tag:joss.theoj.org,2005:/papers/tagged/lungJournal of Open Source Software2023-10-19T10:05:08ZJournal of Open Source Softwarehttps://joss.theoj.orgtag:joss.theoj.org,2005:Paper/42982023-10-19T10:05:08Z2023-10-20T00:00:55ZBaargin: a Nextflow workflow for the automatic analysis of bacterial genomics data with a focus on Antimicrobial Resistanceacceptedv0.12023-03-10 09:09:20 UTC902023-10-19 10:05:08 UTC820235397JulietteHayerMIVEGEC, University of Montpellier, IRD, CNRS, 34394, Montpellier, France, Laboratoire Mixte International Drug Resistance in Southeast Asia0000-0003-4899-9637JacquesDainatMIVEGEC, University of Montpellier, IRD, CNRS, 34394, Montpellier, France0000-0002-6629-0173EllaMarcyMIVEGEC, University of Montpellier, IRD, CNRS, 34394, Montpellier, France, Centre Hospitalier Universitaire (CHU) Lapeyronie, Montpellier, France0009-0002-6000-1665Anne-LaureBañulsMIVEGEC, University of Montpellier, IRD, CNRS, 34394, Montpellier, France, Laboratoire Mixte International Drug Resistance in Southeast Asia0000-0002-2106-866710.21105/joss.05397https://doi.org/10.5281/zenodo.8386399Python, Nextflowhttps://joss.theoj.org/papers/10.21105/joss.05397.pdfWhole Genome Shotgun, Genomics, Long reads sequencing technology, Short reads sequencing technology, Antimicrobial Resistance, Pangenometag:joss.theoj.org,2005:Paper/31472022-03-15T10:12:41Z2022-03-15T10:48:13Zmmrefpoints: Projecting long-term marine mammal abundance with bycatchacceptedv0.1.12021-11-02 00:12:18 UTC712022-03-15 10:12:41 UTC720223888MargaretC.SipleResource Assessment and Conservation Engineering Division, Alaska Fisheries Science Center, National Oceanic and Atmospheric Administration, Seattle, WA, 98115, USA0000-0002-4260-9856AndréE.PuntSchool of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat St, Seattle, WA 981150000-0001-8489-2488TessaB.FrancisPuget Sound Institute, University of Washington Tacoma, 326 East D Street, Tacoma, WA 98421, USA0000-0002-3383-5392PhilipS.HammondSea Mammal Research Unit, Scottish Oceans Institute, University of St Andrews, Fife KY16 8LB, UK0000-0002-2381-8302DennisHeinemannU.S. Marine Mammal Commission, 4340 East-West Hwy, Rm 700, Bethesda, MD 20814, USA0000-0002-1434-2445KristyJ.LongOffice of Protected Resources, NOAA's National Marine Fisheries Service, Silver Spring, MD 20910, USA0000-0001-6970-0935JeffreyMooreProtected Resources Division, NOAA SWFSC, La Jolla, CA 92037, USA0000-0003-3715-7442MaritzaSepúlvedaFacultad de Ciencias, Universidad de Valparaíso, Gran Bretaña 1111, Playa Ancha, Valparaíso, Chile0000-0002-1403-176XRandallR.ReevesOkapi Wildlife Associates, Hudson, Quebec, Canada0000-0002-6512-6507GuðjónMárSigurðssonMarine and Freshwater Research Institute, Skúlagata 4, 121, Reykjavík, Iceland0000-0001-9390-6693GísliVíkingssonMarine and Freshwater Research Institute, Skúlagata 4, 121, Reykjavík, Iceland0000-0002-4501-193XPaulR.WadeMarine Mammal Laboratory, NOAA AFSC, Seattle, WA, 98115-6349, USA0000-0003-2428-9323RobWilliamsOceans Initiative, 117 E. Louisa Street No. 135. Seattle, WA 98102, USA0000-0001-7496-453XAlexandreN.ZerbiniCascadia Research Collective, 218 ½ 4th Ave W, Olympia, WA, 98501, USA0000-0002-9776-660510.21105/joss.03888https://doi.org/10.5281/zenodo.6338110Rhttps://joss.theoj.org/papers/10.21105/joss.03888.pdfShiny, marine mammal bycatchtag:joss.theoj.org,2005:Paper/27672021-09-30T16:22:48Z2022-01-18T12:03:45ZCOVID-19 