tag:joss.theoj.org,2005:/papers/tagged/softwareJournal 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/50422024-02-09T13:51:24Z2024-02-10T00:01:17Zelsa: an elegant framework for tomographic reconstructionaccepted0.8.02023-12-20 14:16:50 UTC942024-02-09 13:51:24 UTC920246174DavidFrankDepartment of Computer Science, TUM School of Computation, Information and Technology, Technical University of Munich, Munich, Germany, Munich Institute of Biomedical Engineering, Technical University of Munich, Munich, Germany0009-0006-4989-2144JonasJeltenDepartment of Computer Science, TUM School of Computation, Information and Technology, Technical University of Munich, Munich, Germany, Munich Institute of Biomedical Engineering, Technical University of Munich, Munich, Germany0000-0002-5167-2419TobiasLasserDepartment of Computer Science, TUM School of Computation, Information and Technology, Technical University of Munich, Munich, Germany, Munich Institute of Biomedical Engineering, Technical University of Munich, Munich, Germany0000-0001-5669-920X10.21105/joss.06174https://doi.org/10.5281/zenodo.10609174Python, C++, JavaScripthttps://joss.theoj.org/papers/10.21105/joss.06174.pdfComputed Tomography, X-ray Computed Tomography, Tomography, Tomographic Reconstruction, Inverse Problems, Software Frameworktag: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/45592024-01-24T16:16:35Z2024-01-25T15:27:07ZSonoUno development: a User-Centered Sonification software for data analysisacceptedv3.12023-06-22 22:35:46 UTC932024-01-24 16:16:35 UTC920245819JohannaCasadoInstituto en Tecnologías de Detección y Astropartículas (CNEA, CONICET, UNSAM), Mendoza, Argentina, Instituto de Bioingeniería, Facultad de Ingeniería, Universidad de Mendoza, Argentina0000-0001-9528-5034Gonzalode la VegaIndependent Researcher, ArgentinaBeatrizGarcíaInstituto en Tecnologías de Detección y Astropartículas (CNEA, CONICET, UNSAM), Mendoza, Argentina, Universidad Tecnológica Nacional - Regional Mendoza, Argentina0000-0003-0919-273410.21105/joss.05819https://doi.org/10.5281/zenodo.10303871Pythonhttps://joss.theoj.org/papers/10.21105/joss.05819.pdfsonification, inclusion, astrophysics, open source, user-centered design, graphic user interfacetag:joss.theoj.org,2005:Paper/44452024-01-23T12:00:48Z2024-01-24T00:01:21ZFoundry-ML - Software and Services to Simplify Access to Machine Learning Datasets in Materials Scienceacceptedv0.5.12023-04-21 18:46:52 UTC932024-01-23 12:00:48 UTC920245467KjSchmidtGlobus, University of Chicago, Chicago, IL, United States of America, Data Science and Learning Division, Argonne National Laboratory, Lemont, IL, United States of America0000-0002-9373-0058AristanaScourtasGlobus, University of Chicago, Chicago, IL, United States of America, Data Science and Learning Division, Argonne National Laboratory, Lemont, IL, United States of America0000-0002-3917-605XLoganWardData Science and Learning Division, Argonne National Laboratory, Lemont, IL, United States of America0000-0002-1323-5939SteveWangenData Science Institute, University of Wisconsin-Madison, Madison, WI, United States of AmericaMarcusSchwartingDepartment of Computer Science, University of Chicago, Chicago, IL, United States of America0000-0001-6817-7265IsaacDarlingDepartment of Computer Science, University of Chicago, Chicago, IL, United States of AmericaEthanTrueloveDepartment of Computer Science, University of Chicago, Chicago, IL, United States of AmericaAaditAmbadkarGlobus, University of Chicago, Chicago, IL, United States of AmericaRibhavBoseGlobus, University of Chicago, Chicago, IL, United States of AmericaZoaKatokGlobus, University of Chicago, Chicago, IL, United States of AmericaJingruiWeiDepartment of Materials Science and Engineering, University of Wisconsin-Madison, Madison, WI, United States of AmericaXiangguoLiDepartment of Materials Science and Engineering, University of Wisconsin-Madison, Madison, WI, United States of AmericaRyanJacobsDepartment of Materials Science and Engineering, University of Wisconsin-Madison, Madison, WI, United States of America0000-0003-2229-6730LaneSchultzDepartment of Materials Science and