tag:joss.theoj.org,2005:/papers/tagged/memoryJournal of Open Source Software2023-07-22T03:05:19ZJournal of Open Source Softwarehttps://joss.theoj.orgtag:joss.theoj.org,2005:Paper/41612023-07-22T03:05:19Z2023-07-23T00:01:35ZBridgeStan: Efficient in-memory access to the methods of a Stan modelacceptedv.1.0.02023-01-10 21:55:16 UTC872023-07-22 03:05:19 UTC820235236EdwardA.RoualdesCalifornia State University, Chico0000-0002-8757-3463BrianWardCenter for Computational Mathematics, Flatiron Institute0000-0002-9841-3342BobCarpenterCenter for Computational Mathematics, Flatiron Institute0000-0002-2433-9688AdrianSeyboldtPyMC Labs0000-0002-4239-4541SethD.AxenCluster of Excellence Machine Learning: New Perspectives for Science, University of Tübingen0000-0003-3933-824710.21105/joss.05236https://doi.org/10.5281/zenodo.8169248R, C, Juliahttps://joss.theoj.org/papers/10.21105/joss.05236.pdfStan, Python, Rust, C++, automatic differentiationtag:joss.theoj.org,2005:Paper/44662023-07-19T18:21:11Z2023-07-20T00:01:39Zshmem4py: OpenSHMEM for Pythonacceptedv0.12023-05-02 19:53:20 UTC872023-07-19 18:21:11 UTC820235444MarcinRogowskiKing Abdullah University of Science and Technology, Saudi Arabia0000-0002-5662-2082LisandroDalcinKing Abdullah University of Science and Technology, Saudi Arabia0000-0001-8086-0155JeffR.HammondNVIDIA Helsinki Oy, Finland0000-0003-3181-8190DavidE.KeyesKing Abdullah University of Science and Technology, Saudi Arabia0000-0002-4052-722410.21105/joss.05444https://doi.org/10.5281/zenodo.8143862Python, Chttps://joss.theoj.org/papers/10.21105/joss.05444.pdfPGAS, OpenSHMEM, shared memory, High Performance Computingtag:joss.theoj.org,2005:Paper/39452022-12-28T09:07:11Z2022-12-29T00:01:16ZMetagenomic classification with KrakenUniq on low-memory computersacceptedv1.0.12022-10-06 17:50:41 UTC802022-12-28 09:07:11 UTC720224908ChristopherPockrandtCenter for Computational Biology, Johns Hopkins University, Baltimore, MD 21218, USA, Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USAAlekseyV.ZiminCenter for Computational Biology, Johns Hopkins University, Baltimore, MD 21218, USA, Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USAStevenL.SalzbergCenter for Computational Biology, Johns Hopkins University, Baltimore, MD 21218, USA, Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA, Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA, Department of Biostatistics, Johns Hopkins University, Baltimore, MD 21218, USA10.21105/joss.04908https://doi.org/10.5281/zenodo.7459217Perlhttps://joss.theoj.org/papers/10.21105/joss.04908.pdfmetagenomics, classification, speciestag:joss.theoj.org,2005:Paper/32942022-06-09T14:33:25Z2022-06-10T00:01:17ZGridapDistributed: a massively parallel finite element toolbox in Juliaacceptedv0.2.42022-01-18 08:34:54 UTC742022-06-09 14:33:25 UTC720224157SantiagoBadiaSchool of Mathematics, Monash University, Clayton, Victoria, 3800, Australia., Centre Internacional de Mètodes Numèrics en Enginyeria, Esteve Terrades 5, E-08860 Castelldefels, Spain.0000-0003-2391-4086AlbertoF.MartínSchool of Mathematics, Monash University, Clayton, Victoria, 3800, Australia.0000-0001-5751-4561FrancescVerdugoCentre Internacional de Mètodes Numèrics en Enginyeria, Esteve Terrades 5, E-08860 Castelldefels, Spain.0000-0003-3667-443X10.21105/joss.04157https://doi.org/10.5281/zenodo.6622081Juliahttps://joss.theoj.org/papers/10.21105/joss.04157.pdfPartial Differential Equations, Finite Elements, Distributed memory parallelization, High Performance Computingtag:joss.theoj.org,2005:Paper/18362021-10-05T12:25:19Z2021-10-06T00:04:29ZThe o80 C++ templated toolbox: Designing customized Python APIs for synchronizing realtime