Lung Segmentationaccepted2.0.02021-06-16 14:26:47 UTC652021-09-30 16:22:48 UTC620213447RiccardoBiondiDepartment of Experimental, Diagnostic and Specialty Medicine of Bologna UniversityNicoCurtieDIMESLab, Department of Experimental, Diagnostic and Specialty Medicine of Bologna University0000-0001-5802-1195EnricoGiampierieDIMESLab, Department of Experimental, Diagnostic and Specialty Medicine of Bologna University0000-0003-2269-2338GastoneCastellaniDepartment of Experimental, Diagnostic and Specialty Medicine of Bologna University0000-0003-4892-925X10.21105/joss.03447https://doi.org/10.5281/zenodo.5535568Python, PowerShellhttps://joss.theoj.org/papers/10.21105/joss.03447.pdfradiomics, artificial-intelligence, machine-learning, deep-learning, medical-imaging, chest-CT, python3tag:joss.theoj.org,2005:Paper/26232021-06-04T21:44:11Z2021-06-05T03:34:21Zdataaimsr: An R Client for the Australian Institute of Marine Science Data Platform API which provides easy access to AIMS Data Platformacceptedv1.0.32021-05-05 08:11:36 UTC622021-06-04 21:44:11 UTC620213282DiegoR.BarnecheAustralian Institute of Marine Science, Crawley, WA 6009, Australia, The Indian Ocean Marine Research Centre, The University of Western Australia, Crawley, WA 6009, Australia0000-0002-4568-2362GregColemanAustralian Institute of Marine Science, Townsville, Qld 4810, AustraliaDuncanFermorAustralian Institute of Marine Science, Townsville, Qld 4810, AustraliaEduardoKleinAustralian Institute of Marine Science, Townsville, Qld 4810, AustraliaTobiasRobinsonAustralian Institute of Marine Science, Townsville, Qld 4810, AustraliaJasonSmithAustralian Institute of Marine Science, Townsville, Qld 4810, AustraliaJeffreyL.SheehanAustralian Institute of Marine Science, Townsville, Qld 4810, AustraliaShannonDowleyAustralian Institute of Marine Science, Townsville, Qld 4810, AustraliaDeanDittonAustralian Institute of Marine Science, Townsville, Qld 4810, AustraliaKevinGunnAustralian Institute of Marine Science, Townsville, Qld 4810, AustraliaGavinEricsonAustralian Institute of Marine Science, Townsville, Qld 4810, AustraliaMurrayLoganAustralian Institute of Marine Science, Townsville, Qld 4810, AustraliaMarkRehbeinAustralian Institute of Marine Science, Townsville, Qld 4810, Australia10.21105/joss.03282https://doi.org/10.5281/zenodo.4782786Rhttps://joss.theoj.org/papers/10.21105/joss.03282.pdfsea surface temperature, weather stations, long-term environmental monitoring, Australia, APItag:joss.theoj.org,2005:Paper/14372020-12-04T18:02:00Z2021-02-15T11:31:09ZAkmedoids R package for generating directionally-homogeneous clusters of longitudinal data setsacceptedv0.1.52020-01-13 14:07:03 UTC562020-12-04 18:02:00 UTC520202379MonsuruAdepejuCrime and Well-being Big Data Centre, Manchester Metropolitan University0000-0002-9006-4934SamuelLangtonCrime and Well-being Big Data Centre, Manchester Metropolitan University0000-0002-1322-1553JonBannisterCrime and Well-being Big Data Centre, Manchester Metropolitan University0000-0002-1350-510X10.21105/joss.02379https://doi.org/10.5281/zenodo.4294266Rhttps://joss.theoj.org/papers/10.21105/joss.02379.pdfAnchored k-medoids, k-means, crime, longitudinal clustering, long-term trendstag:joss.theoj.org,2005:Paper/18522020-11-17T15:49:05Z2021-02-15T11:30:17ZNodePy: A package for the analysis