{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,7]],"date-time":"2026-05-07T03:54:10Z","timestamp":1778126050158,"version":"3.51.4"},"reference-count":36,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2023,8,4]],"date-time":"2023-08-04T00:00:00Z","timestamp":1691107200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Bioinform."],"DOI":"10.3389\/fbinf.2023.1255159","type":"journal-article","created":{"date-parts":[[2023,8,4]],"date-time":"2023-08-04T11:12:55Z","timestamp":1691147575000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":10,"title":["Better research software tools to elevate the rate of scientific discovery or why we need to invest in research software engineering"],"prefix":"10.3389","volume":"3","author":[{"given":"Joran","family":"Deschamps","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Damian","family":"Dalle Nogare","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Florian","family":"Jug","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1965","published-online":{"date-parts":[[2023,8,4]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"295","DOI":"10.12688\/f1000research.23224.1","article-title":"An environment for sustainable research software in Germany and beyond: Current state, open challenges, and call for action","volume":"9","author":"Anzt","year":"2020","journal-title":"F1000Res"},{"key":"B2","unstructured":"Study: Public services need to nurture and sustain vulnerable small projects\n            AroraS. S.\n          2022"},{"key":"B3","doi-asserted-by":"publisher","first-page":"110848","DOI":"10.1016\/j.jss.2020.110848","article-title":"Software engineering practices for scientific software development: A systematic mapping study","volume":"172","author":"Arvanitou","year":"2021","journal-title":"J. Syst. Softw."},{"key":"B4","doi-asserted-by":"publisher","DOI":"10.3389\/fcomp.2022.777728","article-title":"Labkit: Labeling and segmentation toolkit for big image data","volume":"4","author":"Arzt","year":"2022","journal-title":"Front. Comput. Sci."},{"key":"B5","doi-asserted-by":"publisher","first-page":"622","DOI":"10.1038\/s41597-022-01710-x","article-title":"Introducing the FAIR Principles for research software","volume":"9","author":"Barker","year":"2022","journal-title":"Sci. Data"},{"key":"B6","doi-asserted-by":"publisher","first-page":"1226","DOI":"10.1038\/s41592-019-0582-9","article-title":"ilastik: interactive machine learning for (bio)image analysis","volume":"16","author":"Berg","year":"2019","journal-title":"Nat. Methods"},{"key":"B7","doi-asserted-by":"publisher","first-page":"26","DOI":"10.1145\/1656274.1656280","article-title":"Knime - the Konstanz information miner","volume":"11","author":"Berthold","year":"2009","journal-title":"ACM SIGKDD Explor. Newsl."},{"key":"B8","doi-asserted-by":"publisher","first-page":"666","DOI":"10.1038\/nmeth.2073","article-title":"A call for bioimaging software usability","volume":"9","author":"Carpenter","year":"2012","journal-title":"Nat. Methods"},{"key":"B15","article-title":"Essential Open Source Software for science","year":"2019"},{"key":"B10","doi-asserted-by":"publisher","first-page":"14","DOI":"10.1109\/mcse.2023.3258630","article-title":"Research software engineers: Career entry points and training gaps","volume":"24","author":"Cosden","year":"2022","journal-title":"Comput. Sci. Eng."},{"key":"B11","doi-asserted-by":"publisher","first-page":"74","DOI":"10.1109\/mcse.2013.133","article-title":"The software sustainability institute: Changing research software attitudes and practices","volume":"15","author":"Crouch","year":"2013","journal-title":"Comput. Sci. Eng."},{"key":"B12","unstructured":"An open-source rich internet application for collaborative analysis of multi-gigapixel images\n            Cytomine\n          2023"},{"key":"B13","article-title":"Centre for bioimage analysis","year":"2023"},{"key":"B32","article-title":"Call for proposal research software sustainability","year":"2016"},{"key":"B14","doi-asserted-by":"publisher","first-page":"829","DOI":"10.1038\/s41592-022-01507-1","article-title":"TrackMate 7: Integrating state-of-the-art segmentation algorithms into tracking pipelines","volume":"19","author":"Ershov","year":"2022","journal-title":"Nat. Methods"},{"key":"B16","doi-asserted-by":"publisher","first-page":"84","DOI":"10.1109\/mc.2020.2998235","article-title":"Open source research software","volume":"53","author":"Hasselbring","year":"2020","journal-title":"Computer"},{"key":"B17","doi-asserted-by":"publisher","DOI":"10.5281\/zenodo.14809","article-title":"UK Research Software Survey 2014 [Data set]","author":"Hettrick","year":"2014","journal-title":"Zenodo"},{"key":"B18","unstructured":"National facility for data handling and analysis2023"},{"key":"B9","unstructured":"Images processing and analysing2023"},{"key":"B29","unstructured":"Image Analysis Hub2023"},{"key":"B19","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1109\/mcse.2018.108162940","article-title":"Software engineering for computational science: Past, present, future","volume":"20","author":"Johanson","year":"2018","journal-title":"Comput. Sci. Eng."