processesaccepted1.02020-07-07 13:14:58 UTC662021-10-05 12:25:19 UTC620212752VincentBerenzMax Planck Institute for Intelligent Systems, Tübingen, GermanyMaximilienNaveauMax Planck Institute for Intelligent Systems, Tübingen, GermanyFelixWidmaierMax Planck Institute for Intelligent Systems, Tübingen, GermanyManuelWüthrichMax Planck Institute for Intelligent Systems, Tübingen, GermanyJean-ClaudePassyMax Planck Institute for Intelligent Systems, Tübingen, GermanySimonGuistMax Planck Institute for Intelligent Systems, Tübingen, GermanyDieterBüchlerMax Planck Institute for Intelligent Systems, Tübingen, Germany10.21105/joss.02752https://doi.org/10.5281/zenodo.5357876C++https://joss.theoj.org/papers/10.21105/joss.02752.pdfPython, processes, robotics, shared memorytag:joss.theoj.org,2005:Paper/19942020-10-15T12:31:09Z2021-02-15T11:30:04ZPsifr: Analysis and visualization of free recall dataacceptedv0.4.22020-08-28 23:03:38 UTC542020-10-15 12:31:09 UTC520202669NealW.MortonResearch Fellow, Center for Learning and Memory, The University of Texas at Austin0000-0002-2631-271010.21105/joss.02669https://doi.org/10.5281/zenodo.4086188Python, Matlabhttps://joss.theoj.org/papers/10.21105/joss.02669.pdfpsychology, memory, researchtag:joss.theoj.org,2005:Paper/12322019-11-20T18:18:29Z2021-02-15T11:31:34Zmemochange: An R package for estimation procedures and tests for persistent time seriesacceptedv1.0.12019-09-24 21:01:18 UTC432019-11-20 18:18:29 UTC420191820KaiWengerInstitute of Statistics, Leibniz University Hannover0000-0002-6566-0427JanisBeckerInstitute of Statistics, Leibniz University Hannover0000-0001-5104-633010.21105/joss.01820https://doi.org/10.5281/zenodo.3543826Rhttps://joss.theoj.org/papers/10.21105/joss.01820.pdftime series analysis, long memory, structural change, breaks in persistencetag:joss.theoj.org,2005:Paper/11012019-07-30T16:20:45Z2021-02-15T11:31:58ZMemCNN: A Python/PyTorch package for creating memory-efficient invertible neural networksaccepted0.3.32019-07-10 22:18:15 UTC392019-07-30 16:20:45 UTC420191576SilC.van de LeemputRadboud University Medical Center, Department of Radiology and Nuclear Medicine, Nijmegen, The Netherlands0000-0001-6047-3051JonasTeuwenRadboud University Medical Center, Department of Radiology and Nuclear Medicine, Nijmegen, The NetherlandsBramvan GinnekenRadboud University Medical Center, Department of Radiology and Nuclear Medicine, Nijmegen, The NetherlandsRashindraManniesingRadboud University Medical Center, Department of Radiology and Nuclear Medicine, Nijmegen, The Netherlands10.21105/joss.01576https://doi.org/10.5281/zenodo.3353604Pythonhttps://joss.theoj.org/papers/10.21105/joss.01576.pdfMemCNN, PyTorch, machine learning, invertible networks, deep learningtag:joss.theoj.org,2005:Paper/8552019-04-03T15:30:45Z2021-02-15T11:32:32Ziced: fast and memory efficient normalization of contact mapsacceptedv0.5.12019-02-11 16:51:44 UTC362019-04-03 15:30:45 UTC420191286NelleVaroquauxUniversity of California, Berkeley0000-0002-8748-6546NicolasServantInstitut Curie, INSERM U900, Mines ParisTech0000-0003-1678-741010.21105/joss.01286https://doi.org/10.5281/zenodo.2622857PowerShell, Pythonhttps://joss.theoj.org/papers/10.21105/joss.01286.pdfHi-C contact count, Normalizationtag:joss.theoj.org,2005:Paper/4332018-06-18T11:50:17Z2021-02-15T11:33:33Zmmappickle: Python 3 module to store memory-mapped numpy array in pickle formatacceptedv1.0.02018-03-12 10:07:15 UTC262018-06-18 11:50:17 UTC32018651LaurentFasnachtUniversity of Neuchâtel0000-0002-9853-820910.21105/joss.00651https://doi.org/10.5281/zenodo.1291734Pythonhttps://joss.theoj.org/papers/10.21105/joss.00651.pdfmemory-mapped, mmap, memmap, numpy array, pickle