tag:joss.theoj.org,2005:/papers/tagged/particlesJournal of Open Source Software2024-03-16T22:48:59ZJournal of Open Source Softwarehttps://joss.theoj.orgtag:joss.theoj.org,2005:Paper/46292024-03-16T22:48:59Z2024-03-17T00:00:58ZFeenoX: a cloud-first finite-element(ish) computational engineering toolacceptedv0.32023-07-27 16:01:35 UTC952024-03-16 22:48:59 UTC920245846JeremyThelerSeamplex, Argentina, Instituto Balseiro, Argentina0000-0002-4142-498010.21105/joss.05846https://doi.org/10.5281/zenodo.10819606M4, C, GLSLhttps://joss.theoj.org/papers/10.21105/joss.05846.pdfengineering, partial differential equations, differential algebraic equationstag:joss.theoj.org,2005:Paper/41602024-02-29T19:05:35Z2024-03-01T08:13:27ZDAPPER: Data Assimilation with Python: a Package for Experimental Researchacceptedv1.4.02023-01-10 18:54:31 UTC942024-02-29 19:05:35 UTC920245150PatrickN.RaanesNORCE, Bergen, Norway, NERSC, Bergen, Norway0000-0001-5073-6786YumengChenDepartment of Meteorology and NCEO, University of Reading, Reading, UK0000-0002-2319-6937ColinGrudzienCW3E - Scripps Institution of Oceanography, University of California, San Diego, USA, Department of Mathematics and Statistics, University of Nevada, Reno, USA0000-0002-3084-317810.21105/joss.05150https://doi.org/10.5281/zenodo.10710355Python, Fortranhttps://joss.theoj.org/papers/10.21105/joss.05150.pdfdata-assimilation, state-estimation, bayesian-filter, kalman-filtering, enkf, particle-filter, chaos, bayesian-methodstag:joss.theoj.org,2005:Paper/46722023-12-19T23:06:00Z2023-12-21T10:58:00ZSeaduck: A python package for Eulerian and Lagrangian interpolation on ocean datasetsacceptedv0.1.32023-08-02 18:06:07 UTC922023-12-19 23:06:00 UTC820235967WenruiJiangDepartment of Earth and Planetary Sciences, The Johns Hopkins University0009-0000-7319-9469ThomasW. n.HaineDepartment of Earth and Planetary Sciences, The Johns Hopkins University0000-0001-8231-2419MattiaAlmansiB-Open Solutions s.r.l, Italy0000-0001-6849-364710.21105/joss.05967https://doi.org/10.5281/zenodo.10183123Pythonhttps://joss.theoj.org/papers/10.21105/joss.05967.pdfoceanography, interpolation, Lagarangian particletag:joss.theoj.org,2005:Paper/47102023-11-21T14:35:15Z2023-11-22T00:01:03ZPhasik: a Python package to identify system states in partially temporal networksacceptedv1.3.22023-08-19 19:13:03 UTC912023-11-21 14:35:15 UTC820235872MaximeLucasCENTAI Institute, Turin, Italy0000-0001-8087-2981AlexTownsend-TeagueDahlem Center for Complex Quantum Systems, Freie Universitat Berlin, 14195 Berlin, GermanyMatteoNeriCENTAI Institute, Turin, Italy, Institut de Neurosciences de la Timone UMR 7289, Aix Marseille Université, CNRS, Marseille 13005, France0009-0007-0998-552XSimonePoettoCENTAI Institute, Turin, Italy, Center for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Toruń, PolandArthurMorrisTheory of Condensed Matter Group, Cavendish Laboratory, University of Cambridge, J. J. Thomson Avenue, Cambridge CB3 0HE, United KingdomBiancaHabermannAix Marseille University, CNRS, IBDM UMR 7288, Turing Center for Living Systems, Marseille, France0000-0002-2457-7504LaurentTichitAix Marseille University, CNRS, I2M UMR 7373, Turing Center for Living Systems, Marseille, France0000-0002-8350-144610.21105/joss.05872https://doi.org/10.5281/zenodo.10113244Jupyter Notebook, Pythonhttps://joss.theoj.org/papers/10.21105/joss.05872.pdftemporal networkstag:joss.theoj.org,2005:Paper/40302023-10-02T07:49:41Z2023-10-04T15:51:32ZSMITE: