tag:joss.theoj.org,2005:/papers/tagged/Docker?page=1Journal of Open Source Software2024-01-24T17:19:02ZJournal of Open Source Softwarehttps://joss.theoj.orgtag:joss.theoj.org,2005:Paper/49472024-01-24T17:19:02Z2024-02-25T07:02:22ZViash: A meta-framework for building reusable workflow modulesaccepted0.8.12023-11-21 12:26:06 UTC932024-01-24 17:19:02 UTC920246089RobrechtCannoodtData Intuitive, Lebbeke, Belgium, Data Mining and Modelling for Biomedicine group, VIB Center for Inflammation Research, Ghent, Belgium, Department of Applied Mathematics, Computer Science, and Statistics, Ghent University, Ghent, Belgium0000-0003-3641-729XHendrikCannoodtData Intuitive, Lebbeke, Belgium0000-0002-0032-6719DriesSchaumontData Intuitive, Lebbeke, Belgium0000-0002-4389-0440KaiWaldrantData Intuitive, Lebbeke, Belgium0009-0003-8555-1361EricVan de KerckhoveData Intuitive, Lebbeke, BelgiumAndyBoschmansData Intuitive, Lebbeke, Belgium0009-0008-8793-4661DriesDe MaeyerDiscovery Technology and Molecular Pharmacology, Janssen Research & Development, Pharmaceutical Companies of Johnson & Johnson, Beerse, Belgium0000-0002-1314-3348ToniVerbeirenData Intuitive, Lebbeke, Belgium0000-0002-7007-686610.21105/joss.06089https://doi.org/10.5281/zenodo.10563479Scala, Nextflowhttps://joss.theoj.org/papers/10.21105/joss.06089.pdfBioinformatics, Workflows, Software development, Reproducibility, Cloud computing, Dockertag:joss.theoj.org,2005:Paper/34632022-08-05T18:36:00Z2022-08-06T02:57:34ZOpen-Source Hypothalamic-ForniX (OSHy-X) Atlases and Segmentation Tool for 3T and 7Tacceptedv0.32022-04-11 01:36:26 UTC762022-08-05 18:36:00 UTC720224368JerynChangSchool of Biomedical Sciences, The University of Queensland0000-0002-6659-365XFrederikSteynSchool of Biomedical Sciences, The University of Queensland, Department of Neurology, Royal Brisbane and Women's Hospital, Australia, Wesley Medical Research, The Wesley Hospital, UQ Centre for Clinical Research, The University of Queensland0000-0002-4782-3608ShyuanNgoDepartment of Neurology, Royal Brisbane and Women's Hospital, Australia, Wesley Medical Research, The Wesley Hospital, UQ Centre for Clinical Research, The University of Queensland, Australian Institute of Bioengineering and Nanotechnology, The University of Queensland0000-0002-1388-2108RobertHendersonDepartment of Neurology, Royal Brisbane and Women's Hospital, Australia, Wesley Medical Research, The Wesley Hospital, UQ Centre for Clinical Research, The University of Queensland0000-0002-2820-8183ChristineGuoActiGraph, LLC, Pensacola, FL, USASteffenBollmannCentre for Advanced Imaging, The University of Queensland, School of Information Technology and Electrical Engineering, The University of Queensland0000-0002-2909-0906JurgenFrippCSIRO Health and Biosecurity, The Australian eHealth Research Centre, Brisbane, Australia0000-0001-9705-0079MarkusBarthCentre for Advanced Imaging, The University of Queensland, School of Information Technology and Electrical Engineering, The University of Queensland0000-0002-0520-1843ThomasShawDepartment of Neurology, Royal Brisbane and Women's Hospital, Australia, Centre for Advanced Imaging, The University of Queensland, School of Information Technology and Electrical Engineering, The University of Queensland0000-0003-2490-053210.21105/joss.04368https://doi.org/10.5281/zenodo.6874987Pythonhttps://joss.theoj.org/papers/10.21105/joss.04368.pdfDocker, Apptainer, ANTs, MRI, Segmentation, Multi-atlas label fusiontag:joss.theoj.org,2005:Paper/32342022-04-05T03:54:27Z2022-04-06T00:00:44ZADaPT-ML: A Data Programming Template for Machine Learningacceptedv1.0.02021-12-02 22:51:07 UTC722022-04-05 03:54:27 UTC720224038AndreaM.WhittakerUniversity of Alberta0000-0001-8512-181010.21105/joss.04038https://doi.org/10.5281/zenodo.6402630Pythonhttps://joss.theoj.org/papers/10.21105/joss.04038.pdfDocker, MLOps, data