tag:joss.theoj.org,2005:/papers/tagged/3DJournal of Open Source Software2024-03-04T15:38:25ZJournal of Open Source Softwarehttps://joss.theoj.orgtag:joss.theoj.org,2005:Paper/48272024-03-04T15:38:25Z2024-03-05T01:12:22Z$hp\mathrm{3D}$: A Scalable MPI/OpenMP $hp$-Adaptive Finite Element Software Library for Complex Multiphysics Applicationsacceptedv1.0-beta2023-10-02 22:48:04 UTC952024-03-04 15:38:25 UTC920245946StefanHennekingOden Institute, The University of Texas at Austin, USA0000-0003-2177-8519SocratisPetridesLawrence Livermore National Laboratory, USA0000-0002-1284-5495FedericoFuentesInstitute for Mathematical and Computational Engineering, Pontificia Universidad Católica de Chile, Chile0000-0002-4039-082XJacobBadgerOden Institute, The University of Texas at Austin, USA0000-0001-6482-105XLeszekDemkowiczOden Institute, The University of Texas at Austin, USA0000-0001-7839-803710.21105/joss.05946https://doi.org/10.5281/zenodo.10763375Perl, Pythonhttps://joss.theoj.org/papers/10.21105/joss.05946.pdffinite element, hp-adaptivity, DPG methodtag:joss.theoj.org,2005:Paper/47452024-03-03T08:56:11Z2024-03-09T08:34:29ZDICaugment: A Python Package for 3D Medical Imaging Augmentationacceptedv1.0.02023-09-10 23:37:02 UTC952024-03-03 08:56:11 UTC920246120J.McIntoshDivision of Imaging, Diagnostics, and Software Reliability, CDRH, U.S. Food and Drug Administration, Silver Spring, MD 20993, USA0009-0008-2573-180XQianCaoDivision of Imaging, Diagnostics, and Software Reliability, CDRH, U.S. Food and Drug Administration, Silver Spring, MD 20993, USABerkmanSahinerDivision of Imaging, Diagnostics, and Software Reliability, CDRH, U.S. Food and Drug Administration, Silver Spring, MD 20993, USANicholasPetrickDivision of Imaging, Diagnostics, and Software Reliability, CDRH, U.S. Food and Drug Administration, Silver Spring, MD 20993, USAM.MehdiFarhangiDivision of Imaging, Diagnostics, and Software Reliability, CDRH, U.S. Food and Drug Administration, Silver Spring, MD 20993, USA10.21105/joss.06120https://doi.org/10.5281/zenodo.10738855Pythonhttps://joss.theoj.org/papers/10.21105/joss.06120.pdfAugmentation, Deep Learning, Medical, tag:joss.theoj.org,2005:Paper/48132024-02-27T21:24:38Z2024-03-22T14:09:24ZDeepRank2: Mining 3D Protein Structures with Geometric Deep Learningacceptedv2.1.02023-09-22 15:36:51 UTC942024-02-27 21:24:38 UTC920245983GiuliaCrocioniNetherlands eScience Center, Amsterdam, The Netherlands0000-0002-0823-0121DaniL.BodorNetherlands eScience Center, Amsterdam, The Netherlands0000-0003-2109-2349CoosBaakmanThe Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, The Netherlands0000-0003-4317-1566FarzanehM.PariziThe Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, The Netherlands0000-0003-4230-7492Daniel-T.RademakerThe Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, The Netherlands0000-0003-1959-1317GayatriRamakrishnanThe Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, The Netherlands0000-0001-8203-2783SvenA.van der BurgNetherlands eScience Center, Amsterdam, The Netherlands0000-0003-1250-6968DarioF.MarzellaThe Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, The Netherlands0000-0002-0043-3055JoãoM.c.TeixeiraIndependent Researcher0000-0002-9113-0622LiC.XueThe Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, The Netherlands0000-0002-2613-538X10.21105/joss.05983https://doi.org/10.5281/zenodo.10566809Python, Jupyter Notebookhttps://joss.theoj.org/papers/10.21105/joss.05983.pdfPyTorch, structural biology, geometric deep learning, 3D protein structures, protein-protein interfaces, single-residue variants, graph neural networks, convolutional neural networks, DeepRanktag:joss.theoj.org,2005:Paper/45862024-01-16T15:49:05Z2024-01-19T17:33:56ZAmbit – A FEniCS-based cardiovascular multi-physics solveraccepteddevelopment2023-07-07 14:32:49 UTC932024-01-16 15:49:05 UTC920245744MarcHirschvogelDepartment of Biomedical Engineering, School of Biomedical Engineering & Imaging Sciences, King's College London, London, United Kingdom, MOX, Dipartimento di Matematica, Politecnico di Milano, Milan, Italy0000-0002-4575-912010.21105/joss.05744https://doi.org/10.5281/zenodo.10501275Python, Gnuplothttps://joss.theoj.org/papers/10.21105/joss.05744.pdfcardiovascular