tag:joss.theoj.org,2005:/papers/tagged/ModalJournal of Open Source Software2024-03-26T05:48:55ZJournal of Open Source Softwarehttps://joss.theoj.orgtag:joss.theoj.org,2005:Paper/49762024-03-26T05:48:55Z2024-03-27T00:01:16ZHofstadterTools: A Python package for analyzing the Hofstadter modelacceptedv1.0.02023-12-02 03:40:46 UTC952024-03-26 05:48:55 UTC920246356BartholomewAndrewsDepartment of Physics, University of California, Berkeley, USA0000-0002-9079-743310.21105/joss.06356https://doi.org/10.5281/zenodo.10809833Pythonhttps://joss.theoj.org/papers/10.21105/joss.06356.pdftheoretical physics, electromagnetism, fractals, quantum physics, topological materials, mathematical physics, topological order, condensed matter physics, quantum Hall effect, band theorytag:joss.theoj.org,2005:Paper/44352024-03-24T14:42:39Z2024-03-25T00:01:12ZViable North Sea (ViNoS): A NetLogo Agent-based Model of German Small-scale Fisheriesaccepted1.0.02023-04-17 14:17:24 UTC952024-03-24 14:42:39 UTC920245731CarstenLemmenHelmholtz-Zentrum Hereon, Institute of Coastal Systems - Modeling and Analysis, Germany, carsten.lemmen@hereon.de0000-0003-3483-6036SaschaHokampUniversität Hamburg, Centre for Earth System Research and Sustainability (CEN), Germany0000-0002-2192-4013SerraÖreyHochschule Bremerhaven, Research Cluster Life Sciences, Bremerhaven, Germany0000-0003-3483-6036JürgenScheffranUniversität Hamburg, Centre for Earth System Research and Sustainability (CEN), Germany0000-0002-7171-306210.21105/joss.05731https://doi.org/10.5281/zenodo.7928199R, Schemehttps://joss.theoj.org/papers/10.21105/joss.05731.pdfNetLogo, Agent-based Model, ABM, North Sea, Fisheries, MuSSeL project, VIABLE, Plaice, Sole, Shrimptag:joss.theoj.org,2005:Paper/47592024-03-20T16:19:58Z2024-03-21T00:23:03ZPywaterflood: Well connectivity analysis through capacitance-resistance modelingacceptedv0.3.12023-09-16 18:42:32 UTC952024-03-20 16:19:58 UTC920246191FrankMalePennsylvania State University, University Park, PA, USA0000-0002-3402-557810.21105/joss.06191https://doi.org/10.5281/zenodo.10815882Python, Rusthttps://joss.theoj.org/papers/10.21105/joss.06191.pdfwell connectivity analysis, waterfloods, CO2 floods, Geothermal energy, multiphase flowtag:joss.theoj.org,2005:Paper/44762024-03-14T17:04:56Z2024-03-15T00:01:19ZWAVI.jl: Ice Sheet Modelling in Juliaaccepted0.0.012023-05-05 08:02:40 UTC952024-03-14 17:04:56 UTC920245584AlexanderT.BradleyBritish Antarctic Survey, Cambridge, UK0000-0001-8381-5317RobertJ.ArthernBritish Antarctic Survey, Cambridge, UK0000-0002-3762-8219DavidT.BettBritish Antarctic Survey, Cambridge, UK0000-0003-3118-9902C.RosieWilliamsBritish Antarctic Survey, Cambridge, UK0000-0002-8131-4946JamesByrneBritish Antarctic Survey, Cambridge, UK0000-0003-3731-237710.21105/joss.05584https://doi.org/10.5281/zenodo.10723504Juliahttps://joss.theoj.org/papers/10.21105/joss.05584.pdfglaciology, ice sheet modelling, ice shelves, Antarctica, Greenland, climatetag:joss.theoj.org,2005:Paper/46892024-03-12T19:13:10Z2024-03-13T00:00:51ZTide Model Driver for MATLABaccepted3.0.02023-08-09 22:26:21 UTC952024-03-12 19:13:10 UTC920246018ChadA.GreeneInstitute for Geophysics, John A. and Katherine G. Jackson School of Geosciences, University of Texas at Austin, Austin, TX, USA0000-0001-6710-6297SvetlanaErofeevaCollege of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, OR, USA0000-0002-4489-7505LauriePadmanEarth and Space Research, Corvallis, OR, USA0000-0003-2010-642XSusanL.HowardEarth and Space Research, Corvallis, OR, USA0000-0002-9183-0178TylerSutterleyUniversity of Washington Applied Physics Laboratory Polar Science Center, Seattle, WA, 98122, USA0000-0002-6964-1194GaryEgbertCollege of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, OR, USA10.21105/joss.06018https://doi.org/10.5281/zenodo.10724881MATLABhttps://joss.theoj.org/papers/10.21105/joss.06018.pdftides, oceanography, TMDtag:joss.theoj.org,2005:Paper/50672024-03-10T12:27:59Z2024-03-12T10:21:48ZProject RACCOON: Automated construction of PDB files for polymers and polymer peptide conjugatesacceptedv1.0.12024-01-10 16:52:37 UTC952024-03-10 12:27:59 UTC920246293MoritzL.ObenauerDepartment of Chemistry, Johannes Gutenberg-University Mainz, Duesbergweg 10-14, D-55128 Mainz, Germany0009-0003-8140-9907KaiN.SpauszusDepartment of Chemistry, Johannes Gutenberg-University