},{"key":"B20","doi-asserted-by":"publisher","first-page":"302","DOI":"10.12688\/f1000research.52531.1","article-title":"Developing open-source software for bioimage analysis: Opportunities and challenges","volume":"10","author":"Levet","year":"2021","journal-title":"F1000Res"},{"key":"B21","doi-asserted-by":"publisher","first-page":"410","DOI":"10.1038\/d41586-022-01901-x","article-title":"Ex-Google chief\u2019s venture aims to save neglected science software","volume":"607","author":"Matthews","year":"2022","journal-title":"Nature"},{"key":"B22","doi-asserted-by":"publisher","first-page":"e2005970","DOI":"10.1371\/journal.pbio.2005970","article-title":"CellProfiler 3.0: Next-generation image processing for biology","volume":"16","author":"McQuin","year":"2018","journal-title":"PLoS Biol."},{"key":"B23","first-page":"41","article-title":"Position paper: Towards usability as a first-class quality of HPC scientific software","author":"Milewicz","year":""},{"key":"B24","doi-asserted-by":"publisher","first-page":"133","DOI":"10.1038\/d41586-019-02046-0","article-title":"How to support open-source software and stay sane","volume":"571","author":"Nowogrodzki","year":"2019","journal-title":"Nature"},{"key":"B25","doi-asserted-by":"publisher","first-page":"1634","DOI":"10.1038\/s41592-022-01663-4","article-title":"Cellpose 2.0: How to train your own model","volume":"19","author":"Pachitariu","year":"2022","journal-title":"Nat. Methods"},{"key":"B26","doi-asserted-by":"publisher","first-page":"475","DOI":"10.1038\/s41592-023-01776-4","article-title":"MoBIE: A Fiji plugin for sharing and exploration of multi-modal cloud-hosted big image data","volume":"20","author":"Pape","year":"2023","journal-title":"Nat. Methods"},{"key":"B27","doi-asserted-by":"publisher","first-page":"481","DOI":"10.1038\/nmeth.3392","article-title":"BigDataViewer: Visualization and processing for large image data sets","volume":"12","author":"Pietzsch","year":"2015","journal-title":"Nat. Methods"},{"key":"B28","unstructured":"Physics of life\n            PoL\n          2023"},{"key":"B30","doi-asserted-by":"publisher","first-page":"529","DOI":"10.1186\/s12859-017-1934-z","article-title":"ImageJ2: ImageJ for the next generation of scientific image data","volume":"18","author":"Rueden","year":"2017","journal-title":"BMC Bioinforma."},{"key":"B31","doi-asserted-by":"publisher","first-page":"676","DOI":"10.1038\/nmeth.2019","article-title":"Fiji: An open-source platform for biological-image analysis","volume":"9","author":"Schindelin","year":"2012","journal-title":"Nat. Methods"},{"key":"B33","doi-asserted-by":"publisher","DOI":"10.1111\/jmi.13192","article-title":"Challenges and opportunities for bio-image analysis core-facilities","author":"Soltwedel","year":"2023","journal-title":"J. Microsc."},{"key":"B34","doi-asserted-by":"publisher","first-page":"80","DOI":"10.1016\/j.ymeth.2016.09.016","article-title":"TrackMate: An open and extensible platform for single-particle tracking","volume":"115","author":"Tinevez","year":"2017","journal-title":"Methods"},{"key":"B35","unstructured":"Bus factor2023"},{"key":"B36","doi-asserted-by":"publisher","first-page":"160018","DOI":"10.1038\/sdata.2016.18","article-title":"The FAIR Guiding Principles for scientific data management and stewardship","volume":"3","author":"Wilkinson","year":"2016","journal-title":"Sci. Data"}],"container-title":["Frontiers in Bioinformatics"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fbinf.2023.1255159\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,8,4]],"date-time":"2023-08-04T11:13:01Z","timestamp":1691147581000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fbinf.2023.1255159\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,8,4]]},"references-count":36,"alternative-id":["10.3389\/fbinf.2023.1255159"],"URL":"https:\/\/doi.org\/10.3389\/fbinf.2023.1255159","relation":{},"ISSN":["2673-7647"],"issn-type":[{"value":"2673-7647","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,8,4]]},"article-number":"1255159"}}