tag:joss.theoj.org,2005:/papers/edited_by/@ppxasjsmJournal of Open Source Software2024-02-07T22:25:26ZJournal of Open Source Softwarehttps://joss.theoj.orgtag:joss.theoj.org,2005:Paper/46792024-02-07T22:25:26Z2024-02-12T11:55:04ZChi: A Python package for treatment response modellingacceptedv0.2.32023-08-06 13:35:22 UTC942024-02-07 22:25:26 UTC920245925DavidAugustinDepartment of Computer Science, University of Oxford, Oxford, United Kingdom0000-0002-4885-108810.21105/joss.05925https://doi.org/10.5281/zenodo.10510572Pythonhttps://joss.theoj.org/papers/10.21105/joss.05925.pdfpkpd, treatment planning, inference, Bayesian inferencetag:joss.theoj.org,2005:Paper/46312024-02-01T01:34:57Z2024-02-02T00:00:56Ztightbinder: A Python package for semi-empirical tight-binding models of crystalline and disordered solidsacceptedv0.12023-07-28 16:04:25 UTC942024-02-01 01:34:57 UTC920245810AlejandroJoséUría-ÁlvarezDepartamento de Física de la Materia Condensada, Universidad Autónoma de Madrid, 28049 Madrid, Spain0000-0001-6668-7333JuanJoséPalaciosDepartamento de Física de la Materia Condensada, Universidad Autónoma de Madrid, 28049 Madrid, Spain, Instituto Nicolás Cabrera, Condensed Matter Physics Centre (IFIMAC), 28049 Madrid, Spain0000-0003-2378-086610.21105/joss.05810https://doi.org/10.5281/zenodo.10496449Pythonhttps://joss.theoj.org/papers/10.21105/joss.05810.pdfcondensed matter physics, electronic structure, tight-binding, Slater-Kostertag:joss.theoj.org,2005:Paper/45162024-01-31T19:53:10Z2024-02-01T00:00:26Zmpl-interactions: A Python Package for Interactive Matplotlib Figuresaccepted0.23.02023-05-31 18:05:51 UTC932024-01-31 19:53:10 UTC920245651IanHunt-IsaakJohn A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA0000-0002-7591-083XJohnRussellDepartment of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA0009-0002-0402-2306DoekeHekstraJohn A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA, Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA0000-0003-2332-922310.21105/joss.05651https://doi.org/10.5281/zenodo.10211397Pythonhttps://joss.theoj.org/papers/10.21105/joss.05651.pdfMatplotlib, Ipywidgets, Interactive, Visualizationtag:joss.theoj.org,2005:Paper/44832023-09-14T03:02:07Z2023-09-22T03:40:20ZMLMOD: Machine Learning Methods for Data-Driven Modeling in LAMMPSacceptedv1.0.02023-05-12 19:56:27 UTC892023-09-14 03:02:07 UTC820235620PaulJ.AtzbergerPaul J. Atzberger, Professor, University of California Santa Barbara0000-0001-6806-806910.21105/joss.05620https://doi.org/10.5281/zenodo.8327516Python, C++https://joss.theoj.org/papers/10.21105/joss.05620.pdfmachine learning, dynamicstag:joss.theoj.org,2005:Paper/43942023-08-14T09:08:18Z2023-08-16T09:04:23ZPAS: a Python Anesthesia Simulator for drug controlacceptedv0.0.42023-04-07 15:16:16 UTC882023-08-14 09:08:18 UTC820235480BobAubouin-PairaultUniv. Grenoble Alpes, CNRS, Grenoble INP, GIPSA-lab, 38000 Grenoble, France, Univ. Grenoble Alpes, CNRS, Grenoble INP, VERIMAG, 38000 Grenoble, France0000-0003-0029-438XMirkoFiacchiniUniv. Grenoble Alpes, CNRS, Grenoble INP, GIPSA-lab, 38000 Grenoble, France0000-0002-3601-0302ThaoDangUniv. Grenoble Alpes, CNRS, Grenoble INP, VERIMAG, 38000 