tag:joss.theoj.org,2005:/papers/tagged/LC-NEJournal 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/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/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/32822022-03-22T12:33:30Z2022-03-23T00:00:45ZPyPVRPM: Photovoltaic Reliability and Performance Model in Pythonacceptedv1.6.02022-01-13 23:30:03 UTC712022-03-22 12:33:30 UTC720224093BrandonSilvaUniversity of Central FloridaPaulLunisUniversity of Central FloridaMariosTheristisSandia National LaboratoriesHubertSeigneurUniversity of Central Florida10.21105/joss.04093https://doi.org/10.5281/zenodo.6355115Pythonhttps://joss.theoj.org/papers/10.21105/joss.04093.pdfLCOE, Photovoltaic, Solar, Energy, Cost modeltag: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/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, reproducibilitytag:joss.theoj.org,2005:Paper/18722021-06-23T16:08:27Z2021-06-25T03:08:40ZBacting: a next generation, command line version of Bioclipseaccepted0.0.112020-07-22 08:54:08 UTC622021-06-23 16:08:27 UTC620212558EgonWillighagenDept of Bioinformatics - BiGCaT, NUTRIM, Maastricht University0000-0001-7542-028610.21105/joss.02558https://doi.org/10.5281/zenodo.4942022Javahttps://joss.theoj.org/papers/10.21105/joss.02558.pdfbioinformatics, cheminformatics, Bioclipsetag:joss.theoj.org,2005:Paper/25802021-05-17T21:13:13Z2021-05-18T00:00:34ZMCALF: Multi-Component Atmospheric Line Fittingacceptedv0.2.02021-04-19 19:08:29 UTC612021-05-17 21:13:13 UTC620213265ConorD.MacBrideAstrophysics Research Centre, School of Mathematics and Physics, Queen's University Belfast, Belfast, BT7 1NN, UK0000-0002-9901-8723DavidB.JessAstrophysics Research Centre, School of Mathematics and Physics, Queen's University Belfast, Belfast, BT7 1NN, UK, Department of Physics and Astronomy, California State University Northridge, Northridge, CA 91330, U.S.A.0000-0002-9155-803910.21105/joss.03265https://doi.org/10.5281/zenodo.4767888Pythonhttps://joss.theoj.org/papers/10.21105/joss.03265.pdfastronomy, solar physics, spectrum, spectra, fitting, absorption, emission, voigttag:joss.theoj.org,2005:Paper/23732021-04-15T16:28:08Z2021-04-16T00:03:06Zkallisto: A command-line interface to simplify computational modelling and the generation of atomic featuresacceptedv1.0.12021-02-05 11:38:42 UTC602021-04-15 16:28:08 UTC620213050EikeCaldeweyherData Science and Modelling, Pharmaceutical Science, R&D, AstraZeneca, Gothenburg, Sweden0000-0002-3985-595X10.21105/joss.03050https://doi.org/10.5281/zenodo.4692147Pythonhttps://joss.theoj.org/papers/10.21105/joss.03050.pdfPoetry, Atomic Features, Machine Learning, Computational Chemistry, Pharmaceutical Sciencetag:joss.theoj.org,2005:Paper/19172020-08-26T18:23:52Z2022-01-18T11:41:31ZSALSA: A Python Package for Constructing Synthetic Quasar Absorption Line Catalogs from Astrophysical Hydrodynamic Simulationsacceptedv0.1.02020-07-28 15:04:13 UTC522020-08-26 18:23:52 UTC520202581BrendanI.BoydDepartment of Physics and Astronomy, Michigan State UniversityDevinW.SilviaDepartment of Computational Mathematics, Science and Engineering, Michigan State UniversityBrianW.O'SheaDepartment of Physics and Astronomy, Michigan State University, Department of Computational Mathematics, Science and Engineering, Michigan State University, National Superconducting Cyclotron Laboratory, Michigan State UniversityJasonTumlinsonSpace Telescope Science Institute, Department of Physics & Astronomy, Johns Hopkins UniversityMollyS.PeeplesSpace Telescope Science Institute, Department of Physics & Astronomy, Johns Hopkins UniversityNicholasEarlSpace Telescope Science Institute10.21105/joss.02581https://doi.org/10.5281/zenodo.4002067Jupyter Notebook, Pythonhttps://joss.theoj.org/papers/10.21105/joss.02581.pdfastronomy, simulation, spectra