tag:joss.theoj.org,2005:/papers/tagged/brainJournal of Open Source Software2024-01-11T22:46:25ZJournal of Open Source Softwarehttps://joss.theoj.orgtag:joss.theoj.org,2005:Paper/47432024-01-11T22:46:25Z2024-01-12T00:05:23ZPhysioLabXR: A Python Platform for Real-Time, Multi-modal, Brain–Computer Interfaces and Extended Reality Experimentsacceptedv1.0.02023-09-09 02:37:52 UTC932024-01-11 22:46:25 UTC920245854Ziheng'Leo'LiColumbia University, New York, New York, United States of America0000-0001-5187-200XHaowen'John'WeiColumbia University, New York, New York, United States of America0000-0003-1856-5627ZiwenXieColumbia University, New York, New York, United States of America0009-0006-2304-7591YunxiangPengColumbia University, New York, New York, United States of America0009-0000-1824-970XJunePyoSuhColumbia University, New York, New York, United States of America0009-0005-1211-6101StevenFeinerColumbia University, New York, New York, United States of America0000-0001-9978-7090PaulSajdaColumbia University, New York, New York, United States of America0000-0002-9738-134210.21105/joss.05854https://doi.org/10.5281/zenodo.10471500Python, C++, Cythonhttps://joss.theoj.org/papers/10.21105/joss.05854.pdfneuroscience, human–computer interaction, brain-computer interface, multi-modality, virtual augmented realitytag:joss.theoj.org,2005:Paper/45282023-12-04T10:49:39Z2023-12-05T00:00:59ZBidsme: expandable BIDS-ifier of brain imagery datasetsaccepted1.4.0.post42023-06-06 14:11:38 UTC922023-12-04 10:49:39 UTC820235575NikitaBeliyGIGA - Cyclotron Research Centre in vivo imaging, University of Liege, Liege, Belgium0009-0002-0830-3279CamilleGuilleminGIGA - Cyclotron Research Centre in vivo imaging, University of Liege, Liege, Belgium0000-0002-5377-7417EmelinePommierTélécom Physique Strasbourg, Université de Strasbourg, FranceGrégoryHammadGIGA - Cyclotron Research Centre in vivo imaging, University of Liege, Liege, Belgium0000-0003-1083-3869ChristophePhillipsGIGA - Cyclotron Research Centre in vivo imaging, University of Liege, Liege, Belgium0000-0002-4990-425X10.21105/joss.05575https://doi.org/10.5281/zenodo.10185300Pythonhttps://joss.theoj.org/papers/10.21105/joss.05575.pdfBIDS, data management, standardizationtag:joss.theoj.org,2005:Paper/45692023-12-02T08:01:07Z2023-12-04T09:27:34ZPyBCI: A Python Package for Brain-Computer Interface (BCI) Designaccepted1.0.02023-06-27 14:31:44 UTC922023-12-02 08:01:07 UTC820235706LiamBoothFaculty of Science and Engineering, University of Hull, United Kingdom.0000-0002-8749-9726AzizAsgharCentre for Anatomical and Human Sciences, Hull York Medical School, University of Hull, United Kingdom.0000-0002-3735-4449AnthonyBatesonFaculty of Science and Engineering, University of Hull, United Kingdom.0000-0002-4780-445810.21105/joss.05706https://doi.org/10.5281/zenodo.10245437Python, C++https://joss.theoj.org/papers/10.21105/joss.05706.pdfbrain-computer-interface, python, bci, lsl, labstreaminglayer, machinelearningtag:joss.theoj.org,2005:Paper/40712023-10-08T07:45:43Z2023-10-09T09:21:20Zbrains-py, A framework to support research on energy-efficient unconventional hardware for machine learningaccepted1.0.22022-12-04 18:53:21 UTC902023-10-08 07:45:43 UTC820235573UnaiAlegre-IbarraMESA+ Institute for Nanotechnology & BRAINS Center for Brain-Inspired Nano Systems, University of Twente, Netherlands0000-0001-5957-7945Hans-ChristianRuizEulerMESA+ Institute for Nanotechnology & BRAINS Center for Brain-Inspired Nano Systems, University of Twente, NetherlandsHumaidA.MollahMESA+ Institute for Nanotechnology & BRAINS Center for Brain-Inspired Nano Systems, University of Twente, NetherlandsBozhidarP.PetrovMESA+ Institute for Nanotechnology & BRAINS Center for Brain-Inspired Nano Systems, University of Twente, NetherlandsSrikumarS.SastryMESA+ Institute for Nanotechnology & BRAINS Center for Brain-Inspired Nano Systems, University of Twente, NetherlandsMarcusN.BoonMESA+ Institute for Nanotechnology & BRAINS Center for Brain-Inspired Nano Systems, University of Twente, NetherlandsMichelP.de JongMESA+ Institute for Nanotechnology & BRAINS Center for Brain-Inspired Nano Systems, University of Twente, NetherlandsMohamadrezaZolfagharinejadMESA+ Institute for Nanotechnology & BRAINS Center for Brain-Inspired Nano Systems, University of Twente, NetherlandsFlorentinaM. j.UitzetterMESA+ Institute for Nanotechnology & BRAINS Center for Brain-Inspired Nano Systems, University of Twente, NetherlandsBramvan de VenMESA+ Institute for Nanotechnology & BRAINS Center for Brain-Inspired Nano Systems, University of Twente, NetherlandsAntónioJ. Sousade AlmeidaMESA+ Institute for Nanotechnology & BRAINS Center for Brain-Inspired Nano Systems, University of Twente, NetherlandsSachinKingeMESA+ Institute for Nanotechnology & BRAINS Center for Brain-Inspired Nano Systems, University of Twente, NetherlandsWilfredG.van der WielAdvanced Tech., Materials Engineering Div., Toyota Motor Europe, Belgium10.21105/joss.05573https://doi.org/10.5281/zenodo.8410268Pythonhttps://joss.theoj.org/papers/10.21105/joss.05573.pdfDopant network processing units (DNPUs), Material Learning, Machine Learning Hardware design, Efficient Computing, Materials Sciencetag:joss.theoj.org,2005:Paper/44802023-08-04T17:17:18Z2023-08-05T00:01:30ZEcoAssist: A no-code platform to train and deploy custom YOLOv5 object detection modelsacceptedv4.02023-05-11 09:57:40 UTC882023-08-04 17:17:18 UTC820235581Petervan LunterenIndependent Researcher, The Netherlands0000-0001-5488-422510.21105/joss.05581https://doi.org/10.5281/zenodo.7223363Pythonhttps://joss.theoj.org/papers/10.21105/joss.05581.pdfartificial intelligence, machine learning, deep learning, object detection, yolov5, annotation tool, cameratrapstag:joss.theoj.org,2005:Paper/38282023-07-26T13:30:49Z2023-07-27T00:01:46ZAmpTorch: A Python package for scalable fingerprint-based neural network training on multi-element systems with integrated uncertainty quantificationacceptedv0.12022-08-22 16:32:43 UTC872023-07-26 13:30:49 UTC820235035MuhammedShuaibiDepartment of Chemical Engineering, Carnegie Mellon University, United StatesYugeHuDepartment of Chemical and Biomolecular Engineering, Georgia Institute of Technology, United States0000-0003-3648-7749XiangyunLeiDepartment of Chemical and Biomolecular Engineering, Georgia Institute of Technology, United StatesBenjaminM.ComerDepartment of Chemical and Biomolecular Engineering, Georgia Institute of Technology, United StatesMattAdamsDepartment of Chemical Engineering, Carnegie Mellon University, United StatesJacobParasSchool of Physics and School of Computer Science, Georgia Institute of Technology, United StatesRuiQiChenDepartment of Chemical and Biomolecular Engineering, Georgia Institute of Technology, United StatesEricMusaDepartment of Chemical Engineering, University of Michigan, United StatesJosephMusielewiczDepartment of Chemical Engineering, Carnegie Mellon University, United StatesAndrewA.PetersonSchool of Engineering, Brown University, United States0000-0003-2855-9482AndrewJ.MedfordDepartment of Chemical and Biomolecular Engineering, Georgia Institute of Technology, United States0000-0001-8311-9581ZacharyUlissiDepartment of Chemical Engineering, Carnegie Mellon University, United States0000-0002-9401-491810.21105/joss.05035https://doi.org/10.5281/zenodo.8151492Python, C++, C, G-code, GAPhttps://joss.theoj.org/papers/10.21105/joss.05035.pdfmachine