Engineering, University of Wisconsin-Madison, Madison, WI, United States of AmericaDoyeonKimDepartment of Materials Science and Engineering, University of Wisconsin-Madison, Madison, WI, United States of AmericaMichaelFerrisDepartment of Computer Science, University of Wisconsin-Madison, Madison, WI, United States of America0000-0002-7652-6776PaulM.VoylesDepartment of Materials Science and Engineering, University of Wisconsin-Madison, Madison, WI, United States of America0000-0001-9438-4284DaneMorganDepartment of Materials Science and Engineering, University of Wisconsin-Madison, Madison, WI, United States of America0000-0002-4911-0046IanFosterGlobus, University of Chicago, Chicago, IL, United States of America, Data Science and Learning Division, Argonne National Laboratory, Lemont, IL, United States of America, Department of Computer Science, University of Chicago, Chicago, IL, United States of America0000-0003-2129-5269BenBlaiszikGlobus, University of Chicago, Chicago, IL, United States of America, Data Science and Learning Division, Argonne National Laboratory, Lemont, IL, United States of America0000-0002-5326-490210.21105/joss.05467https://doi.org/10.5281/zenodo.10494644Pythonhttps://joss.theoj.org/papers/10.21105/joss.05467.pdfMachine Learning, Artificial Intelligence, Materials Science, Datatag:joss.theoj.org,2005:Paper/46862024-01-22T16:32:03Z2024-01-23T00:01:01ZThe Kestrel software for simulations of morphodynamic Earth-surface flowsaccepted1.02023-08-09 17:30:12 UTC932024-01-22 16:32:03 UTC920246079JakeLanghamSchool of Mathematics, Fry Building, University of Bristol, Bristol, BS8 1UG, UK0000-0001-9857-7016MarkJ.WoodhouseSchool of Earth Sciences, Wills Memorial Building, University of Bristol, Bristol, BS8 1RJ, UK0000-0002-2198-679110.21105/joss.06079https://doi.org/10.5281/zenodo.10477693M4, Fortran, C++https://joss.theoj.org/papers/10.21105/joss.06079.pdfgeophysics, shallow water, debris flow, morphodynamicstag:joss.theoj.org,2005:Paper/45402024-01-12T22:11:20Z2024-01-15T11:54:18Zcellanneal: A user-friendly deconvolution software for transcriptomics dataacceptedv1.0.02023-06-12 17:35:47 UTC932024-01-12 22:11:20 UTC920245610LisaBuchauerDepartment of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel, Department of Infectious Diseases and Respiratory Medicine, Charité-Universitätsmedizin Berlin, Berlin, Germany0000-0002-4722-8390ShalevItzkovitzDepartment of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel0000-0003-0685-252210.21105/joss.05610https://doi.org/10.5281/zenodo.10405043Pythonhttps://joss.theoj.org/papers/10.21105/joss.05610.pdfbioinformatics, computational biology, mixture deconvolution, bulk deconvolution, transcriptomics, RNA sequencing, omics methodstag:joss.theoj.org,2005:Paper/47132024-01-11T17:22:56Z2024-01-12T00:01:07ZLIBSsa: an open source software for analyzing LIBS spectraacceptedv2.1.02023-08-21 20:15:54 UTC932024-01-11 17:22:56 UTC920245961KleydsonStenioDepartment of Biotechnology, Federal University of São Carlos, São Carlos, SP 13563-905, Brazil, Embrapa Instrumentation, São Carlos, SP 13560-970, Brazil0000-0002-1407-9712DéboraMarcondes Bastos PereiraMiloriEmbrapa Instrumentation, São Carlos, SP 13560-970, Brazil0000-0003-1253-717410.21105/joss.05961https://doi.org/10.5281/zenodo.10447382Pythonhttps://joss.theoj.org/papers/10.21105/joss.05961.pdfLIBS, spectroscopy, modeling, automationtag:joss.theoj.org,2005:Paper/47162023-12-15T17:51:50Z2023-12-16T20:57:44ZHNN-core: A Python software for cellular and circuit-level interpretation of human MEG/EEGaccepted0.32023-08-23 18:15:30 UTC922023-12-15 17:51:50 UTC820235848MainakJasAthinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Boston, MA, USA0000-0002-3199-9027RyanThorpeDepartment of Neuroscience, Brown University, Providence, RI, USA, Robert J. and Nancy D. Carney Institute for Brain Science, Brown University, Providence, RI, USA0000-0003-2491-8599NicholasTolleyDepartment of Neuroscience, Brown University, Providence, RI, USA, Robert J. and Nancy D. Carney Institute for Brain Science, Brown University, Providence, RI, USA0000-0003-0358-0074ChristopherBaileyDepartment of Clinical