tag:joss.theoj.org,2005:/papers/tagged/LINKSJournal of Open Source Software2024-02-12T12:06:13ZJournal of Open Source Softwarehttps://joss.theoj.orgtag: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/46092024-02-05T20:21:25Z2024-02-06T00:00:57Zprospect: an R package to link leaf optical properties with their chemical and structural properties with the leaf model PROSPECTacceptedv1.3.02023-07-17 16:12:52 UTC942024-02-05 20:21:25 UTC920246027Jean-BaptisteFéretTETIS, INRAE, AgroParisTech, CIRAD, CNRS, Université Montpellier, Montpellier, France0000-0002-0151-1334Floriande BoissieuTETIS, INRAE, AgroParisTech, CIRAD, CNRS, Université Montpellier, Montpellier, France0000-0002-2185-995210.21105/joss.06027https://doi.org/10.5281/zenodo.10480410Rhttps://joss.theoj.org/papers/10.21105/joss.06027.pdfleaf spectroscopy, vegetation biophysical properties, remote sensing, physical modeling, iterative optimizationtag: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/41672023-04-29T07:05:40Z2023-05-02T07:29:08Zhdt-rs: A Rust library for the Header Dictionary Triples binary RDF compression formataccepted0.0.112023-01-17 15:48:29 UTC842023-04-29 07:05:40 UTC820235114KonradHöffnerInstitute for Medical Informatics, Statistics, and Epidemiology, Medical Faculty, Leipzig University0000-0001-7358-3217TimBaccaertIndependent Researcher, Belgium10.21105/joss.05114https://doi.org/10.5281/zenodo.7871117https://joss.theoj.org/papers/10.21105/joss.05114.pdfRust, HDT, RDF, linked data, semantic webtag:joss.theoj.org,2005:Paper/40862023-03-14T19:50:49Z2023-08-17T10:51:59ZAtramhasis: An online SKOS vocabulary editoraccepted1.2.02022-12-14 11:18:48 UTC832023-03-14 19:50:49 UTC820235040KoenVan DaeleFlanders Heritage Agency, Belgium0000-0002-8153-2978TinneCahyGEO Solutions, BelgiumWimDe ClercqGEO Solutions, BelgiumJonasGeuensFlanders Heritage Agency, Belgium0000-0001-8197-5034BramGoessensFlanders Heritage Agency, Belgium0000-0001-6693-0866JonathanPirauxGEO Solutions, BelgiumBartSaelenGEO Solutions, BelgiumMaartenTaeymansGEO Solutions, BelgiumCedrikVanderhaegenFlanders Heritage Agency, Belgium10.21105/joss.05040https://doi.org/10.5281/zenodo.7733994Python, Mako, Ruby, JavaScripthttps://joss.theoj.org/papers/10.21105/joss.05040.pdfSKOS, thesaurus, vocabulary, linked datatag: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 mappingtag:joss.theoj.org,2005:Paper/32612022-03-11T23:49:25Z2023-01-28T16:53:54Znsink: An R package for flow path nitrogen removal estimationacceptedv1.1.02021-12-20 20:39:12 UTC712022-03-11 23:49:25 UTC720224039JeffreyW.HollisterU. S. Environmental Protection Agency, Atlantic Coastal Environmental Sciences Division, Narragansett, RI 028820000-0002-9254-9740DorothyQ.KelloggUniversity of Rhode Island, Department of Natural Resources Science, Kingston, RI 028810000-0002-9509-4606QianLei-ParentUniversity of Connecticut, Center for Land Use Education and Research, Storrs, CT 062680000-0002-1904-2513EmilyWilsonUniversity of Connecticut, Center for Land Use Education and Research, Storrs, CT 062680000-0003-0035-5752CaryChadwickUniversity of Connecticut, Center for Land Use Education and Research, Storrs, CT 062680000-0002-6952-7535DavidDicksonUniversity of Connecticut, Center for Land Use Education and Research, Storrs, CT 062680000-0002-2660-6460ArthurGoldUniversity of Rhode Island, Department of Natural Resources Science, Kingston, RI 028810000-0002-0290-1377ChesterArnoldUniversity of Connecticut, Center for Land Use Education and Research, Storrs, CT 0626810.21105/joss.04039https://doi.org/10.5281/zenodo.6341565Rhttps://joss.theoj.org/papers/10.21105/joss.04039.pdfnitrogen, nitrogen sinks, landscape, gistag:joss.theoj.org,2005:Paper/31362022-03-03T18:42:06Z2022-03-04T00:01:11Z3D Line Radiative Transfer & Synthetic Observations with Magritteaccepted0.0.12021-10-27 19:03:50 UTC712022-03-03 18:42:06 UTC720223905FrederikDe CeusterDepartment of Physics and Astronomy, University College London, London, UK, Institute of Astronomy, KU Leuven, Leuven, Belgium0000-0001-5887-8498ThomasCeulemansInstitute of Astronomy, KU Leuven, Leuven, BelgiumAtulitSrivastavaInstitute of Astronomy, KU Leuven, Leuven, BelgiumWardHomanInstitut d’Astronomie et d’Astrophysique, Université Libre de Bruxelles, Brussels, Belgium0000-0001-7314-5081JanBolteInstitute of Astronomy, KU Leuven, Leuven, Belgium0000-0002-7991-9663JeremyYatesDepartment of Physics and Astronomy, University College London, London, UK0000-0003-1954-8749LeenDecinInstitute of Astronomy, KU Leuven, Leuven, Belgium, School of Chemistry, University of Leeds, Leeds, UK0000-0002-5342-8612PeterBoyleSchool of Physics and Astronomy, The University of Edinburgh, Edinburgh, UK, Brookhaven National Laboratory, NY, USA0000-0002-8960-1587JamesHetheringtonDepartment of Computer Science, University