programming, machine learning, model lifecycletag:joss.theoj.org,2005:Paper/30602021-11-12T21:11:08Z2021-11-13T00:00:35ZA flexible search system for high-accuracy identification of biological entities and moleculesaccepted0.6.02021-09-10 18:06:43 UTC672021-11-12 21:11:08 UTC620213756MaxFranzThe Donnelly Centre, University of Toronto, Toronto, Ontario, M5S 3E1, Canada0000-0003-0169-0480JeffreyV.WongThe Donnelly Centre, University of Toronto, Toronto, Ontario, M5S 3E1, Canada0000-0002-8912-5699MetinCanSiperComputational Biology Program, Oregon Health and Science University, Portland, OR 97239, USA0000-0002-7556-093XChristianDallagoDepartment of Cell Biology, Harvard Medical School, Boston, MA, 02215, USA, Department of Systems Biology, Harvard Medical School, Boston, MA, 02215, USA, Department of Informatics, Technische Universität München, 85748 Garching, Germany0000-0003-4650-6181JohnGiorgiThe Donnelly Centre, University of Toronto, Toronto, Ontario, M5S 3E1, Canada0000-0001-9621-5046EmekDemirComputational Biology Program, Oregon Health and Science University, Portland, OR 97239, USA0000-0002-3663-7113ChrisSanderDepartment of Cell Biology, Harvard Medical School, Boston, MA, 02215, USA, Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, 02215, USA, Broad Institute of MIT and Harvard, Boston, MA, 02142, USA0000-0001-6059-6270GaryD.BaderThe Donnelly Centre, University of Toronto, Toronto, Ontario, M5S 3E1, Canada, Department of Computer Science, University of Toronto, Ontario, M5S 2E4, Canada, Department of Molecular Genetics, University of Toronto, Ontario, M5S 1A8, Canada, The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, M5G 1X5, Canada, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, M5G 2C1, Canada0000-0003-0185-886110.21105/joss.03756https://doi.org/10.5281/zenodo.4891545JavaScripthttps://joss.theoj.org/papers/10.21105/joss.03756.pdfbiological entities, small molecules, grounding, identifiers, identification, search, Dockertag:joss.theoj.org,2005:Paper/22892021-04-12T01:04:26Z2021-05-18T22:03:03Zminimo: a linked data and metadata storage system for small labsacceptedv1.0.02020-12-29 01:57:48 UTC602021-04-12 01:04:26 UTC620212979JacksonBorchardtUniversity of California San Francisco, Weill Institute for Neurosciences, Department of Neurology0000-0001-9033-6365RaymondDunnUniversity of California San Francisco, Weill Institute for Neurosciences, Department of Neurology0000-0003-4443-5519SaulKatoUniversity of California San Francisco, Weill Institute for Neurosciences, Department of Neurology0000-0003-2990-830610.21105/joss.02979https://doi.org/10.5281/zenodo.4678098JavaScripthttps://joss.theoj.org/papers/10.21105/joss.02979.pdfdata storage, object storage, metadata linkage, MinIO, MongoDB, Traefik, Docker, Node.js, Expresstag:joss.theoj.org,2005:Paper/17602020-09-17T00:14:39Z2021-02-15T11:30:26ZCaliban: Docker-based job manager for reproducible workflowsaccepted0.2.52020-06-22 17:27:34 UTC532020-09-17 00:14:39 UTC520202403SamRitchieGoogle, United States of America0000-0002-0545-6360AmbroseSloneGoogle, United States of AmericaVinayRamaseshGoogle, United States of America0000-0003-0625-332710.21105/joss.02403https://doi.org/10.5281/zenodo.4026612Pythonhttps://joss.theoj.org/papers/10.21105/joss.02403.pdfpython, docker, machine learning, reproducibilitytag:joss.theoj.org,2005:Paper/15772020-09-02T00:00:00Z2022-08-25T16:35:40ZUtopia: A Comprehensive and Collaborative Modeling Framework for Complex and Evolving Systemsacceptedlatest2020-03-07 19:20:06 UTC532020-09-02 00:00:00 UTC520202165LukasRiedelInstitute of Environmental Physics, Heidelberg University, Germany, Interdisciplinary Center for Scientific Computing, Heidelberg University, Germany, Heidelberg Graduate School of Mathematical and Computational