Single Molecule Imaging Toolbox Extraordinaire (MATLAB)acceptedv0.2.02022-11-28 23:42:12 UTC902023-10-02 07:49:41 UTC820235563DavidJ.SchodtDepartment of Physics and Astronomy, University of New Mexico, Albuquerque, United States of America0000-0002-8986-2736MichaelJ.WesterDepartment of Physics and Astronomy, University of New Mexico, Albuquerque, United States of America, Department of Mathematics and Statistics, Albuquerque, University of New Mexico, United States of America0000-0002-3520-7605MohamadrezaFazelDepartment of Physics and Astronomy, University of New Mexico, Albuquerque, United States of America0000-0002-6215-1336SajjadKhanDepartment of Physics and Astronomy, University of New Mexico, Albuquerque, United States of America0000-0002-6910-5199HaniehMazloom-FarsibafDepartment of Physics and Astronomy, University of New Mexico, Albuquerque, United States of America0000-0002-2571-0418SandeepPallikkuthDepartment of Physics and Astronomy, University of New Mexico, Albuquerque, United States of America0009-0003-0400-6389MarjoleinB. m.MeddensDepartment of Physics and Astronomy, University of New Mexico, Albuquerque, United States of America0000-0002-9965-1342FarzinFarzamDepartment of Physics and Astronomy, University of New Mexico, Albuquerque, United States of America0000-0002-9939-1923EricA.BurnsDepartment of Pathology, University of New Mexico Health Sciences Center, Albuquerque, United States of America0000-0002-1625-2400WilliamK.KanagyDepartment of Pathology, University of New Mexico Health Sciences Center, Albuquerque, United States of America0000-0002-5756-9965DerekA.RinaldiDepartment of Pathology, University of New Mexico Health Sciences Center, Albuquerque, United States of America0009-0000-8394-3626EltonJhambaDepartment of Pathology, University of New Mexico Health Sciences Center, Albuquerque, United States of America0000-0002-5272-6466ShengLiuDepartment of Physics and Astronomy, University of New Mexico, Albuquerque, United States of America0000-0003-1225-0763PeterK.RelichDepartment of Physics and Astronomy, University of New Mexico, Albuquerque, United States of America0000-0002-6063-6233MarkJ.OlahDepartment of Physics and Astronomy, University of New Mexico, Albuquerque, United States of AmericaStanlyL.SteinbergDepartment of Mathematics and Statistics, Albuquerque, University of New Mexico, United States of AmericaKeithA.LidkeDepartment of Physics and Astronomy, University of New Mexico, Albuquerque, United States of America0000-0002-9328-431810.21105/joss.05563https://doi.org/10.5281/zenodo.8327409MATLAB, Cuda, C++, Chttps://joss.theoj.org/papers/10.21105/joss.05563.pdfsingle molecule localization microscopy (SMLM), single particle tracking (SPT), super resolutiontag:joss.theoj.org,2005:Paper/43562023-09-11T14:49:33Z2023-09-13T15:13:03ZParticlePhaseSpace: A python package for streamlined import, analysis, and export of particle phase space dataacceptedv0.5.02023-03-21 01:30:44 UTC892023-09-11 14:49:33 UTC820235375BrendanWhelanImage-X Institute, School of Health Sciences, University of Sydney0000-0002-2326-0927LeoEsnaultUniv. Bordeaux-CNRS-CEA, Centre Lasers Intenses et Applications, UMR 5107, 33405 Talence, France0000-0002-0795-995710.21105/joss.05375https://doi.org/10.5281/zenodo.8299964https://joss.theoj.org/papers/10.21105/joss.05375.pdfPython, accelerator physics, topas-mc, phase spacetag:joss.theoj.org,2005:Paper/44462023-09-06T21:43:32Z2023-09-07T13:47:17Zxinvert: A Python