tag:joss.theoj.org,2005:/papers/tagged/ode?page=2Journal of Open Source Software2020-11-17T15:49:05ZJournal of Open Source Softwarehttps://joss.theoj.orgtag: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/16692020-09-07T23:50:55Z2021-02-15T11:30:43ZFlint: a simulator for biological and physiological models in ordinary and stochastic differential equationsacceptedv2.3.02020-05-22 02:28:34 UTC532020-09-07 23:50:55 UTC520202331TakeshiAbeGraduate School of Medicine, Yamaguchi University0000-0002-7074-4561YoshiyukiAsaiGraduate School of Medicine, Yamaguchi University0000-0001-5519-430610.21105/joss.02331https://doi.org/10.5281/zenodo.4017040M4, C++, Chttps://joss.theoj.org/papers/10.21105/joss.02331.pdfbiology, physiology, numerical analysis, simulation, ODE, SDEtag:joss.theoj.org,2005:Paper/12722020-07-20T20:17:00Z2021-02-15T11:31:33Zpylustrator: code generation for reproducible figures for publicationacceptedv0.12.02019-10-04 08:52:20 UTC512020-07-20 20:17:00 UTC520201989RichardGerumDepartment of Physics, University of Erlangen-Nürnberg, Germany0000-0001-5893-265010.21105/joss.01989https://doi.org/10.5281/zenodo.3952417Pythonhttps://joss.theoj.org/papers/10.21105/joss.01989.pdfreproducibility, code generation, interactive, matplotlib, plotting, drag, styletag:joss.theoj.org,2005:Paper/15282020-06-19T06:23:19Z2021-02-15T11:30:57ZLTRpred: de novo annotation of intact retrotransposonsacceptedv1.1.02020-02-28 12:49:43 UTC502020-06-19 06:23:19 UTC520202170Hajk-GeorgDrostThe Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge CB2 1LR, UK, Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tuebingen, Germany0000-0002-1567-306X10.21105/joss.02170https://doi.org/10.5281/zenodo.3895754R, UnrealScripthttps://joss.theoj.org/papers/10.21105/joss.02170.pdfretrotransposon annotation, de novo functional annotation of retrotransposons, meta-genome scale retrotransposon annotation, transposable elements, mobile transposable elements, genome dynamicstag:joss.theoj.org,2005:Paper/13812020-03-20T00:32:09Z2021-02-15T11:31:19ZAnnotation Sniffer: A tool to Extract Code Annotations Metricsacceptedv2.0.02019-11-29 13:29:48 UTC472020-03-20 00:32:09 UTC520201960PhyllipeLimaCDG, National Institute of Telecommunications - INATEL, Brazil, LAC, National Institute for Space Research - INPE, Brazil0000-0002-8358-4405EduardoGuerraLAC, National Institute for Space Research - INPE, Brazil0000-0001-5555-3487PauloMeirellesEPM, Federal University of São Paulo - UNIFESP, Brazil, IME, University of São Paulo - USP, Brazil0000-0002-8923-281410.21105/joss.01960https://doi.org/10.5281/zenodo.3701910Java, Pythonhttps://joss.theoj.org/papers/10.21105/joss.01960.pdfmetadata, annotations, software-engineering, source-code-analysistag:joss.theoj.org,2005:Paper/8502020-02-16T12:29:51Z2021-02-15T11:32:32ZRclean: A Tool for Writing Cleaner, More Transparent Codeacceptedv1.0.12019-02-07 21:53:10 UTC462020-02-16 12:29:51 UTC520201312MatthewK.LauHarvard Forest, Harvard University0000-0003-3758-2406ThomasF. J.-M PasquierDepartment of Computer Science, University of Bristol, School of Engineering and Applied Science, Harvard University0000-0001-6876-1306MargoSeltzerDepartment of Computer Science, University of British Columbia0000-0002-2165-465810.21105/joss.01312https://doi.org/10.5281/zenodo.3665732Rhttps://joss.theoj.org/papers/10.21105/joss.01312.pdfreproducibility, transparency, code cleaning, data provenancetag:joss.theoj.org,2005:Paper/12732019-12-20T01:51:18Z2021-02-15T11:31:33ZOwlDE: making ODEs first-class Owl citizensacceptedv0.2.02019-10-04 14:05:03 UTC442019-12-20 01:51:18 UTC420191812MarcelloSeriBernoulli Institute for Mathematics, Computer Science and Artificial Intelligence, University of Groningen0000-0002-8563-5894Ta-ChuKaoComputational and Biological Learning Lab, Department of Engineering, University of Cambridge10.21105/joss.01812https://doi.org/10.5281/zenodo.3584264OCamlhttps://joss.theoj.org/papers/10.21105/joss.01812.pdfOrdinary differential equations, Geometric integration, Numerical integration, Neural ODEtag:joss.theoj.org,2005:Paper/11472019-09-20T00:00:00Z2021-02-15T11:31:49ZSBMLtoODEpy: A software program for converting SBML models into ODE models in Pythonacceptedv.1.0.22019-08-02 14:48:58 UTC532019-09-20 00:00:00 UTC520201643SteveM.RuggieroSchool of Chemical Engineering, Oklahoma State UniversityAshleeN. FordVersyptSchool of Chemical Engineering, Oklahoma State University0000-0001-9059-570310.21105/joss.01643https://doi.org/10.5281/zenodo.3441677Jupyter Notebook, JavaScripthttps://joss.theoj.org/papers/10.21105/joss.01643.pdfPython, Systems Biology, Modelingtag:joss.theoj.org,2005:Paper/9912019-08-10T12:45:50Z2021-02-15T11:32:12ZOnToCode: Template-based code-generation from ontologiesaccepted1.0.02019-05-08 05:42:28 UTC402019-08-10 12:45:50 UTC420191513PhilippMatthiasSchäferDLR Institute of Data Science, Mälzerstraße 3, 07745 Jena, Germany0000-0003-3931-667010.21105/joss.01513https://doi.org/10.5281/zenodo.3361131Python, JavaScripthttps://joss.theoj.org/papers/10.21105/joss.01513.pdfcode generation, semantic modeling, software engineering