tag:joss.theoj.org,2005:/papers/tagged/miningJournal of Open Source Software2024-02-27T21:24:38ZJournal of Open Source Softwarehttps://joss.theoj.orgtag:joss.theoj.org,2005:Paper/48132024-02-27T21:24:38Z2024-03-22T14:09:24ZDeepRank2: Mining 3D Protein Structures with Geometric Deep Learningacceptedv2.1.02023-09-22 15:36:51 UTC942024-02-27 21:24:38 UTC920245983GiuliaCrocioniNetherlands eScience Center, Amsterdam, The Netherlands0000-0002-0823-0121DaniL.BodorNetherlands eScience Center, Amsterdam, The Netherlands0000-0003-2109-2349CoosBaakmanThe Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, The Netherlands0000-0003-4317-1566FarzanehM.PariziThe Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, The Netherlands0000-0003-4230-7492Daniel-T.RademakerThe Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, The Netherlands0000-0003-1959-1317GayatriRamakrishnanThe Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, The Netherlands0000-0001-8203-2783SvenA.van der BurgNetherlands eScience Center, Amsterdam, The Netherlands0000-0003-1250-6968DarioF.MarzellaThe Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, The Netherlands0000-0002-0043-3055JoãoM.c.TeixeiraIndependent Researcher0000-0002-9113-0622LiC.XueThe Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, The Netherlands0000-0002-2613-538X10.21105/joss.05983https://doi.org/10.5281/zenodo.10566809Python, Jupyter Notebookhttps://joss.theoj.org/papers/10.21105/joss.05983.pdfPyTorch, structural biology, geometric deep learning, 3D protein structures, protein-protein interfaces, single-residue variants, graph neural networks, convolutional neural networks, DeepRanktag:joss.theoj.org,2005:Paper/49062024-02-12T12:06:13Z2024-02-13T00:01:22ZFasten: a toolkit for streaming operations on fastq filesacceptedv0.7.22023-10-30 19:01:17 UTC942024-02-12 12:06:13 UTC920246030LeeS.KatzEnteric Diseases Laboratory Branch (EDLB), Centers for Disease Control and Prevention, Atlanta, GA, United States of America, Center for Food Safety, University of Georgia, Griffin, GA, United States of America0000-0002-2533-9161JohnPhanGeneral Dynamics Information Technology Inc., Atlanta, GA, United States of America0000-0002-4670-2660HenkC. denBakkerEnteric Diseases Laboratory Branch (EDLB), Centers for Disease Control and Prevention, Atlanta, GA, United States of America0000-0002-4086-158010.21105/joss.06030https://doi.org/10.5281/zenodo.10621531Rusthttps://joss.theoj.org/papers/10.21105/joss.06030.pdfcommand line, fastq manipulation, interleaved fastqtag:joss.theoj.org,2005:Paper/38102024-01-09T15:42:20Z2024-01-10T00:01:06ZScarlet: Scalable Anytime Algorithms for Learning Fragments of Linear Temporal Logicacceptedv0.0.12022-08-10 18:27:58 UTC932024-01-09 15:42:20 UTC920245052RitamRahaUniversity of Antwerp, Antwerp, Belgium, CNRS, LaBRI and Université de Bordeaux, France0000-0003-1467-1182RajarshiRoyMax Planck Institute for Software Systems, Kaiserslautern, Germany0000-0002-0202-1169NathanaëlFijalkowCNRS, LaBRI and Université de Bordeaux, France0000-0002-6576-4680DanielNeiderTU Dortmund University, Dortmund, Germany, Center for Trustworthy Data Science and Security, University Alliance Ruhr, Germany0000-0001-9276-634210.21105/joss.05052https://doi.org/10.5281/zenodo.10419514Pythonhttps://joss.theoj.org/papers/10.21105/joss.05052.pdflinear temporal logic (LTL), Explainable AI (XAI), specification mining, Formal Methodstag:joss.theoj.org,2005:Paper/45892023-08-18T19:47:48Z2023-08-19T08:54:38ZA Java Library for Itemset Mining with Choco-solveracceptedv1.0.22023-07-09 13:14:01 UTC882023-08-18 19:47:48 UTC820235654CharlesVernereyTASC, IMT-Atlantique, LS2N-CNRS, Nantes, France0000-0002-2922-2833SamirLoudniTASC, IMT-Atlantique, LS2N-CNRS, Nantes, France0000-0001-6245-766110.21105/joss.05654https://doi.org/10.5281/zenodo.8263971Javahttps://joss.theoj.org/papers/10.21105/joss.05654.pdfConstraint Programming, Itemset Mining, Multi-Objective Optimisationtag:joss.theoj.org,2005:Paper/39102023-05-10T21:56:30Z2023-05-11T09:10:10ZSPyCi-PDB: A modular command-line interface for back-calculating experimental datatypes of protein structures.acceptedv0.1.102022-09-21 16:08:40 UTC852023-05-10 21:56:30 UTC820234861ZiHaoLiuMolecular Medicine Program, Hospital for Sick Children, Toronto, Ontario, Canada, Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada0000-0002-8357-8507OufanZhangPitzer Center for Theoretical Chemistry, University of California, Berkeley, California, United States of America, Department of Chemistry, University of California, Berkeley, California, United States of AmericaJoãoM.c.TeixeiraDepartment of Biomedical Sciences, University of Padua, Padova, Italy0000-0002-9113-0622JieLiPitzer Center for Theoretical Chemistry, University of California, Berkeley, California, United States of America, Department of Chemistry, University of California, Berkeley, California, United States of America0000-0002-4727-1786TeresaHead-GordonPitzer Center for Theoretical Chemistry, University of California, Berkeley, California, United States of America, Department of Chemistry, University of California, Berkeley, California, United States of America, Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California, United States of America, Department of