tag:joss.theoj.org,2005:/papers/by/Andre%20SJournal of Open Source Software2024-03-26T15:54:37ZJournal of Open Source Softwarehttps://joss.theoj.orgtag:joss.theoj.org,2005:Paper/48572024-03-26T15:54:37Z2024-03-27T00:01:22ZMold: a LAMMPS package to compute interfacial free energies and nucleation ratesacceptedLAMMPS 20232023-10-20 08:11:09 UTC952024-03-26 15:54:37 UTC920246083AndresR.TejedorYusuf Hamied Department of Chemistry, University of Cambridge, United Kingdom, Departamento de Química Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Spain0000-0002-9437-6169IgnacioSanchez-BurgosCavendish Laboratory, Department of Physics, University of Cambridge, United Kingdom0000-0002-1160-3945EduardoSanzDepartamento de Química Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Spain0000-0001-6474-5835CarlosVegaDepartamento de Química Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Spain0000-0002-2417-9645FelipeJ.BlasLaboratorio de Simulacion Molecular y Quimica Computacional, CIQSO-Centro de Investigacion en Quimica Sostenible and Departamento de Ciencias Integradas, Universidad de Huelva, Spain0000-0001-9030-040XRuslanL.DavidchackSchool of Computing and Mathematical Sciences, University of Leicester, United Kingdom0000-0001-9418-5322NicodemoDi PasqualeDepartment of Chemical Engineering, Brunel University London, United Kingdom, Dipartimento di Chimica Industriale, Università di Bologna, Italy0000-0001-5676-8527JorgeRamirezDepartment of Chemical Engineering, Universidad Politécnica de Madrid, Spain0000-0002-8946-3786JorgeR.EspinosaDepartamento de Química Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Spain0000-0001-9530-265810.21105/joss.06083https://doi.org/10.5281/zenodo.10843863C++https://joss.theoj.org/papers/10.21105/joss.06083.pdfLAMMPS, Molecular simulations, Phase Transitions, Nucleation theorytag:joss.theoj.org,2005:Paper/49082024-02-14T15:41:34Z2024-02-15T00:01:24ZThe MOOSE Thermal Hydraulics Moduleacceptedv1.0.02023-10-30 21:51:40 UTC942024-02-14 15:41:34 UTC920246146JoshuaHanselIdaho National Laboratory0000-0001-6782-5275DavidAndrsIdaho National Laboratory0000-0002-8913-902XLiseCharlotIdaho National Laboratory0000-0002-6343-6990GuillaumeGiudicelliIdaho National Laboratory0000-0001-9714-438210.21105/joss.06146https://doi.org/10.5281/zenodo.10651363Python, C, Fortranhttps://joss.theoj.org/papers/10.21105/joss.06146.pdfC++, multiphysics, system analysis, thermal hydraulicstag:joss.theoj.org,2005:Paper/40252023-05-16T14:36:36Z2023-05-17T01:09:38ZMulti-view-AE: A Python package for multi-view autoencoder modelsacceptedv1.0.02022-11-25 14:36:25 UTC852023-05-16 14:36:36 UTC820235093AnaLawryAguilaCentre for Medical Image Computing (CMIC), Medical Physics and Biomedical Engineering, University College London (UCL), London, UK0000-0003-0727-3274AlejandraJaymeEngineering Mathematics and Computing Lab (EMCL), Heidelberg, GermanyNinaMontaña-BrownCentre for Medical Image Computing (CMIC), Medical Physics and Biomedical Engineering, University College London (UCL), London, UK0000-0001-5685-971XVincentHeuvelineEngineering Mathematics and Computing Lab (EMCL), Heidelberg, GermanyAndreAltmannCentre for Medical Image Computing (CMIC), Medical Physics and Biomedical Engineering, University College London (UCL), London, UK0000-0002-9265-239310.21105/joss.05093https://doi.org/10.5281/zenodo.7871099Pythonhttps://joss.theoj.org/papers/10.21105/joss.05093.pdfAutoencoders, Multi-view, Unsupervised learning, Representation learning, Data generationtag:joss.theoj.org,2005:Paper/33382023-02-01T16:22:20Z2023-02-02T00:00:37ZJOAN: a framework for human-automated vehicle interaction