tag:joss.theoj.org,2005:/papers/tagged/SIRJournal of Open Source Software2023-06-22T15:55:09ZJournal of Open Source Softwarehttps://joss.theoj.orgtag:joss.theoj.org,2005:Paper/39662023-06-22T15:55:09Z2023-06-23T00:01:36ZAirTrafficSim: An open-source web-based air traffic simulation platform.acceptedv0.0.02022-10-17 08:18:35 UTC862023-06-22 15:55:09 UTC820234916KaYiuHuiDepartment of Mechanical and Aerospace Engineering, The Hong Kong University of Science and Technology, Hong Kong SARChrisHc.NguyenDepartment of Mechanical and Aerospace Engineering, The Hong Kong University of Science and Technology, Hong Kong SARGoNamLuiDepartment of Mechanical and Aerospace Engineering, The Hong Kong University of Science and Technology, Hong Kong SARRheaP.LiemDepartment of Mechanical and Aerospace Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR10.21105/joss.04916https://doi.org/10.5281/zenodo.8070119https://joss.theoj.org/papers/10.21105/joss.04916.pdfPython, Aviation, Air traffic management, Multi-agent simulation, Data visualizationtag:joss.theoj.org,2005:Paper/37432022-12-21T19:48:09Z2022-12-22T00:00:50ZPACMAN: A pipeline to reduce and analyze Hubble Wide Field Camera 3 IR Grism dataacceptedv0.1-alpha2022-07-25 15:59:23 UTC802022-12-21 19:48:09 UTC720224838SebastianZiebaMax-Planck-Institut für Astronomie, Königstuhl 17, D-69117 Heidelberg, Germany, Leiden Observatory, Leiden University, Niels Bohrweg 2, 2333CA Leiden, The Netherlands0000-0003-0562-6750LauraKreidbergMax-Planck-Institut für Astronomie, Königstuhl 17, D-69117 Heidelberg, Germany0000-0003-0514-114710.21105/joss.04838https://doi.org/10.5281/zenodo.7465579Pythonhttps://joss.theoj.org/papers/10.21105/joss.04838.pdfHST, python, astronomy, exoplanets, spectroscopy, photometrytag:joss.theoj.org,2005:Paper/36102022-09-05T10:04:38Z2022-10-11T06:54:05ZBTE: a Python module for pandemic-scale mutation-annotated phylogenetic treesacceptedv0.8.12022-05-17 23:22:33 UTC772022-09-05 10:04:38 UTC720224433JakobMcBroomeDepartment of Biomolecular Engineering, University of California Santa Cruz. Santa Cruz, CA 95064, USA, Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA0000-0002-5002-5156YatishTurakhiaDepartment of Electrical and Computer Engineering, University of California, San Diego; San Diego, CA 92093, USA0000-0001-5600-2900RussellCorbett-DetigDepartment of Biomolecular Engineering, University of California Santa Cruz. Santa Cruz, CA 95064, USA, Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA0000-0001-6535-247810.21105/joss.04433https://doi.org/10.5281/zenodo.7036163Python, C++, Cythonhttps://joss.theoj.org/papers/10.21105/joss.04433.pdfphylogenetics, epidemiology, SARS-CoV-2tag:joss.theoj.org,2005:Paper/31872022-03-22T12:46:38Z2022-03-23T00:59:20ZRainbow: Automated Air-Liquid Interface Cell Culture Analysis Using Deep Optical Flowaccepted0.1.02021-11-22 10:26:07 UTC712022-03-22 12:46:38 UTC720224080AlphonsGwatimbaWal-yan Respiratory Research Centre, Telethon Kids Institute, University of Western Australia, Nedlands, 6009, Western Australia, Australia, School of Computer Science and Software Engineering, University of Western Australia, Nedlands, 6009, Western Australia, Australia0000-0002-9607-2839JosephHoWal-yan Respiratory Research Centre, Telethon Kids Institute, University of Western Australia, Nedlands, 6009, Western Australia, Australia, School of Computer Science and Software Engineering, University of Western Australia, Nedlands, 6009, Western Australia, Australia0000-0002-9496-506XThomasIosifidisWal-yan Respiratory Research Centre, Telethon Kids Institute, University of Western Australia, Nedlands, 6009, Western Australia, Australia, Centre for Cell Therapy and Regenerative Medicine, School of Medicine, University of Western Australia, Nedlands, 6009, Western Australia, Australia, School of Population Health, Curtin University, Bentley, 6102, Western Australia, Australia0000-0001-8462-5865YuliyaV.KarpievitchWal-yan Respiratory Research Centre, Telethon Kids Institute, University of Western Australia, Nedlands, 6009, Western Australia, Australia, School of Molecular Sciences, University of Western Australia, Nedlands, 6009, Western Australia, Australia0000-0003-2586-335810.21105/joss.04080https://doi.org/10.5281/zenodo.6355080Python, Jupyter Notebookhttps://joss.theoj.org/papers/10.21105/joss.04080.pdfpython, jupyter notebook, bioinformatics, deep learning, biology, optical flow, image analysis, bioimage informaticstag:joss.theoj.org,2005:Paper/31182022-02-14T13:56:48Z2022-02-17T23:07:39ZMetaWards: A flexible metapopulation framework for modelling disease spreadacceptedv1.6.12021-10-20 15:14:37 UTC702022-02-14 13:56:48 UTC720223914ChristopherWoodsResearch Software Engineering, Advanced Computing Research Centre, University of Bristol, UK0000-0001-6563-9903LesterHedgesResearch Software Engineering, Advanced Computing Research Centre, University of Bristol, UK0000-0002-5624-0500ChristopherEdsallResearch