Methods for the Sciences, Heidelberg University, Germany0000-0002-4667-3652BenjaminHerdeanuInstitute of Environmental Physics, Heidelberg University, Germany, Heidelberg Graduate School for Physics, Heidelberg University, Germany0000-0001-6343-3004HaraldMackInstitute of Environmental Physics, Heidelberg University, Germany0000-0001-7787-9496YunusSevinchanInstitute of Environmental Physics, Heidelberg University, Germany0000-0003-3858-0904JulianWeningerDepartment of Biochemistry, University of Geneva, Switzerland10.21105/joss.02165https://doi.org/10.5281/zenodo.4011979C++, Pythonhttps://joss.theoj.org/papers/10.21105/joss.02165.pdfComplex Systems, Agent-based Models, Modeling Framework, Computational Science, Docker, GitLab, HDF5, YAMLtag:joss.theoj.org,2005:Paper/15992020-08-24T00:00:00Z2022-08-29T08:53:25ZDORiE: A Discontinuous Galerkin Solver for Soil Water Flow and Passive Solute Transport Based on DUNEacceptedv2.02020-05-20 12:39:58 UTC522020-08-24 00:00:00 UTC520202313LukasRiedelInstitute of Environmental Physics, Heidelberg University, Interdisciplinary Center for Scientific Computing, Heidelberg University, Heidelberg Graduate School of Mathematical and Computational Methods for the Sciences, Heidelberg University0000-0002-4667-3652SantiagoOspina LosDe RíosInterdisciplinary Center for Scientific Computing, Heidelberg University, Heidelberg Graduate School of Mathematical and Computational Methods for the Sciences, Heidelberg University0000-0003-0814-9670DionHäfnerNiels Bohr Institute, University of Copenhagen, Institute of Environmental Physics, Heidelberg University0000-0002-4465-7317OleKleinInterdisciplinary Center for Scientific Computing, Heidelberg University0000-0002-3295-734710.21105/joss.02313https://doi.org/10.5281/zenodo.3997152C++, Pythonhttps://joss.theoj.org/papers/10.21105/joss.02313.pdfSoil Hydrology, Porous Media, Solute Transport, Discontinuous Galerkin Method, Finite Element Method, Dockertag:joss.theoj.org,2005:Paper/14472020-01-23T15:03:14Z2021-02-15T11:31:07Zoutsider: Install and run programs, outside of R, inside of Racceptedv0.1.12020-01-21 10:58:32 UTC452020-01-23 15:03:14 UTC520202038DominicJ.BennettGothenburg Global Biodiversity Centre, Box 461, SE-405 30 Gothenburg, Sweden, Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, SE-405 30 Gothenburg, Sweden0000-0003-2722-1359HannesHettlingNaturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands0000-0003-4144-2238DanieleSilvestroGothenburg Global Biodiversity Centre, Box 461, SE-405 30 Gothenburg, Sweden, Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, SE-405 30 Gothenburg, Sweden0000-0003-0100-0961RutgerVosNaturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands0000-0001-9254-7318AlexandreAntonelliGothenburg Global Biodiversity Centre, Box 461, SE-405 30 Gothenburg, Sweden, Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, SE-405 30 Gothenburg, Sweden, Royal Botanic Gardens, Kew, TW9 3AE, Richmond, Surrey, UK0000-0003-1842-929710.21105/joss.02038https://doi.org/10.5281/zenodo.3615177Rhttps://joss.theoj.org/papers/10.21105/joss.02038.pdfDocker, GitHub, GitLab, BitBucket, Reproducibility, Workflow, Integrationtag:joss.theoj.org,2005:Paper/11282019-08-21T17:12:06Z2021-02-15T11:31:54Zcontainerit: Generating Dockerfiles for reproducible research with Racceptedv0.5.02019-07-25 08:02:50 UTC402019-08-21 17:12:06 UTC420191603DanielNüstInstitute for Geoinformatics, University of Münster, Germany0000-0002-0024-5046MatthiasHinzProfessorship for Geoinformatics and Geodesy, Faculty of Agricultural and Environmental Sciences, University of Rostock, Germany0000-0001-6837-940610.21105/joss.01603https://doi.org/10.5281/zenodo.3373289R, Rebolhttps://joss.theoj.org/papers/10.21105/joss.01603.pdfcontainerisation, Docker, sandbox, reproducibility, reproducible research