experiments in a virtual reality driving simulatoracceptedV1.1.02022-02-14 16:47:16 UTC822023-02-01 16:22:20 UTC820234250NiekBeckersHuman-Robot Interaction group, Department of Cognitive Robotics, Faculty 3mE, Delft University of Technology, Mekelweg 2, 2628 CD Delft, The Netherlands0000-0001-7077-9812OlgerSiebingaHuman-Robot Interaction group, Department of Cognitive Robotics, Faculty 3mE, Delft University of Technology, Mekelweg 2, 2628 CD Delft, The Netherlands0000-0002-5614-1262JorisGiltayHuman-Robot Interaction group, Department of Cognitive Robotics, Faculty 3mE, Delft University of Technology, Mekelweg 2, 2628 CD Delft, The NetherlandsAndrévan der KraanHuman-Robot Interaction group, Department of Cognitive Robotics, Faculty 3mE, Delft University of Technology, Mekelweg 2, 2628 CD Delft, The Netherlands10.21105/joss.04250https://doi.org/10.4121/21975335Pythonhttps://joss.theoj.org/papers/10.21105/joss.04250.pdfHuman-automated vehicle interaction, Automated driving, Human factors experiments, Simulation, Virtual Reality, CARLAtag:joss.theoj.org,2005:Paper/39642022-12-16T13:14:37Z2022-12-17T00:01:04Zhstrat: a Python Package for phylogenetic inference on distributed digital evolution populationsacceptedv1.0.32022-10-16 23:14:14 UTC802022-12-16 13:14:37 UTC720224866MatthewAndresMorenoMichigan State University0000-0003-4726-4479EmilyDolsonMichigan State University0000-0001-8616-4898CharlesOfriaMichigan State University0000-0003-2924-173210.21105/joss.04866https://doi.org/10.5281/zenodo.7416592Pythonhttps://joss.theoj.org/papers/10.21105/joss.04866.pdfartificial life, digital evolution, distributed computingtag:joss.theoj.org,2005:Paper/39492022-12-13T23:25:17Z2022-12-14T11:08:15ZInspectorCell: Finding Ground Truth in Multiplexed Microscopy Imagesaccepted0.3.12022-10-07 18:08:15 UTC802022-12-13 23:25:17 UTC720224949AndreGosselinkInstitute of Medical Statistics and Computational Biology, Faculty of Medicine, University of Cologne, Cologne, Germany, R&D Department, Miltenyi Biotec B.V. & Co. KG, Bergisch Gladbach, Germany0000-0003-0181-456XTatsianaHoferCenter for Integrative Bioinformatics Vienna, Max Perutz Labs, University of Vienna, Medical University of Vienna, Vienna, AustriaElviraCriado-MoronatiR&D Department, Miltenyi Biotec B.V. & Co. KG, Bergisch Gladbach, GermanyArndtvon HaeselerCenter for Integrative Bioinformatics Vienna, Max Perutz Labs, University of Vienna, Medical University of Vienna, Vienna, Austria, Faculty of Computer Science, University of Vienna, Vienna, AustriaJuttaKolletR&D Department, Miltenyi Biotec B.V. & Co. KG, Bergisch Gladbach, Germany10.21105/joss.04949https://doi.org/10.5281/zenodo.7434875Pythonhttps://joss.theoj.org/papers/10.21105/joss.04949.pdfbiology, multiplex, microscopy, annotationtag:joss.theoj.org,2005:Paper/31472022-03-15T10:12:41Z2022-03-15T10:48:13Zmmrefpoints: Projecting long-term marine mammal abundance with bycatchacceptedv0.1.12021-11-02 00:12:18 UTC712022-03-15 10:12:41 UTC720223888MargaretC.SipleResource Assessment and Conservation Engineering Division, Alaska Fisheries Science Center, National Oceanic and Atmospheric Administration, Seattle, WA, 98115, USA0000-0002-4260-9856AndréE.PuntSchool of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat St, Seattle, WA 981150000-0001-8489-2488TessaB.FrancisPuget Sound Institute, University of Washington Tacoma, 326 East D Street, Tacoma, WA 98421, USA0000-0002-3383-5392PhilipS.HammondSea Mammal Research Unit, Scottish Oceans Institute, University of St Andrews, Fife KY16 8LB, UK0000-0002-2381-8302DennisHeinemannU.S. Marine Mammal Commission, 4340 East-West Hwy, Rm 700, Bethesda, MD 