Bioengineering, University of California, Berkeley, California, United States of America0000-0003-0025-8987JulieD.Forman-KayMolecular Medicine Program, Hospital for Sick Children, Toronto, Ontario, Canada, Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada0000-0001-8265-972X10.21105/joss.04861https://doi.org/10.5281/zenodo.7887039Pythonhttps://joss.theoj.org/papers/10.21105/joss.04861.pdfNMR, SAXS, smFRET, Back-calculator, PDB, Structural Biology, Proteins, Biochemistrytag:joss.theoj.org,2005:Paper/41772023-04-12T07:57:07Z2023-04-13T00:02:38ZSDGdetector: an R-based text mining tool for quantifying efforts toward Sustainable Development Goalsacceptedv0.1.02023-01-23 18:53:40 UTC842023-04-12 07:57:07 UTC820235124YingjieLiCenter for Systems Integration and Sustainability, Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI 48823, United States, Environmental Science and Policy Program, Michigan State University, East Lansing, MI 48823, United States, Natural Capital Project, Woods Institute for the Environment, Stanford University, Stanford, CA, 94305, United States0000-0002-8401-0649VeronicaF.FransCenter for Systems Integration and Sustainability, Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI 48823, United States, Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI 48824, United States, W.K. Kellogg Biological Station, Michigan State University, Hickory Corners, MI 49060, United States0000-0002-5634-3956YongzeSongSchool of Design and the Built Environment, Curtin University, Perth, WA, 6102, Australia0000-0003-3420-9622MengCaiSchool of Planning, Design and Construction, Michigan State University, East Lansing, MI, 48824, United States, Department of Civil and Environmental Engineering, Technical University of Darmstadt, Darmstadt 64287, Germany0000-0002-8318-572XYuqianZhangCenter for Systems Integration and Sustainability, Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI 48823, United States, Environmental Science and Policy Program, Michigan State University, East Lansing, MI 48823, United States0000-0001-7576-2526JianguoLiuCenter for Systems Integration and Sustainability, Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI 48823, United States, Environmental Science and Policy Program, Michigan State University, East Lansing, MI 48823, United States0000-0001-6344-008710.21105/joss.05124https://doi.org/10.5281/zenodo.7775019Rhttps://joss.theoj.org/papers/10.21105/joss.05124.pdfSustainability, Sustainable Development Goals (SDGs), Text mining, Text analysistag:joss.theoj.org,2005:Paper/36302022-11-25T07:51:09Z2022-12-01T15:37:03ZTLViz: Visualising and analysing tensor decomposition models with Pythonacceptedv0.1.12022-05-26 07:53:29 UTC792022-11-25 07:51:09 UTC720224754MarieRoaldSimula Metropolitan Center for Digital Engineering, Norway, Oslo Metropolitan University, Norway0000-0002-9571-8829YngveMardalMoeIndependent Researcher, Norway0000-0002-5159-901210.21105/joss.04754https://doi.org/10.5281/zenodo.7274925Pythonhttps://joss.theoj.org/papers/10.21105/joss.04754.pdftensor decompositions, data mining, data visualisation, TensorLytag:joss.theoj.org,2005:Paper/37382022-10-09T08:04:24Z2022-10-10T00:01:29ZPatchView: A Python Package for Patch-clamp Data Analysis and Visualizationacceptedv0.2.22022-07-22 00:03:39 UTC782022-10-09 08:04:24 UTC720224706MingHuDepartment of Neuroscience, Baylor College of Medicine, Houston, TX, Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston,TX, USA0000-0002-5254-5315XiaolongJiangDepartment of Neuroscience, Baylor College of Medicine, Houston, TX, Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston,TX, USA, Department of Ophthalmology, Baylor College of Medicine, Houston, TX10.21105/joss.04706https://doi.org/10.5281/zenodo.7149877Python, AGS Scripthttps://joss.theoj.org/papers/10.21105/joss.04706.pdfneuroscience, patch-clamp, mini-event, Heka, Axon instrumentstag:joss.theoj.org,2005:Paper/35212022-09-29T21:20:38Z2022-09-30T00:00:37ZNiaARM: A minimalistic framework for Numerical Association Rule Miningaccepted0.1.62022-04-27 18:52:09 UTC772022-09-29 21:20:38 UTC720224448ŽigaStupanUniversity of Maribor, Faculty of Electrical Engineering and Computer Science0000-0001-9847-7306IztokFisterUniversity of Maribor, Faculty of Electrical Engineering and Computer Science0000-0002-6418-127210.21105/joss.04448https://doi.org/10.5281/zenodo.7123879Pythonhttps://joss.theoj.org/papers/10.21105/joss.04448.pdfassociation rule mining, data mining, evolutionary algorithms, numerical association rule mining, visualizationtag:joss.theoj.org,2005:Paper/31622022-07-12T10:00:56Z2022-07-12T10:02:12ZlimHaloPT: A Numerical Package for Accurate Modeling of Line Intensity Power Spectrumacceptedv1.0.02021-11-09 10:29:27 UTC752022-07-12 10:00:56 UTC720224173AzadehMoradinezhad DizgahDepartment of Theoretical Physics, University of Geneva, 24 quai Ernest Ansermet, 1211 Geneva 4, Switzerland0000-0001-8841-9989AlbertoVallinottoIndependent Researcher, ItalyFarnikNikakhtarDepartment of Physics and Astronomy, University of Pennsylvania, 209 S. 33rd St., Philadelphia, PA 19104, USA0000-0002-3641-436610.21105/joss.04173https://doi.org/10.5281/zenodo.6762607Chttps://joss.theoj.org/papers/10.21105/joss.04173.pdfC language, cosmology, intensity mapping