package for inversion problems in geophysical fluid dynamicsacceptedv0.1.02023-04-21 22:00:51 UTC892023-09-06 21:43:32 UTC820235510Yu-KunQianState Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China0000-0001-5660-761910.21105/joss.05510https://doi.org/10.5281/zenodo.8320324Pythonhttps://joss.theoj.org/papers/10.21105/joss.05510.pdfgeophysics, atmosphere, ocean, geophysical fluid dynamics, steady state problem, second-order partial differential equation, successive over relaxationtag:joss.theoj.org,2005:Paper/40032023-08-25T03:11:09Z2023-08-26T00:01:24ZGNS: A generalizable Graph Neural Network-based simulator for particulate and fluid modelingacceptedv1.0.12022-11-13 22:08:21 UTC882023-08-25 03:11:09 UTC820235025KrishnaKumarAssistant Professor, University of Texas at Austin, Texas, USA0000-0003-2144-5562JosephVantasselAssistant Professor, Virginia Tech, Virginia, USA, Texas Advanced Computing Center, University of Texas at Austin, Texas, USA0000-0002-1601-335410.21105/joss.05025https://doi.org/10.5281/zenodo.8249813Python, Jupyter Notebookhttps://joss.theoj.org/papers/10.21105/joss.05025.pdfmachine learning, simulationtag:joss.theoj.org,2005:Paper/42952023-06-21T19:36:56Z2023-06-22T00:01:24ZSarracen: a Python package for analysis and visualization of smoothed particle hydrodynamics dataacceptedv1.1.02023-03-09 19:28:13 UTC862023-06-21 19:36:56 UTC820235263AndrewHarrisMemorial University of Newfoundland, CanadaTerrenceS.TriccoMemorial University of Newfoundland, Canada0000-0002-6238-909610.21105/joss.05263https://doi.org/10.5281/zenodo.8034448Pythonhttps://joss.theoj.org/papers/10.21105/joss.05263.pdfJupyter Notebook, smoothed particle hydrodynamics, astronomy, astrophysics, data visualization, data sciencetag:joss.theoj.org,2005:Paper/39442023-05-12T12:14:29Z2023-05-13T00:01:21ZGraphNeT: Graph neural networks for neutrino telescope event reconstructionacceptedv0.2.22022-10-06 11:55:25 UTC852023-05-12 12:14:29 UTC820234971AndreasSøgaardNiels Bohr Institute, University of Copenhagen, Denmark0000-0002-0823-056XRasmusF.ØrsøeNiels Bohr Institute, University of Copenhagen, Denmark, Technical University of Munich, Germany0000-0001-8890-4124MortenHolmNiels Bohr Institute, University of Copenhagen, Denmark0000-0003-1383-2810LeonBozianuNiels Bohr Institute, University of Copenhagen, Denmark0000-0002-1243-9980AskeRostedChiba University, Japan0000-0003-2410-400XTroelsC.PetersenNiels Bohr Institute, University of Copenhagen, Denmark0000-0003-0221-3037KaareEndrupIversenNiels Bohr Institute, University of Copenhagen, Denmark0000-0001-6533-4085AndreasHermansenNiels Bohr Institute, University of Copenhagen, Denmark0009-0006-1162-9770TimGuggenmosTechnical University of Munich, GermanyPeterAndresenNiels Bohr Institute, University of Copenhagen, Denmark0009-0008-5759-0490MartinHaMinhTechnical University of Munich, Germany0000-0001-7776-4875LudwigNesteTechnical University of Dortmund, Germany0000-0002-4829-3469MoustHolmesNiels Bohr Institute, University of Copenhagen, Denmark0009-0000-8530-7041AxelPonténUppsala University, Sweden0009-0008-2463-2930KaylaLeonardDeHoltonPennsylvania State University, USA0000-0002-8795-0601PhilippEllerTechnical University of Munich, Germany0000-0001-6354-520910.21105/joss.04971https://doi.org/10.5281/zenodo.7928487Pythonhttps://joss.theoj.org/papers/10.21105/joss.04971.pdfmachine learning, deep learning, neural networks, graph neural networks, astrophysics, particle physics, neutrinos