Mainz, Duesbergweg 10-14, D-55128 Mainz, Germany0009-0006-0650-2273PolBeseniusDepartment of Chemistry, Johannes Gutenberg-University Mainz, Duesbergweg 10-14, D-55128 Mainz, Germany0000-0001-7478-4459FriederikeSchmidInstitute of Physics, Johannes Gutenberg University, Staudingerweg 9, 55128 Mainz, Germany0000-0002-5536-671810.21105/joss.06293https://doi.org/10.5281/zenodo.10776652Jupyter Notebook, Python, Bikeshedhttps://joss.theoj.org/papers/10.21105/joss.06293.pdfcheminformatics, molecular-dynamics-simulatiom, pdb-files, molecular-modelingtag:joss.theoj.org,2005:Paper/48522024-03-09T21:38:19Z2024-03-11T01:37:29ZHyperNetX: A Python package for modeling complex network data as hypergraphsacceptedv2.0.52023-10-16 19:38:03 UTC952024-03-09 21:38:19 UTC920246016BrendaPraggastisPacific Northwest National Laboratory, USA0000-0003-1344-0497SinanAksoyPacific Northwest National Laboratory, USA0000-0002-3466-3334DustinArendtPacific Northwest National Laboratory, USA0000-0003-2466-199XMarkBonicilloPacific Northwest National Laboratory, USA0009-0003-9764-2180CliffJoslynPacific Northwest National Laboratory, USA0000-0002-5923-5547EmiliePurvinePacific Northwest National Laboratory, USA0000-0003-2069-5594MadelynShapiroPacific Northwest National Laboratory, USA0000-0002-2786-7056JiYoungYunPacific Northwest National Laboratory, USA10.21105/joss.06016https://doi.org/10.5281/zenodo.10795225Pythonhttps://joss.theoj.org/papers/10.21105/joss.06016.pdfhypergraph, network science, simplicial-complexes, knowledge graph, simplicial-homology, s-linegraph, property hypergraphtag:joss.theoj.org,2005:Paper/46832024-03-09T08:42:01Z2024-03-10T00:01:18ZPerMetrics: A Framework of Performance Metrics for Machine Learning Modelsacceptedv1.4.22023-08-08 05:27:41 UTC952024-03-09 08:42:01 UTC920246143NguyenVan ThieuFaculty of Computer Science, Phenikaa University, Yen Nghia, Ha Dong, Hanoi, 12116, Vietnam.0000-0001-9994-874710.21105/joss.06143https://doi.org/10.5281/zenodo.3951205Pythonhttps://joss.theoj.org/papers/10.21105/joss.06143.pdfmodel assessment tools, performance metrics, classification validation metrics, regression evaluation criteria, clustering criterion indices, machine learning metricstag:joss.theoj.org,2005:Paper/48582024-03-06T17:32:25Z2024-03-07T00:00:24Zcalorine: A Python package for constructing and sampling neuroevolution potential modelsacceptedv2.02023-10-21 15:02:27 UTC952024-03-06 17:32:25 UTC920246264EricLindgrenDepartment of Physics, Chalmers University of Technology, Gothenburg 412 96, Sweden0000-0002-8549-6839MagnusRahmDepartment of Physics, Chalmers University of Technology, Gothenburg 412 96, Sweden0000-0002-6777-0371ErikFranssonDepartment of Physics, Chalmers University of Technology, Gothenburg 412 96, Sweden0000-0001-5262-3339FredrikErikssonDepartment of Physics, Chalmers University of Technology, Gothenburg 412 96, Sweden0000-0002-7945-5483NicklasÖsterbackaDepartment of Physics, Chalmers University of Technology, Gothenburg 412 96, Sweden0000-0002-6043-4607ZheyongFanCollege of Physical Science and Technology, Bohai University, Jinzhou 121013, P. R. China0000-0002-2253-8210PaulErhartDepartment of Physics, Chalmers University of Technology, Gothenburg 412 96, Sweden0000-0002-2516-606110.21105/joss.06264https://doi.org/10.5281/zenodo.10723374Python, C++, Jupyter Notebookhttps://joss.theoj.org/papers/10.21105/joss.06264.pdfcondensed matter, machine learning, interatomic potentials, force fields, molecular dynamics, neuroevolution, neural networktag:joss.theoj.org,2005:Paper/44002024-03-05T10:10:26Z2024-03-06T00:00:49ZWorldDynamics.jl: A Julia Package for Developing and Simulating Integrated Assessment Modelsacceptedv0.4.22023-04-13 20:15:11 UTC952024-03-05 10:10:26 UTC920245772PierluigiCrescenziGran Sasso Science Institute, L’Aquila, Italy, COATI, INRIA d’Université Côte d’Azur, Sophia Antipolis, France0000-0001-8789-3195EmanueleNataleCOATI, INRIA d’Université Côte d’Azur, Sophia Antipolis, France0000-0002-8755-3892AuroraRossiCOATI, INRIA d’Université Côte d’Azur, Sophia Antipolis, France0009-0001-3302-0468PauloBrunoSerafimGran Sasso Science Institute, L’Aquila, Italy0000-0002-5980-814910.21105/joss.05772https://doi.org/10.5281/zenodo.10684579Juliahttps://joss.theoj.org/papers/10.21105/joss.05772.pdfIntegrated Assessment Model, Modeling and Simulation, Scientific Computing