tag:joss.theoj.org,2005:/papers/tagged/PipelineJournal of Open Source Software2024-03-25T09:10:44ZJournal of Open Source Softwarehttps://joss.theoj.orgtag:joss.theoj.org,2005:Paper/48492024-03-25T09:10:44Z2024-03-26T00:00:59ZAcanthophis: a comprehensive plant hologenomics pipelineacceptedv1.0.02023-10-15 07:16:35 UTC952024-03-25 09:10:44 UTC920246062KevinD.MurrayMax Planck Institute for Biology Tübingen, 72076 Tübingen, Germany0000-0002-2466-1917JustinO.BorevitzResearch School of Biology, Australian National University, Canberra, Australia0000-0001-8408-3699DetlefWeigelMax Planck Institute for Biology Tübingen, 72076 Tübingen, Germany0000-0002-2114-7963NormanWarthmannResearch School of Biology, Australian National University, Canberra, Australia, FAO/IAEA Joint Centre of Nuclear Techniques in Food and Agriculture, Plant Breeding and Genetics Laboratory, Seibersdorf, Austria0000-0002-1178-840910.21105/joss.06062https://doi.org/10.5281/zenodo.10795245Pythonhttps://joss.theoj.org/papers/10.21105/joss.06062.pdfpython, snakemake, plants, metagenomics, variant calling, population genomics, reference-free classificationtag:joss.theoj.org,2005:Paper/43002024-02-21T08:51:15Z2024-02-23T09:04:14ZReducing the efforts to create reproducible analysis code with FieldTripacceptedhttps://github.com/fieldtrip/fieldtrip/commit/9cfc0a7e7b7871a1d9938552ce60041c59f3a5532023-03-10 17:12:47 UTC942024-02-21 08:51:15 UTC920245566MatsW.j.van EsDonders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen, The Netherlands, Oxford Centre for Human Brain Activity, Department of Psychiatry, University of Oxford, United Kingdom, Wellcome Centre for Integrative Neuroimaging, University of Oxford, Oxford, United Kingdom0000-0002-7133-509XEelkeSpaakDonders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen, The Netherlands0000-0002-2018-3364Jan-MathijsSchoffelenDonders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen, The Netherlands0000-0003-0923-6610RobertOostenveldDonders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen, The Netherlands, NatMEG, Karolinska Institutet, Stockholm, Sweden0000-0002-1974-129310.21105/joss.05566https://doi.org/10.5281/zenodo.10495308MATLAB, Mathematicahttps://joss.theoj.org/papers/10.21105/joss.05566.pdfFieldTrip Toolbox, reproducibility, analysis pipeline, open science, MEG, EEGtag:joss.theoj.org,2005:Paper/33022023-10-27T15:31:05Z2023-10-28T00:00:41ZUncertainSCI: A Python Package for Noninvasive Parametric Uncertainty Quantification of Simulation Pipelinesacceptedv0.2.0b2022-01-21 23:18:23 UTC902023-10-27 15:31:05 UTC820234249JessTateScientific Computing and Imaging Institute, University of Utah, Salt Lake City, UT, USA0000-0002-2934-1453ZexinLiuScientific Computing and Imaging Institute, University of Utah, Salt Lake City, UT, USA, Mathematics Department, University of Utah, Salt Lake City, UT, USA0000-0003-3409-5709JakeA.BergquistScientific Computing and Imaging Institute, University of Utah, Salt Lake City, UT, USA, Biomedical Engineering Department , University of Utah, Salt Lake City, UT, USA, Nora Eccles Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, UT, USA0000-0002-4586-6911SumientraRampersadPhysics Department, University of Massachusetts, Boston, MA, USA, Electrical and Computer Engineering Department, Northeastern University, Boston, MA, USA0000-0001-9860-4459DanWhiteScientific Computing and Imaging Institute, University of Utah, Salt Lake City, UT, USAChantelCharleboisScientific Computing and Imaging Institute, University of Utah, Salt Lake City, UT, USA, Biomedical Engineering Department , University of Utah, Salt Lake City, UT, USA0000-0002-4139-3539LindsayRuppScientific Computing and Imaging Institute, University of Utah, Salt Lake City, UT, USA, Biomedical Engineering Department , University of Utah, Salt Lake City, UT, USA, Nora Eccles Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, UT, USA0000-0002-2688-7688DanaH.BrooksElectrical