tag:joss.theoj.org,2005:/papers/tagged/Mode%20SJournal of Open Source Software2024-03-24T14:42:39ZJournal of Open Source Softwarehttps://joss.theoj.orgtag: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/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/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/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/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 Computingtag:joss.theoj.org,2005:Paper/47752024-02-23T15:40:17Z2024-02-24T00:03:16Zstemflow: A Python Package for Adaptive Spatio-Temporal Exploratory Modelacceptedv1.0.02023-09-21 07:39:41 UTC942024-02-23 15:40:17 UTC920246158YangkangChenKey Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China, University of Chinese Academy of Sciences, Beijing, ChinaZhongruGuKey Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China, Cardiff University-Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, Beijing, ChinaXiangjiangZhanKey Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China, University of Chinese Academy of Sciences, Beijing, China, Cardiff University-Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, Beijing, China, Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China10.21105/joss.06158https://doi.org/10.6084/m9.figshare.24669132Pythonhttps://joss.theoj.org/papers/10.21105/joss.06158.pdfecology, spatio-temporal big data, citizen science, modeling, seasonal migrationtag:joss.theoj.org,2005:Paper/43002024-02-21T08:51:15Z2024-02-23T09:04:14ZReducing the efforts to create reproducible analysis code with FieldTripacceptedhttps://github.com/fieldtrip/fieldtrip/commit/9cfc0a7e7b7871a1d9938552ce60041c59f3a5532023-03-10 17:12:47 UTC942024-02-21 08:51:15 UTC920245566MatsW.j.van EsDonders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen, The Netherlands, Oxford Centre for Human Brain Activity, Department of Psychiatry, University of Oxford, United Kingdom, Wellcome Centre for Integrative Neuroimaging, University of Oxford, Oxford, United Kingdom0000-0002-7133-509XEelkeSpaakDonders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen, The Netherlands0000-0002-2018-3364Jan-MathijsSchoffelenDonders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen, The Netherlands0000-0003-0923-6610RobertOostenveldDonders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen, The Netherlands, NatMEG, Karolinska Institutet, Stockholm, Sweden0000-0002-1974-129310.21105/joss.05566https://doi.org/10.5281/zenodo.10495308MATLAB, Mathematicahttps://joss.theoj.org/papers/10.21105/joss.05566.pdfFieldTrip Toolbox, reproducibility, analysis pipeline, open science, MEG, EEGtag:joss.theoj.org,2005:Paper/49992024-02-15T18:47:42Z2024-02-19T16:12:18ZgrowR: R Implementation of the Vegetation Model ModVegeacceptedv1.2.02023-12-15 07:54:47 UTC942024-02-15 18:47:42 UTC920246260KevinP.KramerAgroscope, Climate and Agriculture Group, Reckenholzstrasse 191, CH-8046 Zürich, Switzerland0000-0001-5523-6924PierluigiCalancaAgroscope, Climate and Agriculture Group, Reckenholzstrasse 191, CH-8046 Zürich, Switzerland0000-0003-3113-288510.21105/joss.06260https://doi.org/10.5281/zenodo.10658193Rhttps://joss.theoj.org/papers/10.21105/joss.06260.pdfagronomy, grasslands, agroecology, modellingtag:joss.theoj.org,2005:Paper/46092024-02-05T20:21:25Z2024-02-06T00:00:57Zprospect: an R package to link leaf optical properties with their chemical and structural properties with the leaf model PROSPECTacceptedv1.3.02023-07-17 16:12:52 UTC942024-02-05 20:21:25 UTC920246027Jean-BaptisteFéretTETIS, INRAE, AgroParisTech, CIRAD, CNRS, Université Montpellier, Montpellier, France0000-0002-0151-1334Floriande BoissieuTETIS, INRAE, AgroParisTech, CIRAD, CNRS, Université Montpellier, Montpellier, France0000-0002-2185-995210.21105/joss.06027https://doi.org/10.5281/zenodo.10480410Rhttps://joss.theoj.org/papers/10.21105/joss.06027.pdfleaf spectroscopy, vegetation biophysical properties, remote sensing, physical modeling, iterative optimizationtag: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 coupling