of numerical ODE solversaccepted0.92020-07-13 11:13:47 UTC552020-11-17 15:49:05 UTC520202515DavidI.KetchesonKing Abdullah University of Science and Technology0000-0002-1212-126XHendrikRanochaKing Abdullah University of Science and Technology0000-0002-3456-2277MatteoParsaniKing Abdullah University of Science and Technology0000-0001-7300-1280UmairBinWaheedKing Fahd University of Petroleum & Minerals0000-0002-5189-0694YiannisHadjimichaelEötvös Loránd Tudományegyetem0000-0003-3517-855710.21105/joss.02515https://doi.org/10.5281/zenodo.4275158Pythonhttps://joss.theoj.org/papers/10.21105/joss.02515.pdfnumerical analysis, differential equations, Runge-Kutta method, linear multistep methodtag:joss.theoj.org,2005:Paper/18682020-10-30T19:17:32Z2021-02-15T11:30:15ZRK-Opt: A package for the design of numerical ODE solversacceptedv1.0.02020-07-21 06:05:44 UTC542020-10-30 19:17:32 UTC520202514DavidI.KetchesonKing Abdullah University of Science and Technology, Saudi Arabia0000-0002-1212-126XMatteoParsaniKing Abdullah University of Science and Technology, Saudi Arabia0000-0001-7300-1280ZacharyJ.GrantOak Ridge National Laboratory, USA0000-0002-1293-4770AronJ.AhmadiaCapital One, USA0000-0002-2573-2481HendrikRanochaKing Abdullah University of Science and Technology, Saudi Arabia0000-0002-3456-227710.21105/joss.02514https://doi.org/10.5281/zenodo.4146740Matlab, Mathematica, Pythonhttps://joss.theoj.org/papers/10.21105/joss.02514.pdfnumerical analysis, differential equations, Runge-Kutta method, linear multistep method, strong stability preservation, absolute stabilitytag:joss.theoj.org,2005:Paper/16932020-10-10T17:32:12Z2021-02-15T11:30:37ZExploring meaningful visual effects and quantities of interest from dynamic models through dynamacacceptedv0.1.102020-05-27 17:24:48 UTC542020-10-10 17:32:12 UTC520202528SorenJordanAssistant Professor, Department of Political Science, Auburn University0000-0003-4201-1085AndrewQ.PhilipsAssistant Professor, Department of Political Science, University of Colorado Boulder10.21105/joss.02528https://doi.org/10.5281/zenodo.4057108Rhttps://joss.theoj.org/papers/10.21105/joss.02528.pdftime series, methodology, long-run effects, simulations, quantities of interesttag:joss.theoj.org,2005:Paper/12152020-03-13T12:31:02Z2021-02-15T11:31:38ZChaste: Cancer, Heart and Soft Tissue Environmentaccepted2019.12019-09-13 15:00:50 UTC472020-03-13 12:31:02 UTC520201848FergusR.CooperWolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Oxford, UK0000-0002-6221-4288RuthE.BakerWolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Oxford, UK0000-0002-6304-9333MiguelO.BernabeuCentre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, United Kingdom0000-0002-6456-3756RafelBordasDepartment of Computer Science, University of Oxford, Oxford, UK0000-0002-0856-544XLouiseBowlerDepartment of Computer Science, University of Oxford, Oxford, UK0000-0002-4910-9205AlfonsoBueno-OrovioDepartment of Computer Science, University of Oxford, Oxford, UK0000-0002-1634-3601HelenM.ByrneWolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Oxford, UK0000-0003-1771-5910ValentinaCarapellaDivision of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK0000-0001-9750-9425LouieCardone-NoottDepartment of Computer Science, University of Oxford, Oxford, UKJonathanCooperResearch IT Services, University College