tag:joss.theoj.org,2005:/papers/tagged/scienceJournal of Open Source Software2024-03-28T11:28:09ZJournal of Open Source Softwarehttps://joss.theoj.orgtag:joss.theoj.org,2005:Paper/45762024-03-28T11:28:09Z2024-03-28T15:40:29ZsimChef: High-quality data science simulations in Racceptedv0.0.32023-07-03 18:14:27 UTC952024-03-28 11:28:09 UTC920246156JamesDuncanGraduate Group in Biostatistics, University of California, Berkeley, United States of America0000-0003-3297-681XTiffanyTangDepartment of Statistics, University of California, Berkeley, United States of America0000-0002-8079-6867CorrineF.ElliottDepartment of Statistics, University of California, Berkeley, United States of America0000-0001-7935-9945PhilippeBoileauGraduate Group in Biostatistics, University of California, Berkeley, United States of America0000-0002-4850-2507BinYuGraduate Group in Biostatistics, University of California, Berkeley, United States of America, Department of Statistics, University of California, Berkeley, United States of America, Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, United States of America, Center for Computational Biology, University of California, Berkeley, United States of America0000-0002-8888-406010.21105/joss.06156https://doi.org/10.5281/zenodo.10845638R, JavaScripthttps://joss.theoj.org/papers/10.21105/joss.06156.pdfsimulations, data sciencetag: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/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/48972024-02-14T14:57:13Z2024-02-19T16:23:56ZPyTASER: Simulating transient absorption spectroscopy (TAS) for crystals from first principlesacceptedv2.2.02023-10-24 15:23:57 UTC942024-02-14 14:57:13 UTC920245999SavyasanchiAggarwalThomas Young Centre and Department of Materials, Imperial College London, London, United Kingdom, Thomas Young Centre and Department of Chemistry, University College London, London, United Kingdom0009-0007-7128-3465SeánR.KavanaghThomas Young Centre and Department of Materials, Imperial College London, London, United Kingdom, Thomas Young Centre and Department of Chemistry, University College London, London, United Kingdom0000-0003-4577-9647YoungWonWooThomas Young Centre and Department of Materials, Imperial College London, London, United Kingdom, Department of Materials Science and Engineering, Yonsei University, Seoul, KoreaLucasG.VergaThomas Young Centre and Department of Materials, Imperial College London, London, United Kingdom0000-0002-7453-238XAlexM.GanoseDepartment of Chemistry, Imperial College London, London, United Kingdom0000-0002-4486-3321AronWalshThomas Young Centre and Department of Materials, Imperial College London, London, United Kingdom0000-0001-5460-703310.21105/joss.05999https://doi.org/10.5281/zenodo.10634762Pythonhttps://joss.theoj.org/papers/10.21105/joss.05999.pdfmaterials science, first-principles, optics, differential-absorption, spectroscopy, density functional theorytag:joss.theoj.org,2005:Paper/45912024-01-28T18:34:03Z2024-01-29T08:05:01Zmatscipy: materials science at the atomic scale with Pythonaccepted0.8.02023-07-10 11:58:56 UTC932024-01-28 18:34:03 UTC920245668PetrGrigorevAix-Marseille Université, CNRS, CINaM UMR 7325, Campus de Luminy, 13288 Marseille, France0000-0002-6409-9092LucasFrérotDepartment of Microsystems Engineering, University of Freiburg, 79110 Freiburg, Germany0000-0002-4138-1052FraserBirksWarwick Centre for Predictive Modelling, School of Engineering, University of Warwick, Coventry CV4 7AL, United Kingdom0009-0008-9117-0393AdrienGolaDepartment of Microsystems Engineering, University of Freiburg, 79110 Freiburg, Germany, Institute for Applied Materials, Karlsruhe Institute of Technology, Engelbert-Arnold-Straße 4, 76131 Karlsruhe, Germany0000-0002-5102-1931JacekGolebiowskiDepartment of Materials, Imperial College London, London SW7 2AZ, United Kingdom0000-0001-8053-8318JanGrießerDepartment of Microsystems Engineering, University of Freiburg, 79110 Freiburg, Germany0000-0003-2149-6730JohannesL.HörmannDepartment of Microsystems Engineering, University of Freiburg, 79110 Freiburg, Germany, Cluster of Excellence livMatS, Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany0000-0001-5867-695XAndreasKlemenzFraunhofer IWM, MikroTribologie Centrum µTC, Wöhlerstraße 11, 79108 Freiburg, Germany0000-0001-5677-5639GianpietroMorasFraunhofer IWM, MikroTribologie Centrum µTC, Wöhlerstraße 11, 79108 Freiburg, Germany0000-0002-4623-2881WolframG.NöhringDepartment of Microsystems Engineering, University of