Grenoble, France0000-0002-3637-141510.21105/joss.05480https://doi.org/10.5281/zenodo.8171326Pythonhttps://joss.theoj.org/papers/10.21105/joss.05480.pdfAnesthesia, Drug Control, Drug effect modelling, Test pipelinetag:joss.theoj.org,2005:Paper/39682023-07-29T09:43:49Z2023-07-30T15:43:15ZLightshow: a Python package for generating computational x-ray absorption spectroscopy input filesacceptedv0.0.142022-10-18 01:07:43 UTC872023-07-29 09:43:49 UTC820235182MatthewR.CarboneComputational Science Initiative, Brookhaven National Laboratory, Upton, New York 11973, United States0000-0002-5181-9513FanchenMengCenter for Functional Nanomaterials, Brookhaven National Laboratory, Upton, New York 11973, United States0000-0001-9869-9005ChristianVorwerkPritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, United States0000-0002-2516-9553BenediktMaurerPhysics Department and IRIS Adlershof, Humboldt-Universität zu Berlin, D-12489 Berlin, Germany0000-0001-9152-7390FabianPeschelPhysics Department and IRIS Adlershof, Humboldt-Universität zu Berlin, D-12489 Berlin, Germany0000-0003-0619-6713XiaohuiQuCenter for Functional Nanomaterials, Brookhaven National Laboratory, Upton, New York 11973, United States0000-0001-5651-8405EliStavitskiNational Synchrotron Light Source II, Brookhaven National Laboratory, Upton, New York 11973, United States0000-0002-3337-2930ClaudiaDraxlPhysics Department and IRIS Adlershof, Humboldt-Universität zu Berlin, D-12489 Berlin, Germany0000-0003-3523-6657JohnVinsonMaterial Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States0000-0002-7619-7060DeyuLuCenter for Functional Nanomaterials, Brookhaven National Laboratory, Upton, New York 11973, United States0000-0003-4351-608510.21105/joss.05182https://doi.org/10.5281/zenodo.8118592Python, Jupyter Notebookhttps://joss.theoj.org/papers/10.21105/joss.05182.pdfcomputational spectroscopy, condensed matter physics, materials sciencetag:joss.theoj.org,2005:Paper/42912023-05-22T16:30:20Z2023-06-02T13:39:53Zchombo-discharge: An AMR code for gas discharge simulations in complex geometriesaccepted1.0.02023-03-09 10:09:17 UTC852023-05-22 16:30:20 UTC820235335RobertMarskarSINTEF Energy Research, Norway0000-0003-1706-973610.21105/joss.05335https://doi.org/10.5281/zenodo.7950220C++, Python, Gnuplothttps://joss.theoj.org/papers/10.21105/joss.05335.pdfastronomy, dynamics, galactic dynamics, milky waytag: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/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 simulationstag:joss.theoj.org,2005:Paper/36822022-11-28T08:23:39Z2022-11-29T00:01:08Zstrucscan: A lightweight Python-based framework for high-throughput material simulationaccepted1.02022-06-27 12:33:03 UTC792022-11-28 08:23:39 UTC720224719IsabelPietkaInterdisciplinary Centre for Advanced Materials Simulation (ICAMS), Ruhr University Bochum, Bochum, GermanyRalfDrautzInterdisciplinary Centre for Advanced Materials Simulation (ICAMS), Ruhr University Bochum, Bochum, GermanyThomasHammerschmidtInterdisciplinary Centre for Advanced Materials Simulation (ICAMS), Ruhr University Bochum, Bochum, Germany10.21105/joss.04719https://doi.org/10.5281/zenodo.7313602Pythonhttps://joss.theoj.org/papers/10.21105/joss.04719.pdfmaterial simulation, high-throughput, ab initio