learning interatomic potentials, neural networks, molecular dynamicstag:joss.theoj.org,2005:Paper/32712023-04-22T07:17:47Z2023-04-26T19:28:11ZHylleraasMD: Massively parallel hybrid particle-field molecular dynamics in Pythonacceptedv1.0.32022-01-07 23:14:41 UTC842023-04-22 07:17:47 UTC820234149MortenLedumDepartment of Chemistry, and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, PO Box 1033 Blindern, 0315 Oslo, Norway0000-0003-4244-4876ManuelCarrerDepartment of Chemistry, and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, PO Box 1033 Blindern, 0315 Oslo, Norway0000-0002-8777-4310SamiranSenDepartment of Chemistry, and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, PO Box 1033 Blindern, 0315 Oslo, Norway0000-0002-1922-7796XinmengLiDepartment of Chemistry, and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, PO Box 1033 Blindern, 0315 Oslo, Norway0000-0002-6863-6078MicheleCascellaDepartment of Chemistry, and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, PO Box 1033 Blindern, 0315 Oslo, Norway0000-0003-2266-5399SigbjørnLølandBoreDepartment of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States of America0000-0002-8620-488510.21105/joss.04149https://doi.org/10.5281/zenodo.7839898Python, Fortranhttps://joss.theoj.org/papers/10.21105/joss.04149.pdfchemistry, physics, molecular dynamics, coarse-grained, hybrid particle-fieldtag:joss.theoj.org,2005:Paper/34192023-04-11T15:47:05Z2023-06-08T19:07:56ZFlowSieve: A Coarse-Graining Utility for Geophysical Flows on the Sphereacceptedv3.0.02022-03-11 16:47:12 UTC842023-04-11 15:47:05 UTC820234277BenjaminA.StorerDepartment of Mechanical Engingeering, University of Rochester, USA0000-0001-5955-2158HusseinAluieDepartment of Mechanical Engingeering, University of Rochester, USA0000-0003-3516-369710.21105/joss.04277https://doi.org/10.5281/zenodo.7818192C++, C, Pythonhttps://joss.theoj.org/papers/10.21105/joss.04277.pdfcoarse graining, scale decomposition, fluid dynamicstag:joss.theoj.org,2005:Paper/41732023-03-26T19:04:39Z2023-03-27T00:03:22ZMelodie: Agent-based Modeling in Pythonacceptedv0.6.02023-01-21 11:43:17 UTC832023-03-26 19:04:39 UTC820235100SongminYuFraunhofer Institute for Systems and Innovation Research, Germany0000-0001-6062-4382ZhanyiHouSchool of Reliability and Systems Engineering, Beihang University, China0000-0001-8524-537010.21105/joss.05100https://doi.org/10.5281/zenodo.7771397Python, Cython, Chttps://joss.theoj.org/papers/10.21105/joss.05100.pdfagent-based modeling, complex system, automatic calibration, evolutionary trainingtag:joss.theoj.org,2005:Paper/37082023-01-21T16:46:39Z2023-01-22T21:38:20ZoxDNA: coarse-grained simulations of nucleic acids made simpleacceptedv3.2.22022-07-07 09:39:51 UTC812023-01-21 16:46:39 UTC820234693ErikPoppletonSchool of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, United States of America0000-0002-5146-5970MichaelMatthiesSchool of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, United States of AmericaDebeshMandalDepartment of Materials, Imperial College London, United KingdomFlavioRomanoDipartimento di Scienze Molecolari e Nanosistemi, Universitá Ca Foscari di Venezia, ItalyPetrŠulcSchool of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, United States of America0000-0003-1565-6769LorenzoRovigattiDepartment of Physics, Sapienza University of Rome, Italy, CNR-ISC UoS Sapienza, Rome, Italy0000-0001-5017-282910.21105/joss.04693https://doi.org/10.5281/zenodo.7556035Python, C, Cythonhttps://joss.theoj.org/papers/10.21105/joss.04693.pdfC++, DNA, DNA nanotechnology, Molecular simulations