mechanics, finite strain solid mechanics, nonlinear elastodynamics, fluid dynamics, 0D lumped models, fluid-solid interaction, fsi, multi-physics couplingtag:joss.theoj.org,2005:Paper/36092023-06-28T15:48:02Z2023-06-29T00:01:31ZHallThruster.jl: a Julia package for 1D Hall thruster discharge simulationacceptedv0.1.02022-05-17 20:47:49 UTC862023-06-28 15:48:02 UTC820234672ThomasMarksPlasmadynamics and Electric Propulsion Laboratory, University of Michigan, Ann Arbor, USA0000-0003-3614-6127PaulSchedlerETH Zurich, Zurich, SwitzerlandBenjaminJornsPlasmadynamics and Electric Propulsion Laboratory, University of Michigan, Ann Arbor, USA0000-0001-9296-204410.21105/joss.04672https://doi.org/10.5281/zenodo.8066246Juliahttps://joss.theoj.org/papers/10.21105/joss.04672.pdfPlasma physics, Low temperature magnetized plasma, CFD, Hall Thruster, Electric Propulsiontag:joss.theoj.org,2005:Paper/40002023-05-18T13:10:37Z2023-05-30T08:52:39ZPyBullet Industrial: A process-aware robot simulationacceptedv1.0.02022-11-11 15:27:01 UTC852023-05-18 13:10:37 UTC820235174JanBaumgärtnerwbk Institute of Production Science0000-0002-7825-3476MalteHansjostenwbk Institute of Production ScienceDominikSchönhofenIndependent ResearcherProf.Dr.-Ing. JürgenFleischerwbk Institute of Production Science0000-0003-0961-767510.21105/joss.05174https://doi.org/10.5281/zenodo.7833292https://joss.theoj.org/papers/10.21105/joss.05174.pdfPython, robotics, simulation, milling, force calculation, 3D printing, production processestag:joss.theoj.org,2005:Paper/33352023-04-21T16:59:33Z2023-04-22T00:02:29ZFEM_2D: A Rust Package for 2D Finite Element Method Computations with Extensive Support for hp-refinementaccepted0.1.02022-02-13 23:19:40 UTC842023-04-21 16:59:33 UTC820234172JeremiahCorradoDepartment of Electrical and Computer Engineering, Colorado State University, USA0000-0003-2688-0600JakeJ.HarmonDepartment of Electrical and Computer Engineering, Colorado State University, USAMilanM.IlicDepartment of Electrical and Computer Engineering, Colorado State University, USA, School of Electrical Engineering, University of Belgrade, SerbiaBranislavM.NotarošDepartment of Electrical and Computer Engineering, Colorado State University, USA10.21105/joss.04172https://doi.org/10.5281/zenodo.7849878Rusthttps://joss.theoj.org/papers/10.21105/joss.04172.pdfFEM, CEM, hp-refinement, PDE Solverstag:joss.theoj.org,2005:Paper/42072023-04-11T14:04:20Z2023-04-12T00:02:56ZRegl-Scatterplot: A Scalable Interactive JavaScript-based Scatter Plot Libraryacceptedv1.5.12023-02-15 02:21:06 UTC842023-04-11 14:04:20 UTC820235275FritzLekschasIndependent Researcher, USA0000-0001-8432-483510.21105/joss.05275https://doi.org/10.5281/zenodo.7796642JavaScript, GLSLhttps://joss.theoj.org/papers/10.21105/joss.05275.pdfscatter plot, 2D scatter, interactive data visualization, embedding plot, WebGLtag:joss.theoj.org,2005:Paper/39612023-01-30T10:25:42Z2023-01-31T12:33:59ZFijiRelax: Fast and noise-corrected estimation of MRI relaxation maps in 3D + tacceptedv4.0.22022-10-14 14:29:38 UTC812023-01-30 10:25:42 UTC820234981RomainFernandezCIRAD, UMR AGAP Institut, F-34398 Montpellier, France, AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France.0000-0003-3670-044XCedricMoisyIFV, French Institute of Vine and Wine, UMT Géno-Vigne, UMR AGAP, F-34398 Montpellier, France.0000-0003-4637-471310.21105/joss.04981https://doi.org/10.5281/zenodo.7554691Java, MATLAB, Pythonhttps://joss.theoj.org/papers/10.21105/joss.04981.pdfFiji, Image analysis, MRI, Relaxometry, Phenotypingtag:joss.theoj.org,2005:Paper/34052022-09-13T12:03:32Z2022-09-13T12:03:36ZDuoDIC: 3D Digital Image Correlation in MATLABacceptedv1.0.02022-03-01 12:05:28 UTC742022-09-13 12:03:32 UTC720224279DanaSolavFaculty of Mechanical Engineering, Technion, Haifa, Israel0000-0003-3215-0401AsafSilversteinFaculty of Mechanical Engineering, Technion, Haifa, Israel10.21105/joss.04279https://doi.org/10.5281/zenodo.6673060MATLAB, Java, C++https://joss.theoj.org/papers/10.21105/joss.04279.pdfdigital image correlation, material testing, full-field strain, full-field deformations, Ncorr, Stereo camera calibration