tag:joss.theoj.org,2005:/papers/tagged/ReproductionJournal of Open Source Software2024-02-21T08:51:15ZJournal of Open Source Softwarehttps://joss.theoj.orgtag:joss.theoj.org,2005:Paper/43002024-02-21T08:51:15Z2024-02-23T09:04:14ZReducing the efforts to create reproducible analysis code with FieldTripacceptedhttps://github.com/fieldtrip/fieldtrip/commit/9cfc0a7e7b7871a1d9938552ce60041c59f3a5532023-03-10 17:12:47 UTC942024-02-21 08:51:15 UTC920245566MatsW.j.van EsDonders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen, The Netherlands, Oxford Centre for Human Brain Activity, Department of Psychiatry, University of Oxford, United Kingdom, Wellcome Centre for Integrative Neuroimaging, University of Oxford, Oxford, United Kingdom0000-0002-7133-509XEelkeSpaakDonders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen, The Netherlands0000-0002-2018-3364Jan-MathijsSchoffelenDonders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen, The Netherlands0000-0003-0923-6610RobertOostenveldDonders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen, The Netherlands, NatMEG, Karolinska Institutet, Stockholm, Sweden0000-0002-1974-129310.21105/joss.05566https://doi.org/10.5281/zenodo.10495308MATLAB, Mathematicahttps://joss.theoj.org/papers/10.21105/joss.05566.pdfFieldTrip Toolbox, reproducibility, analysis pipeline, open science, MEG, EEGtag:joss.theoj.org,2005:Paper/47702024-01-25T22:35:43Z2024-01-26T10:44:05Zstanscofi and benchscofi: a new standard for drug repurposing by collaborative filteringacceptedv2.0.02023-09-20 18:28:20 UTC932024-01-25 22:35:43 UTC920245973ClémenceRédaDepartment of Systems Biology and Bioinformatics, University of Rostock, Rostock, G-18051, Germany0000-0003-3238-0258Jill-JênnVieSoda Team, Inria Saclay, F-91120 Palaiseau, France0000-0002-9304-2220OlafWolkenhauerDepartment of Systems Biology and Bioinformatics, University of Rostock, Rostock, G-18051, Germany, Leibniz-Institute for Food Systems Biology, Freising, G-85354, Germany, Stellenbosch Institute of Advanced Study, Wallenberg Research Centre, Stellenbosch, SA-7602, South Africa0000-0001-6105-293710.21105/joss.05973https://doi.org/10.5281/zenodo.10561760Pythonhttps://joss.theoj.org/papers/10.21105/joss.05973.pdfdrug repurposing, collaborative filtering, open science, science reproducibilitytag: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/48632023-12-19T12:19:57Z2024-01-11T16:55:09ZMiscMetabar: an R package to facilitate visualization and reproducibility in metabarcoding analysisacceptedv0.52023-10-23 15:45:54 UTC922023-12-19 12:19:57 UTC820236038AdrienTaudièreIdEst, Saint-Bonnet-de-Salendrinque, 30460 France0000-0003-1088-118210.21105/joss.06038https://doi.org/10.5281/zenodo.10370781Rhttps://joss.theoj.org/papers/10.21105/joss.06038.pdfBioinformatic, Metagenomics, Barcoding, Reproducibilitytag:joss.theoj.org,2005:Paper/45652023-10-01T12:42:45Z2023-10-02T00:01:29ZPyDGN: a Python Library for Flexible and Reproducible Research on Deep Learning for Graphsacceptedv1.3.12023-06-26 18:09:02 UTC902023-10-01 12:42:45 UTC820235713FedericoErricaNEC Laboratories Europe, Germany0000-0001-5181-2904DavideBacciuUniversity of Pisa, Italy0000-0001-5213-2468AlessioMicheliUniversity of Pisa, Italy0000-0001-5764-523810.21105/joss.05713https://doi.org/10.5281/zenodo.8396373Pythonhttps://joss.theoj.org/papers/10.21105/joss.05713.pdfMachine Learning, Graph Networks, Deep Learning for Graphstag:joss.theoj.org,2005:Paper/46782023-09-11T12:47:07Z2023-09-12T00:01:30Zeinprot: flexible, easy-to-use, reproducible workflows for statistical analysis of quantitative proteomics dataaccepted0.7.62023-08-05 20:14:11 UTC892023-09-11 12:47:07 UTC820235750CharlotteSonesonFriedrich Miescher Institute for Biomedical Research, Basel, Switzerland, SIB Swiss Institute of Bioinformatics, Basel, Switzerland0000-0003-3833-2169VytautasIesmantaviciusFriedrich Miescher Institute for Biomedical Research, Basel, Switzerland0000-0002-2512-9957DanielHessFriedrich Miescher