "issn": "2046-1402", "issue": null, "pages": "2824", "title": "F1000Res", "issn-l": "2046-1402"}, "abstract": "Pipeline tools are becoming increasingly important within the field of bioinformatics. Using a pipeline manager to manage and run workflows comprised of multiple tools reduces workload and makes analysis results more reproducible. Existing tools require significant work to install and get running, typically needing pipeline scripts to be written from scratch before running any analysis. We present Cluster Flow, a simple and flexible bioinformatics pipeline tool designed to be quick and easy to install. Cluster Flow comes with 40 modules for common NGS processing steps, ready to work out of the box. Pipelines are assembled using these modules with a simple syntax that can be easily modified as required. Core helper functions automate many common NGS procedures, making running pipelines simple. Cluster Flow is available with an GNU GPLv3 license on GitHub. Documentation, examples and an online demo are available at http://clusterflow.io.", "doi": "10.12688/f1000research.10335.2", "pmid": "28299179", "labels": {"National Genomics Infrastructure": "Collaborative", "NGI Stockholm (Genomics Applications)": "Collaborative", "NGI Stockholm (Genomics Production)": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC5310375"}], "notes": [], "created": "2020-06-30T12:52:40.081Z", "modified": "2021-07-07T15:22:42.766Z"}], "created": "2017-10-04T15:14:48.626Z", "modified": "2020-11-27T13:14:08.817Z"}