London, London, UK0000-0001-6009-3542SaraDuttaDepartment of Computer Science, University of Oxford, Oxford, UKBenjaminD.EvansCentre for Biomedical Modelling and Analysis, Living Systems Institute, University of Exeter, Exeter, UK, School of Psychological Science, University of Bristol, Bristol, UK0000-0002-1734-6070AlexanderG.FletcherSchool of Mathematics & Statistics, University of Sheffield, Sheffield, UK, Bateson Centre, University of Sheffield, Sheffield, UK0000-0003-0525-4336JamesA.GroganWolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Oxford, UKWenxianGuoDepartment of Computer Science, University of Saskatchewan, Canada0000-0001-8130-3326DanielG.HarveyDepartment of Computer Science, University of Oxford, Oxford, UKMauriceHendrixCentre for Mathematical Medicine & Biology, School of Mathematical Sciences, University of Nottingham, Nottingham, UK, Digital Research Service, University of Nottingham, Nottingham, UK0000-0002-6621-7996DavidKayDepartment of Computer Science, University of Oxford, Oxford, UK0000-0003-4984-3669JochenKursaweFaculty of Biology, Medicine and Health, University of Manchester, Manchester, UK0000-0002-0314-9623PhilipK.MainiWolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Oxford, UK0000-0002-0146-9164BethMcMillanDepartment of Computer Science, University of Oxford, Oxford, UK0000-0002-2605-1733GaryR.MiramsCentre for Mathematical Medicine & Biology, School of Mathematical Sciences, University of Nottingham, Nottingham, UK0000-0002-4569-4312JamesM.OsborneSchool of Mathematics and Statistics, University of Melbourne, Victoria, Australia0000-0002-5622-0104PrasPathmanathanOffice of Science and Engineering Laboratories (OSEL), Center for Devices and Radiological Health (CDRH), U.S. Food and Drug Administration (FDA), Silver Spring, MD 20993, USA0000-0003-2111-6689JoeM.Pitt-FrancisDepartment of Computer Science, University of Oxford, Oxford, UK0000-0002-5094-5403MartinRobinsonDepartment of Computer Science, University of Oxford, Oxford, UK0000-0002-1572-6782BlancaRodriguezDepartment of Computer Science, University of Oxford, Oxford, UK0000-0002-3435-7388RaymondJ.SpiteriDepartment of Computer Science, University of Saskatchewan, CanadaDavidJ.GavaghanDepartment of Computer Science, University of Oxford, Oxford, UK0000-0001-8311-320010.21105/joss.01848https://doi.org/10.5281/zenodo.3708497Python, Java, Matlabhttps://joss.theoj.org/papers/10.21105/joss.01848.pdfC++, cardiac electrophysiology, monodomain, bidomain, simulation, cancer, heart, lung, cell-basedtag:joss.theoj.org,2005:Paper/13402019-12-11T23:26:26Z2021-02-15T11:31:21Zalignparse: A Python package for parsing complex features from high-throughput long-read sequencingaccepted0.1.02019-11-19 23:52:10 UTC442019-12-11 23:26:26 UTC420191915KatharineH.d.CrawfordBasic Sciences and Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA, Department of Genome Sciences and Medical Scientist Training Program, University of Washington, Seattle, Washington, USA0000-0002-6223-4019JesseD.BloomBasic Sciences and Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA, Howard Hughes Medical Institute, Seattle, Washington, USA0000-0003-1267-340810.21105/joss.01915https://doi.org/10.5281/zenodo.3569587Python, Jupyter Notebookhttps://joss.theoj.org/papers/10.21105/joss.01915.pdfPacBio, deep mutational scanning, single-cell virus sequencing, genomics, sequencing