tag:joss.theoj.org,2005:/papers?page=28Journal of Open Source Software2023-12-15T17:52:44ZJournal of Open Source Softwarehttps://joss.theoj.orgtag:joss.theoj.org,2005:Paper/48562023-12-15T17:52:44Z2023-12-18T20:30:09ZFlowerMD: Flexible Library of Organic Workflows and Extensible Recipes for Molecular Dynamicsacceptedv1.0.02023-10-18 20:22:59 UTC922023-12-15 17:52:44 UTC820235989MarjanAlbooyehBoise State University, Boise, ID, United States of America0009-0001-9565-3076ChrisJonesBoise State University, Boise, ID, United States of America0000-0002-6196-5274RainierBarrettBoise State University, Boise, ID, United States of America0000-0002-5728-9074EricJankowskiBoise State University, Boise, ID, United States of America0000-0002-3267-141010.21105/joss.05989https://doi.org/10.5281/zenodo.10215501Python, Jupyter Notebookhttps://joss.theoj.org/papers/10.21105/joss.05989.pdfmolecular simulation, materials science, molecular dynamics, polymers, HOOMD-bluetag:joss.theoj.org,2005:Paper/48542024-03-18T12:28:23Z2024-03-19T00:01:17ZImbalance: A comprehensive multi-interface Julia toolbox to address class imbalanceacceptedv0.1.22023-10-17 14:48:00 UTC952024-03-18 12:28:23 UTC920246310EssamWisamCairo University, Egypt0009-0009-1198-7166AnthonyBlaomUniversity of Auckland, New Zealand0000-0001-6689-886X10.21105/joss.06310https://doi.org/10.5281/zenodo.10823254Juliahttps://joss.theoj.org/papers/10.21105/joss.06310.pdfmachine learning, classification, class imbalance, resampling, oversampling, undersampling, juliatag: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/48512023-11-05T18:10:00Z2023-11-06T00:00:24ZMachine Learning Validation via Rational Dataset Sampling with astartesacceptedv1.1.3.post12023-10-16 18:19:35 UTC912023-11-05 18:10:00 UTC820235996JacksonW.BurnsCenter for Computational Science and Engineering, Massachusetts Institute of Technology, Department of Chemical Engineering, Massachusetts Institute of Technology, United States0000-0002-0657-9426KevinA.SpiekermannDepartment of Chemical Engineering, Massachusetts Institute of Technology, United States0000-0002-9484-9253HimaghnaBhattacharjeeDepartment of Chemical and Biomolecular Engineering, University of Delaware, United States0000-0002-6598-3939DionisiosG.VlachosDepartment of Chemical and Biomolecular Engineering, University of Delaware, United States0000-0002-6795-8403WilliamH.GreenDepartment of Chemical Engineering, Massachusetts Institute of Technology, United States0000-0003-2603-969410.21105/joss.05996https://doi.org/10.5281/zenodo.8147205Pythonhttps://joss.theoj.org/papers/10.21105/joss.05996.pdfmachine learning, sampling, interpolation, extrapolation, data splits, cheminformaticstag:joss.theoj.org,2005:Paper/48492024-03-25T09:10:44Z2024-03-26T00:00:59ZAcanthophis: a comprehensive plant hologenomics pipelineacceptedv1.0.02023-10-15 07:16:35 UTC952024-03-25 09:10:44 UTC920246062KevinD.MurrayMax Planck Institute for Biology Tübingen, 72076 Tübingen, Germany0000-0002-2466-1917JustinO.BorevitzResearch School of Biology, Australian National University, Canberra, Australia0000-0001-8408-3699DetlefWeigelMax Planck Institute for Biology Tübingen, 72076 Tübingen, Germany0000-0002-2114-7963NormanWarthmannResearch School of Biology, Australian National University, Canberra, Australia, FAO/IAEA Joint Centre of Nuclear Techniques in Food and Agriculture, Plant Breeding and Genetics Laboratory, Seibersdorf, Austria0000-0002-1178-840910.21105/joss.06062https://doi.org/10.5281/zenodo.10795245Pythonhttps://joss.theoj.org/papers/10.21105/joss.06062.pdfpython, snakemake, plants, metagenomics, variant calling, population genomics, reference-free classificationtag:joss.theoj.org,2005:Paper/48482024-02-29T09:57:40Z2024-03-01T00:00:27ZSurjectors: surjection layers for density estimation with normalizing flowsacceptedv0.0.32023-10-14 