College London, London, UK0000-0001-6993-031910.21105/joss.03905https://doi.org/10.5281/zenodo.6320469Python, C++https://joss.theoj.org/papers/10.21105/joss.03905.pdfastronomy, radiative transfertag:joss.theoj.org,2005:Paper/16202021-11-04T21:51:50Z2021-11-05T00:00:21Zgrlc: the git repository linked data API constructor.acceptedv1.3.42020-05-20 18:05:44 UTC672021-11-04 21:51:50 UTC620212731AlbertMeroño-PeñuelaKing's College London0000-0003-4646-5842CarlosMartinez-OrtizNetherlands eScience Center0000-0001-5565-757710.21105/joss.02731https://doi.org/10.5281/zenodo.5644276Python, JavaScripthttps://joss.theoj.org/papers/10.21105/joss.02731.pdflinked data, API buildertag:joss.theoj.org,2005:Paper/26212021-07-01T04:49:26Z2021-07-02T00:01:30ZDataLad: distributed system for joint management of code, data, and their relationshipaccepted0.14.32021-05-03 19:52:41 UTC632021-07-01 04:49:26 UTC620213262YaroslavO.HalchenkoCenter for Open Neuroscience, Department of Psychological and Brain Sciences, Dartmouth College, Hanover, NH, USA0000-0003-3456-2493KyleMeyerCenter for Open Neuroscience, Department of Psychological and Brain Sciences, Dartmouth College, Hanover, NH, USABenjaminPoldrackInstitute of Neuroscience and Medicine, Brain & Behaviour (INM-7), Research Center Jülich, Jülich, Germany0000-0001-7628-0801DebanjumSinghSolankyCenter for Open Neuroscience, Department of Psychological and Brain Sciences, Dartmouth College, Hanover, NH, USA0000-0002-0774-6564AdinaS.WagnerInstitute of Neuroscience and Medicine, Brain & Behaviour (INM-7), Research Center Jülich, Jülich, Germany0000-0003-2917-3450JasonGorsCenter for Open Neuroscience, Department of Psychological and Brain Sciences, Dartmouth College, Hanover, NH, USADaveMacFarlaneMcGill Center for Integrative Neuroscience, Montreal, CanadaDorianPustinaCHDI Management/CHDI Foundation, Princeton, NJ, USA0000-0002-2834-7220VanessaSochatLawrence Livermore National Lab, Livermore, CA, USA0000-0002-4387-3819SatrajitS.GhoshMassachusetts Institute of Technology, Cambridge, MA, USA0000-0002-5312-6729ChristianMönchInstitute of Neuroscience and Medicine, Brain & Behaviour (INM-7), Research Center Jülich, Jülich, Germany0000-0002-3092-0612ChristopherJ.MarkiewiczStanford University, Stanford, CA, USA0000-0002-6533-164XLauraWaiteInstitute of Neuroscience and Medicine, Brain & Behaviour (INM-7), Research Center Jülich, Jülich, Germany0000-0003-2213-7465IlyaShlyakhterQuest Diagnostics, Marlborough, MA, USA0000-0002-9854-5118Alejandrode la VegaThe University of Austin at Austin, Austin, TX, USA0000-0001-9062-3778SoichiHayashiIndiana University, Bloomington, IN, USA0000-0003-3641-3491ChristianOlafHäuslerInstitute of Neuroscience and Medicine, Brain & Behaviour (INM-7), Research Center Jülich, Jülich, Germany, Institute of Systems Neuroscience, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany0000-0002-0936-317XJean-BaptistePolineFaculty of Medicine and Health Sciences, McConnell Brain Imaging Center, McGill University, Montreal, Canada0000-0002-9794-749XTobiasKadelkaInstitute of Neuroscience and Medicine, Brain & Behaviour (INM-7), Research Center Jülich, Jülich, Germany0000-0002-0152-3490KustiSkyténUniversity of Oslo, Oslo, Norway0000-0001-7460-1157DorotaJareckaMassachusetts Institute of Technology, Cambridge, MA, USA0000-0001-8282-2988DavidKennedyUniversity of Massachusetts Medical School, Worcester, MA, USA0000-0002-9377-0797TedStraussMontreal Neurological Institute, McGill University, Montreal, Canada0000-0002-1927-666XMattCieslakUniversity of Pennsylvania, Philadelphia, PA0000-0002-1931-4734PeterVavraDepartment of Biological Psychology, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany0000-0001-8432-5459Horea-IoanIoanasDepartment of Biological Engineering, Massachusetts Institute of Technology, Cambridge, USA0000-0001-7037-2449RobinSchneiderIndependent Developer, Germany0000-0003-1952-5459MikaPflügerPotsdam Institute for Climate Impact Research (PIK) e. V., Potsdam, Germany0000-0002-7814-8916JamesV.HaxbyCenter for Open Neuroscience, Department of Psychological and Brain Sciences, Dartmouth College, Hanover, NH, USASimonB.EickhoffInstitute of Neuroscience and Medicine, Brain & Behaviour (INM-7), Research Center Jülich, Jülich, Germany, Institute of Systems Neuroscience, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany0000-0001-6363-2759MichaelHankeInstitute of Neuroscience and Medicine, Brain & Behaviour (INM-7), Research Center Jülich, Jülich, Germany, Institute of Systems Neuroscience, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany0000-0001-6398-637010.21105/joss.03262https://doi.org/10.5281/zenodo.5034875https://joss.theoj.org/papers/10.21105/joss.03262.pdfPython, command line, version control, data management, data distribution, data provenance, reproducibility