Medicine, Aarhus University, Aarhus, Denmark0000-0003-3318-3344StevenBrandtDepartment of Neuroscience, Brown University, Providence, RI, USA, Robert J. and Nancy D. Carney Institute for Brain Science, Brown University, Providence, RI, USABlakeCaldwellBassett Medical Center, Cooperstown, NY, USA0000-0002-6882-6998HuziChengDepartment of Psychological and Brain Sciences, Indiana University Bloomington, Bloomington, IN, USADylanDanielsRobert J. and Nancy D. Carney Institute for Brain Science, Brown University, Providence, RI, USA0009-0008-1958-353XCarolinaFernandezPujolDepartment of Biomedical Engineering, University of Miami, Coral Gables, FL, USA0009-0003-0611-1270MostafaKhalilDepartment of Psychiatry and Behavioral Health, Penn State Milton S. Hershey Medical Center, Penn State College of Medicine, Hershey, PA, USASamikaKanekarWarren Alpert Medical, Brown University, Providence, RI0000-0002-6111-4461CarmenKohlRobert J. and Nancy D. Carney Institute for Brain Science, Brown University, Providence, RI, USA0000-0001-7585-595XOrsolyaKolozsváriDepartment of Psychology, University of Jyväskylä, Jyväskylä, Finland, Jyväskylä Centre for Interdisciplinary Brain Research, University of Jyväskylä, Jyväskylä, Finland0000-0002-1619-6314KaisuLankinenAthinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Boston, MA, USA, Department of Radiology, Harvard Medical School, Boston, MA, USA0000-0003-2210-2385KennethLoiRobert J. and Nancy D. Carney Institute for Brain Science, Brown University, Providence, RI, USA, Department of Molecular and Cell Biology; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USASamNeymotinCenter for Biomedical Imaging and Neuromodulation, Nathan S. Kline Institute for Psychiatric Research, Orangeburg, NY, USA, Department of Psychiatry, New York University Grossman School of Medicine, New York, NY, USA0000-0003-3646-5195RajatPartaniDepartment of Computer Science and Engineering, National Institute of Technology Karnataka, Karnataka, India0000-0002-6863-7046MattanPelahRobert J. and Nancy D. Carney Institute for Brain Science, Brown University, Providence, RI, USA, Florida State University, Tallahassee, FL, USAAlexRockhillDepartment of Human Physiology, University of Oregon, Eugene, OR, USA0000-0003-3868-7453MohamedSherifDepartment of Psychiatry and Human Behavior, Brown University, Providence, RI, USA, Rhode Island Hospital, Providence, RI, USA0000-0002-8951-1645MattiHamalainenDepartment of Neuroscience and Biomedical Engineering, Aalto University, Espoo, Finland0000-0001-6841-112XStephanieJonesDepartment of Neuroscience, Brown University, Providence, RI, USA, Robert J. and Nancy D. Carney Institute for Brain Science, Brown University, Providence, RI, USA0000-0001-6760-530110.21105/joss.05848https://doi.org/10.5281/zenodo.10289164Python, Jupyter Notebook, AMPLhttps://joss.theoj.org/papers/10.21105/joss.05848.pdfneuroscience, EEG, MEG, modeling, neocortextag:joss.theoj.org,2005:Paper/38572023-11-20T17:37:21Z2023-11-25T01:16:15ZSoftware Design and User Interface of ESPnet-SE++: Speech Enhancement for Robust Speech Processingacceptedv.2022072022-09-07 13:11:51 UTC912023-11-20 17:37:21 UTC820235403Yen-JuLuJohns Hopkins University, USA0000-0001-8400-4188XuankaiChangCarnegie Mellon University, USA0000-0002-5221-5412ChendaLiShanghai Jiao Tong University, Shanghai0000-0003-0299-9914WangyouZhangShanghai Jiao Tong University, Shanghai0000-0003-4500-3515SamueleCornellCarnegie Mellon University, USA, Universita\` Politecnica delle Marche, Italy0000-0002-5358-1844ZhaohengNiMeta AI, USAYoshikiMasuyamaCarnegie Mellon University, USA, Tokyo Metropolitan University, JapanBrianYanCarnegie Mellon University, USARobinScheiblerLINE Corporation, Japan0000-0002-5205-8365Zhong-QiuWangCarnegie Mellon University, USA0000-0002-4204-9430YuTsaoAcademia Sinica, Taipei0000-0001-6956-0418YanminQianShanghai Jiao Tong University, Shanghai0000-0002-0314-3790ShinjiWatanabeCarnegie Mellon University, USA0000-0002-5970-863110.21105/joss.05403https://doi.org/10.5281/zenodo.10048174Python, Perl, MATLABhttps://joss.theoj.org/papers/10.21105/joss.05403.pdfESPnet, speech processing, speech enhancement