Institute for Biomedical Research, Basel, Switzerland0000-0002-1642-5404MichaelB.StadlerFriedrich Miescher Institute for Biomedical Research, Basel, Switzerland, SIB Swiss Institute of Bioinformatics, Basel, Switzerland, University of Basel, Switzerland0000-0002-2269-4934JanSeebacherFriedrich Miescher Institute for Biomedical Research, Basel, Switzerland0000-0002-7858-272010.21105/joss.05750https://doi.org/10.5281/zenodo.8298657Rhttps://joss.theoj.org/papers/10.21105/joss.05750.pdfproteomicstag:joss.theoj.org,2005:Paper/33942023-05-08T14:20:35Z2023-05-09T00:01:32ZClimate variability indices for ecological and crop models in R: the climatrends packageacceptedv0.22022-02-23 15:55:36 UTC852023-05-08 14:20:35 UTC820234405Kauêde SousaDepartment of Agricultural Sciences, Inland Norway University of Applied Sciences, Hamar, Norway, Digital Inclusion, Bioversity International, Montpellier, France0000-0002-7571-7845Jacobvan EttenDigital Inclusion, Bioversity International, Montpellier, France0000-0001-7554-2558MagneNebyDepartment of Agricultural Sciences, Inland Norway University of Applied Sciences, Hamar, Norway0000-0003-2098-7650SveinØ.SolbergDepartment of Agricultural Sciences, Inland Norway University of Applied Sciences, Hamar, Norway0000-0002-4491-448310.21105/joss.04405https://doi.org/10.5281/zenodo.7884366Rhttps://joss.theoj.org/papers/10.21105/joss.04405.pdfclimate data, climatology, earth science, precipitation data, reproducibility, weather datatag:joss.theoj.org,2005:Paper/41502023-03-29T11:52:06Z2023-03-30T00:03:07Zunfold: removing the barriers to sharing and reproducing prospective life-cycle assessment databasesaccepted1.0.02023-01-05 17:49:49 UTC832023-03-29 11:52:06 UTC820235198RomainSacchiPaul Scherrer Institute, Villigen, Switzerland0000-0003-1440-090510.21105/joss.05198https://doi.org/10.5281/zenodo.7777717Jupyter Notebook, Pythonhttps://joss.theoj.org/papers/10.21105/joss.05198.pdflife cycle assessment, prospective, database, premise, scenariotag:joss.theoj.org,2005:Paper/39292023-03-07T15:19:21Z2023-03-08T00:04:22ZHydroMT: Automated and reproducible model building and analysisacceptedv0.5.02022-09-28 08:56:15 UTC832023-03-07 15:19:21 UTC820234897DirkEilanderDeltares, The Netherlands, Institution for Environmental Studies (IVM), Vrije Universiteit Amsterdam, The Netherlands0000-0002-0951-8418HélèneBoisgontierDeltares, The NetherlandsLaurèneJ. e.BouazizDeltares, The Netherlands0000-0003-0597-8051JoostBuitinkDeltares, The NetherlandsAnaïsCouasnonDeltares, The Netherlands, Institution for Environmental Studies (IVM), Vrije Universiteit Amsterdam, The Netherlands0000-0001-9372-841XBrendanDalmijnDeltares, The NetherlandsMarkHegnauerDeltares, The NetherlandsTjallingde JongDeltares, The NetherlandsSibrenLoosDeltares, The NetherlandsIndraMarthDeltares, The NetherlandsWillemvan VerseveldDeltares, The Netherlands0000-0003-3311-738X10.21105/joss.04897https://doi.org/10.5281/zenodo.7663065Pythonhttps://joss.theoj.org/papers/10.21105/joss.04897.pdfreproducible model building, model analysis, hydrology, hydrodynamics, gistag:joss.theoj.org,2005:Paper/36792023-01-13T19:54:53Z2023-01-14T00:00:57ZRHEA: an open-source Reproducible Hybrid-architecture flow solver Engineered for Academiaacceptedv1.0.02022-06-24 17:38:19 UTC812023-01-13 19:54:53 UTC820234637LluísJofreDepartment of Fluid Mechanics, Universitat Politècnica de Catalunya · BarcelonaTech (UPC), Barcelona 08019, Spain0000-0003-2437-259XAhmedAbdellatifDepartment of Fluid Mechanics, Universitat Politècnica de Catalunya · BarcelonaTech (UPC), Barcelona 08019, Spain0000-0002-8810-7480GuillermoOyarzunDepartment of Computer Applications in Science & Engineering, Barcelona Supercomputing Center, Barcelona 08034, Spain0000-0001-9524-378210.21105/joss.04637https://doi.org/10.5281/zenodo.7525886JavaScripthttps://joss.theoj.org/papers/10.21105/joss.04637.pdfCompressible flow, Fluid mechanics, Ideal- & real-gas thermodynamics, Turbulence, C++, MPI, OpenACC, HDF5, YAML