Software Engineering, Research Computing Services, University of Cambridge, UK0000-0001-6863-2184EllenBrooks-PollockDepartment of Engineering Mathematics, University of Bristol, UK0000-0002-5984-4932ChristopherParton-FentonCollege of Engineering, Mathematics and Physical Sciences, University of Exeter, UK0000-0003-0052-8430TrevelyanJ.McKinleyCollege of Medicine and Health, University of Exeter, UK0000-0002-9485-3236MattJ.KeelingZeeman Institute (SBIDER), University of Warwick, Coventry, UK0000-0003-4639-4765LeonDanonDepartment of Engineering Mathematics, University of Bristol, UK0000-0002-7076-187110.21105/joss.03914https://doi.org/10.5281/zenodo.5562738Python, Chttps://joss.theoj.org/papers/10.21105/joss.03914.pdfepidemiology, epidemics, sir-model, compartmental transmission model, covid, python, cythontag:joss.theoj.org,2005:Paper/28212022-01-29T00:53:03Z2022-01-31T13:03:47Zrfasst: An R tool to estimate air pollution impacts on health and agricultureacceptedv1.12021-06-24 18:44:55 UTC692022-01-29 00:53:03 UTC720223820JonSampedroJoint Global Change Research Institute, Pacific Northwest National Laboratory, College Park, MD, USA0000-0002-2277-1530ZarrarKhanJoint Global Change Research Institute, Pacific Northwest National Laboratory, College Park, MD, USA0000-0002-8147-8553ChrisR.VernonJoint Global Change Research Institute, Pacific Northwest National Laboratory, College Park, MD, USA0000-0002-3406-6214StevenJ.SmithJoint Global Change Research Institute, Pacific Northwest National Laboratory, College Park, MD, USA0000-0003-3248-5607StephanieWaldhoffJoint Global Change Research Institute, Pacific Northwest National Laboratory, College Park, MD, USA0000-0002-8073-0868RitaVan DingenenEuropean Commission, Joint Research Centre (JRC), Ispra, Italy0000-0003-2521-497210.21105/joss.03820https://doi.org/10.5281/zenodo.5838361Rhttps://joss.theoj.org/papers/10.21105/joss.03820.pdfemissionstag:joss.theoj.org,2005:Paper/25822022-01-29T00:08:44Z2022-01-31T10:50:21ZSenSARP: A pipeline to pre-process Sentinel-1 SLC data by using ESA SNAP Sentinel-1 Toolboxaccepted0.12021-04-20 14:24:27 UTC692022-01-29 00:08:44 UTC720223337ThomasWeißDepartment of Geography, Ludwig-Maximilians-Universität München, 80333 Munich, Germany0000-0001-5278-8379TonioFinckeBrockmann Consult GmbH, 21029 Hamburg, Germany;10.21105/joss.03337https://doi.org/10.5281/zenodo.5903483Pythonhttps://joss.theoj.org/papers/10.21105/joss.03337.pdfSentinel-1, SAR, SNAPtag:joss.theoj.org,2005:Paper/29982021-10-14T11:05:41Z2021-10-15T00:03:59ZShUShER: private browser-based placement of sensitive genome samples on phylogenetic treesacceptedv0.5.02021-08-27 01:47:30 UTC662021-10-14 11:05:41 UTC620213677AlexanderKramerDepartment of Biomolecular Engineering, University of California Santa Cruz. Santa Cruz, CA 95064, USA, Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA0000-0003-3630-3209YatishTurakhiaDepartment of Electrical and Computer Engineering, University of California, San Diego; San Diego, CA 92093, USA0000-0001-5600-2900RussellCorbett-DetigDepartment of Biomolecular Engineering, University of California Santa Cruz. Santa Cruz, CA 95064, USA, Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA0000-0001-6535-247810.21105/joss.03677https://doi.org/10.5281/zenodo.5567374Python, JavaScripthttps://joss.theoj.org/papers/10.21105/joss.03677.pdfphylogenetics, WebAssembly, React, SARS-CoV-2tag:joss.theoj.org,2005:Paper/28002021-07-23T14:51:42Z2021-07-24T00:03:18Zpollucheck v1.0: A package to explore open-source air pollution dataaccepted1.0.02021-06-18 04:15:50 UTC632021-07-23 14:51:42 UTC620213435AdithiR.UpadhyaILK Labs, Bengaluru, India0000-0002-1764-1379PratyushAgrawalILK Labs, Bengaluru, IndiaSreekanthVakacherlaCenter for Study of Science, Technology and Policy, Bengaluru, India0000-0003-0400-6584MeenakshiKushwahaILK Labs, Bengaluru, India10.21105/joss.03435https://doi.org/10.5281/zenodo.5128607Rhttps://joss.theoj.org/papers/10.21105/joss.03435.pdfopen-source, air quality, shinytag:joss.theoj.org,2005:Paper/26732021-07-15T14:28:41Z2021-07-15T14:28:41Zcovidregionaldata: Subnational data for COVID-19 epidemiologyaccepted0.9.12021-05-12 15:00:05 UTC632021-07-15 14:28:41 UTC620213290JosephPalmerDepartment of Biological Sciences, Royal Holloway University of London0000-0002-5593-9352KatharineSherrattCentre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine0000-0003-2049-3423RichardMartin-NielsenNoneJonnieBevanTessellaHamishGibbsCentre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine0000-0003-4413-453XCmmidCOVID-19 WorkingGroupCentre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical MedicineSebastianFunkCentre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical MedicineSamAbbottCentre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine0000-0001-8057-803710.21105/joss.03290https://doi.org/10.5281/zenodo.5059988Rhttps://joss.theoj.org/papers/10.21105/joss.03290.pdfCOVID-19, Open data, rstats, Sars-Cov-2