23:34:59 UTC942024-02-29 09:57:40 UTC920246188SimonDirmeierSwiss Data Science Center, Zurich, Switzerland, ETH Zurich, Zurich, Switzerland10.21105/joss.06188https://doi.org/10.5281/zenodo.10679869Pythonhttps://joss.theoj.org/papers/10.21105/joss.06188.pdfJAX, Density estimation, Normalizing flow, Machine learning, Statisticstag:joss.theoj.org,2005:Paper/48472023-10-13T22:21:48Z2024-02-16T00:47:30ZSODA: Software to Support the Curation and Sharing 1 of FAIR Autonomic Nervous System Dataunder_reviewv12.3.12023-10-13 22:21:48 UTCtag:joss.theoj.org,2005:Paper/48462023-10-13T13:08:56Z2024-03-25T07:41:41ZETHOS.FINE: A Framework for Integrated Energy System Assessmentunder_reviewv2.3.02023-10-13 13:08:56 UTCtag:joss.theoj.org,2005:Paper/48442023-10-12T14:43:59Z2024-02-25T03:09:48Z A C++ template library for polynomials algebra over discrete euclidean domains under_reviewv1.12023-10-12 14:43:59 UTCtag:joss.theoj.org,2005:Paper/48432024-01-07T20:40:46Z2024-01-08T00:00:30ZJobflow: Computational Workflows Made Simpleaccepted0.1.142023-10-10 17:26:07 UTC932024-01-07 20:40:46 UTC920245995AndrewS.RosenDepartment of Materials Science and Engineering, University of California, Berkeley, Berkeley, CA, USA, Materials Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA0000-0002-0141-7006MaxGallantDepartment of Materials Science and Engineering, University of California, Berkeley, Berkeley, CA, USA, Materials Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA0009-0008-4099-6144JanineGeorgeFederal Institute for Materials Research and Testing, Department Materials Chemistry, Berlin, Germany, Friedrich Schiller University Jena, Institute of Condensed Matter Theory and Solid-State Optics, Jena, Germany0000-0001-8907-0336JanoshRiebesellMaterials Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA, Department of Physics, University of Cambridge, Cambridge, UK0000-0001-5233-3462HrushikeshSahasrabuddheDepartment of Materials Science and Engineering, University of California, Berkeley, Berkeley, CA, USA, Energy Storage and Distributed Resources Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA0000-0001-7346-4568Jimmy-XuanShenMaterials Science Division, Lawrence Livermore National Laboratory, Livermore, CA, USA0000-0002-2743-7531MingjianWenWilliam A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA0000-0003-0013-575XMatthewL.EvansMatgenix SRL, rue Armand Bury 185, 6534 Gozée, Belgium, Institut de la Matière Condensée et des Nanosciences, Université catholique de Louvain, Chemin des Étoiles 8, Louvain-la-Neuve 1348, Belgium0000-0002-1182-9098GuidoPetrettoMatgenix SRL, rue Armand Bury 185, 6534 Gozée, BelgiumDavidWaroquiersMatgenix SRL, rue Armand Bury 185, 6534 Gozée, Belgium, Institut de la Matière Condensée et des Nanosciences, Université catholique de Louvain, Chemin des Étoiles 8, Louvain-la-Neuve 1348, Belgium0000-0001-8943-9762Gian-MarcoRignaneseMatgenix SRL, rue Armand Bury 185, 6534 Gozée, Belgium, Institut de la Matière Condensée et des Nanosciences, Université catholique de Louvain, Chemin des Étoiles 8, Louvain-la-Neuve 1348, Belgium, School of Materials Science and Engineering, Northwestern Polytechnical University, No. 127 Youyi West Road, Xi’an 710072 Shaanxi, PR China0000-0002-1422-1205KristinA.PerssonDepartment of Materials Science and Engineering, University of California, Berkeley, Berkeley, CA, USA, Materials Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA, Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA0000-0002-7212-6310AnubhavJainEnergy Storage and Distributed Resources Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA0000-0001-5893-9967AlexM.GanoseDepartment of Chemistry, Imperial College London, London, UK0000-0002-4486-332110.21105/joss.05995https://doi.org/10.5281/zenodo.10466868Pythonhttps://joss.theoj.org/papers/10.21105/joss.05995.pdfWorkflows