and Computer Engineering Department, Northeastern University, Boston, MA, USA0000-0003-3231-6715RobS.MacLeodScientific Computing and Imaging Institute, University of Utah, Salt Lake City, UT, USA, Biomedical Engineering Department , University of Utah, Salt Lake City, UT, USA, Nora Eccles Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, UT, USA0000-0002-0000-0356AkilNarayanScientific Computing and Imaging Institute, University of Utah, Salt Lake City, UT, USA, Mathematics Department, University of Utah, Salt Lake City, UT, USA0000-0002-5914-420710.21105/joss.04249https://doi.org/10.5281/zenodo.8226383Pythonhttps://joss.theoj.org/papers/10.21105/joss.04249.pdfuncertainty quantification, computer modeling, polynomial chaos, bioelectricitytag:joss.theoj.org,2005:Paper/42822023-10-23T10:25:02Z2023-10-24T00:01:06ZQuaC: A Pipeline Implementing Quality Control Best Practices for Genome Sequencing and Exome Sequencing Dataaccepted1.32023-03-06 22:06:16 UTC902023-10-23 10:25:02 UTC820235313ManavalanGajapathyCenter for Computational Genomics and Data Science, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America, Department of Genetics, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America0000-0002-8606-0113BrandonM.WilkCenter for Computational Genomics and Data Science, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America, Department of Genetics, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America0000-0002-4110-2324ElizabethA.WortheyCenter for Computational Genomics and Data Science, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America, Department of Genetics, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America0000-0003-4083-776410.21105/joss.05313https://doi.org/10.5281/zenodo.10002036Jinja, Pythonhttps://joss.theoj.org/papers/10.21105/joss.05313.pdfsnakemake, quality control, genome sequencing, exome sequencing, QC review, multiqc, singularity, bam, vcftag:joss.theoj.org,2005:Paper/43942023-08-14T09:08:18Z2023-08-16T09:04:23ZPAS: a Python Anesthesia Simulator for drug controlacceptedv0.0.42023-04-07 15:16:16 UTC882023-08-14 09:08:18 UTC820235480BobAubouin-PairaultUniv. Grenoble Alpes, CNRS, Grenoble INP, GIPSA-lab, 38000 Grenoble, France, Univ. Grenoble Alpes, CNRS, Grenoble INP, VERIMAG, 38000 Grenoble, France0000-0003-0029-438XMirkoFiacchiniUniv. Grenoble Alpes, CNRS, Grenoble INP, GIPSA-lab, 38000 Grenoble, France0000-0002-3601-0302ThaoDangUniv. Grenoble Alpes, CNRS, Grenoble INP, VERIMAG, 38000 Grenoble, France0000-0002-3637-141510.21105/joss.05480https://doi.org/10.5281/zenodo.8171326Pythonhttps://joss.theoj.org/papers/10.21105/joss.05480.pdfAnesthesia, Drug Control, Drug effect modelling, Test pipelinetag:joss.theoj.org,2005:Paper/42882023-05-19T14:59:08Z2023-05-20T00:01:17ZVaMPy: An Automated and Objective Pipeline for Modeling Vascular Geometriesacceptedv1.0.12023-03-08 11:08:28 UTC852023-05-19 14:59:08 UTC820235278HenrikA.KjeldsbergDepartment of Computational Physiology, Simula Research Laboratory, Oslo, Norway0000-0002-7764-4248AslakW.BergersenDepartment of Computational Physiology, Simula Research Laboratory, Oslo, Norway0000-0001-5063-3680KristianValen-SendstadDepartment of Computational Physiology, Simula Research Laboratory, Oslo, Norway0000-0002-2907-017110.21105/joss.05278https://doi.org/10.5281/zenodo.7950605Pythonhttps://joss.theoj.org/papers/10.21105/joss.05278.pdfpre-processing, computational fluid dynamics, post-processing, vascular modeling, automated objective pipelinetag:joss.theoj.org,2005:Paper/42622023-05-11T08:31:02Z2023-05-12T00:01:06ZfRAT: an interactive, Python-based tool for region-of-interest summaries of functional imaging dataaccepted1.0.02023-02-24 14:54:52 UTC852023-05-11 08:31:02 UTC820235200ElliotHowleySchool of Psychology, University of Nottingham, Nottingham, United Kingdom0000-0002-3868-2516SusanFrancisSir