20814, USA0000-0002-1434-2445KristyJ.LongOffice of Protected Resources, NOAA's National Marine Fisheries Service, Silver Spring, MD 20910, USA0000-0001-6970-0935JeffreyMooreProtected Resources Division, NOAA SWFSC, La Jolla, CA 92037, USA0000-0003-3715-7442MaritzaSepúlvedaFacultad de Ciencias, Universidad de Valparaíso, Gran Bretaña 1111, Playa Ancha, Valparaíso, Chile0000-0002-1403-176XRandallR.ReevesOkapi Wildlife Associates, Hudson, Quebec, Canada0000-0002-6512-6507GuðjónMárSigurðssonMarine and Freshwater Research Institute, Skúlagata 4, 121, Reykjavík, Iceland0000-0001-9390-6693GísliVíkingssonMarine and Freshwater Research Institute, Skúlagata 4, 121, Reykjavík, Iceland0000-0002-4501-193XPaulR.WadeMarine Mammal Laboratory, NOAA AFSC, Seattle, WA, 98115-6349, USA0000-0003-2428-9323RobWilliamsOceans Initiative, 117 E. Louisa Street No. 135. Seattle, WA 98102, USA0000-0001-7496-453XAlexandreN.ZerbiniCascadia Research Collective, 218 ½ 4th Ave W, Olympia, WA, 98501, USA0000-0002-9776-660510.21105/joss.03888https://doi.org/10.5281/zenodo.6338110Rhttps://joss.theoj.org/papers/10.21105/joss.03888.pdfShiny, marine mammal bycatchtag:joss.theoj.org,2005:Paper/31142021-12-13T17:08:35Z2021-12-21T10:36:39ZflowTorch - a Python library for analysis and reduced-order modeling of fluid flowsacceptedv1.02021-10-18 13:47:35 UTC682021-12-13 17:08:35 UTC620213860AndreWeinerTechnische Universität Braunschweig, Institute of Fluid Mechanics, Flow Modeling and Control Group0000-0001-5617-1560RichardSemaanTechnische Universität Braunschweig, Institute of Fluid Mechanics, Flow Modeling and Control Group0000-0002-3219-054510.21105/joss.03860https://doi.org/10.5281/zenodo.5770244Python, C++https://joss.theoj.org/papers/10.21105/joss.03860.pdfPyTorch, fluid flows, reduced-order modeling, modal analysistag:joss.theoj.org,2005:Paper/23612021-04-21T06:16:21Z2021-04-22T00:02:25ZGeophysicalFlows.jl: Solvers for geophysical fluid dynamics problems in periodic domains on CPUs & GPUsacceptedv0.11.32021-01-29 21:35:44 UTC602021-04-21 06:16:21 UTC620213053NavidC.ConstantinouAustralian National University, ARC Centre of Excellence for Climate Extremes0000-0002-8149-4094GregoryLeClaireWagnerMassachussetts Institute of Technology0000-0001-5317-2445LiaSiegelmanUniversity of California San Diego0000-0003-3330-082XBrodieC.PearsonOregon State University0000-0002-0202-0481AndréPalóczyUniversity of Oslo0000-0001-8231-829810.21105/joss.03053https://doi.org/10.5281/zenodo.4695260Juliahttps://joss.theoj.org/papers/10.21105/joss.03053.pdfgeophysical fluid dynamics, computational fluid dynamics, Fourier methods, pseudospectral, gputag:joss.theoj.org,2005:Paper/19292020-10-17T15:27:38Z2021-02-15T11:30:10ZDARE Platform: a Developer-Friendly and Self-Optimising Workflows-as-a-Service Framework for e-Science on the Cloudaccepted3.42020-08-05 14:33:56 UTC542020-10-17 15:27:38 UTC520202664IraklisA.KlampanosNational Centre for Scientific Research “Demokritos”, Greece0000-0003-0478-4300ChrysoulaThemeliNational Centre for Scientific Research “Demokritos”, Greece0000-0002-6759-4136AlessandroSpinusoKoninklijk Nederlands Meteorologisch Instituut, the NetherlandsRosaFilgueiraThe University of Edinburgh, UKMalcolmAtkinsonThe University of Edinburgh, UKAndréGemündFraunhofer-Institut für Algorithmen und Wissenschaftliches Rechnen (SCAI), GermanyVangelisKarkaletsisNational Centre for Scientific Research “Demokritos”, Greece10.21105/joss.02664https://doi.org/10.5281/zenodo.4095463Ruby, Smarty, Python, JavaScripthttps://joss.theoj.org/papers/10.21105/joss.02664.pdfCWL, Worfklows-as-a-Service, Kubernetes, Cloud, e-infrastructures