Freiburg, 79110 Freiburg, Germany0000-0003-4203-755XJonasA.OldenstaedtDepartment of Microsystems Engineering, University of Freiburg, 79110 Freiburg, Germany0000-0002-7475-3019PunitPatelWarwick Centre for Predictive Modelling, School of Engineering, University of Warwick, Coventry CV4 7AL, United KingdomThomasReichenbachFraunhofer IWM, MikroTribologie Centrum µTC, Wöhlerstraße 11, 79108 Freiburg, Germany0000-0001-7477-6248ThomasRockeWarwick Centre for Predictive Modelling, School of Engineering, University of Warwick, Coventry CV4 7AL, United Kingdom0000-0002-4612-9112LakshmiShenoyWarwick Centre for Predictive Modelling, School of Engineering, University of Warwick, Coventry CV4 7AL, United Kingdom0000-0001-5760-3345MichaelWalterCluster of Excellence livMatS, Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany0000-0001-6679-2491SimonWengertFritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195 Berlin, Germany0000-0002-8008-1482LeiZhangEngineering and Technology Institute Groningen, Faculty of Science and Engineering, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands0000-0003-4414-7111JamesR.KermodeWarwick Centre for Predictive Modelling, School of Engineering, University of Warwick, Coventry CV4 7AL, United Kingdom0000-0001-6755-6271LarsPastewkaDepartment of Microsystems Engineering, University of Freiburg, 79110 Freiburg, Germany, Cluster of Excellence livMatS, Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany0000-0001-8351-733610.21105/joss.05668https://doi.org/10.5281/zenodo.10564956C++, C, Meson, Python, Rubyhttps://joss.theoj.org/papers/10.21105/joss.05668.pdfMaterial Science, Atomistic simulationstag:joss.theoj.org,2005:Paper/47702024-01-25T22:35:43Z2024-01-26T10:44:05Zstanscofi and benchscofi: a new standard for drug repurposing by collaborative filteringacceptedv2.0.02023-09-20 18:28:20 UTC932024-01-25 22:35:43 UTC920245973ClémenceRédaDepartment of Systems Biology and Bioinformatics, University of Rostock, Rostock, G-18051, Germany0000-0003-3238-0258Jill-JênnVieSoda Team, Inria Saclay, F-91120 Palaiseau, France0000-0002-9304-2220OlafWolkenhauerDepartment of Systems Biology and Bioinformatics, University of Rostock, Rostock, G-18051, Germany, Leibniz-Institute for Food Systems Biology, Freising, G-85354, Germany, Stellenbosch Institute of Advanced Study, Wallenberg Research Centre, Stellenbosch, SA-7602, South Africa0000-0001-6105-293710.21105/joss.05973https://doi.org/10.5281/zenodo.10561760Pythonhttps://joss.theoj.org/papers/10.21105/joss.05973.pdfdrug repurposing, collaborative filtering, open science, science reproducibilitytag: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/48252024-01-19T21:37:47Z2024-01-20T00:00:44Zpymatgen-analysis-defects: A Python package for analyzing point defects in crystalline materialsacceptedv2023.08.222023-10-02 01:54:09 UTC932024-01-19 21:37:47 UTC920245941Jimmy-XuanShenLawrence Livermore National Laboratory, Livermore, California 94550, United States0000-0002-2743-7531JoelVarleyLawrence Livermore National Laboratory, Livermore, California 94550, United States0000-0002-5384-524810.21105/joss.05941https://doi.org/10.5281/zenodo.6994437Python, Jupyter Notebookhttps://joss.theoj.org/papers/10.21105/joss.05941.pdfpython, materials science, point defects, finite-size corrections, database buildingtag:joss.theoj.org,2005:Paper/47492024-01-15T13:46:58Z2024-01-19T07:49:00Zeasyunfold: A Python package for unfolding electronic band structuresacceptedv0.3.02023-09-12 14:37:55 UTC932024-01-15 13:46:58 UTC920245974BonanZhuDepartment of Chemistry, University College London, London, United Kingdom, Thomas Young Centre, University College London, London, United Kingdom, The Faraday Institution, Didcot, United Kingdom0000-0001-5601-6130SeánR.KavanaghDepartment of Chemistry, University College London, London, United Kingdom, Thomas Young Centre, University College London, London, United Kingdom, Department of Materials, Imperial College London, London, United Kingdom0000-0003-4577-9647DavidScanlonDepartment of Chemistry, University College London, London, United Kingdom, Thomas Young Centre, University College London, London, United Kingdom, The Faraday Institution, Didcot, United Kingdom, School of Chemistry, University of Birmingham, Birmingham, United Kingdom0000-0001-9174-860110.21105/joss.05974https://doi.org/10.5281/zenodo.10510884Pythonhttps://joss.theoj.org/papers/10.21105/joss.05974.pdfmaterials science, first-principles, density functional theory