Peter Mansfield Imaging Centre, University of Nottingham, Nottingham, United Kingdom, NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham, United Kingdom0000-0003-0903-7507DenisSchluppeckSchool of Psychology, University of Nottingham, Nottingham, United Kingdom0000-0002-0634-771310.21105/joss.05200https://doi.org/10.5281/zenodo.7877605Python, JavaScripthttps://joss.theoj.org/papers/10.21105/joss.05200.pdffMRI, Neuroscience, Nipype, Pipelinetag:joss.theoj.org,2005:Paper/38582023-02-20T17:45:21Z2023-04-18T07:24:31ZMetaGenePipe: An Automated, Portable Pipeline for Contig-based Functional and Taxonomic Analysisacceptedv.1.0.02022-09-08 01:21:00 UTC822023-02-20 17:45:21 UTC820234851BabakShabanMelbourne Data Analytics Platform, The University of Melbourne0000-0002-7393-810XMaria del MarQuirogaMelbourne Data Analytics Platform, The University of Melbourne0000-0002-8943-2808RobertTurnbullMelbourne Data Analytics Platform, The University of Melbourne0000-0003-1274-6750EdoardoTescariMelbourne Data Analytics Platform, The University of Melbourne0000-0003-1157-4897Kim-AnhLêCaoSchool of Mathematics and Statistics, Melbourne Integrative Genomics, The University of Melbourne0000-0003-3923-1116HeroenVerbruggenSchool of BioSciences, The University of Melbourne0000-0002-6305-474910.21105/joss.04851https://doi.org/10.26188/22032425wdl, Jupyter Notebook, Pythonhttps://joss.theoj.org/papers/10.21105/joss.04851.pdfmetagenomics, WDL, Singularity, Containerizationtag:joss.theoj.org,2005:Paper/39092023-02-20T08:07:25Z2023-02-21T00:00:54ZBlenderProc2: A Procedural Pipeline for Photorealistic Renderingacceptedv2.4.12022-09-21 11:36:12 UTC822023-02-20 08:07:25 UTC820234901MaximilianDenningerGerman Aerospace Center (DLR), Technical University of Munich (TUM)0000-0002-1557-2234DominikWinkelbauerGerman Aerospace Center (DLR), Technical University of Munich (TUM)0000-0001-7443-1071MartinSundermeyerGerman Aerospace Center (DLR), Technical University of Munich (TUM)0000-0003-0587-9643WoutBoerdijkGerman Aerospace Center (DLR), Technical University of Munich (TUM)0000-0003-0789-5970MarkusKnauerGerman Aerospace Center (DLR)0000-0001-8229-9410KlausH.StroblGerman Aerospace Center (DLR)0000-0001-8123-0606MatthiasHumtGerman Aerospace Center (DLR), Technical University of Munich (TUM)0000-0002-1523-9335RudolphTriebelGerman Aerospace Center (DLR), Technical University of Munich (TUM)0000-0002-7975-036X10.21105/joss.04901https://doi.org/10.5281/zenodo.7654630Pythonhttps://joss.theoj.org/papers/10.21105/joss.04901.pdfBlender, Photorealistic rendering, Simulation, Pipeline, Dataset creation, Neural networks, Indoor Scenetag:joss.theoj.org,2005:Paper/38152023-02-13T13:47:30Z2023-02-14T00:00:52Ztpcp: Tiny Pipelines for Complex Problems - A set of framework independent helpers for algorithms development and evaluationacceptedv0.9.02022-08-11 08:06:31 UTC822023-02-13 13:47:30 UTC820234953ArneKüderleMachine Learning and Data Analytics Lab (MaD Lab), Department Artificial Intelligence in Biomedical Engineering (AIBE), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)0000-0002-5686-281XRobertRicherMachine Learning and Data Analytics Lab (MaD Lab), Department Artificial Intelligence in Biomedical Engineering (AIBE), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)0000-0003-0272-5403RaulC.SîmpetruNeuromuscular Physiology and Neural Interfacing (N-squared) Laboratory, Department Artificial Intelligence in Biomedical Engineering (AIBE), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)0000-0003-0455-0168BjoernM.EskofierMachine Learning and Data Analytics Lab (MaD Lab), Department Artificial Intelligence in Biomedical Engineering (AIBE), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)0000-0002-0417-033610.21105/joss.04953https://doi.org/10.17605/OSF.IO/GKY2UPythonhttps://joss.theoj.org/papers/10.21105/joss.04953.pdfMachine Learning, Data Analysis