tag:joss.theoj.org,2005:/papers/edited_by/@brainstormJournal of Open Source Software2020-01-16T18:52:14ZJournal of Open Source Softwarehttps://joss.theoj.orgtag:joss.theoj.org,2005:Paper/10782020-01-16T18:52:14Z2021-02-15T11:32:02ZAdeft: Acromine-based Disambiguation of Entities from Text with applications to the biomedical literatureaccepted0.3.02019-06-25 18:46:30 UTC452020-01-16 18:52:14 UTC520201708AlbertSteppiLaboratory of Systems Pharmacology, Harvard Medical School0000-0001-5871-6245BenjaminM.GyoriLaboratory of Systems Pharmacology, Harvard Medical School0000-0001-9439-5346JohnA.BachmanLaboratory of Systems Pharmacology, Harvard Medical School0000-0001-6095-246610.21105/joss.01708https://doi.org/10.5281/zenodo.3610528Python, JavaScript, Jupyter Notebookhttps://joss.theoj.org/papers/10.21105/joss.01708.pdfnatural language processing, text mining, named entity disambiguation, acronyms, Acrominetag:joss.theoj.org,2005:Paper/10932019-10-01T23:48:40Z2021-02-15T11:31:59Zneurone_loader: A Python module for loading EEG data recorded with Bittium NeurOneacceptedv1.1.02019-07-06 17:10:38 UTC422019-10-01 23:48:40 UTC420191626FelixA.HeilmeyerTranslational Neurotechnology Lab, Department of Neurosurgery, University of Freiburg–Medical Center, Freiburg im Breisgau, Germany0000-0002-9068-2679TonioBallTranslational Neurotechnology Lab, Department of Neurosurgery, University of Freiburg–Medical Center, Freiburg im Breisgau, Germany10.21105/joss.01626https://doi.org/10.5281/zenodo.3468534Pythonhttps://joss.theoj.org/papers/10.21105/joss.01626.pdfneuroscience, neurophysiology, healthcare, EEG, file formatstag:joss.theoj.org,2005:Paper/7112019-06-17T19:05:22Z2021-02-15T11:32:50ZQComms QKD Software Toolkitaccepted0.32018-10-29 19:55:15 UTC382019-06-17 19:05:22 UTC420191119RichardCollinsUniversity of Bristol0000-0002-6238-990XDjeylanAktasUniversity of Bristol0000-0002-5747-058610.21105/joss.01119https://doi.org/10.5281/zenodo.3247364XSLThttps://joss.theoj.org/papers/10.21105/joss.01119.pdfc++, qkd, physics, security, quantumtag:joss.theoj.org,2005:Paper/9212019-06-10T11:52:03Z2021-02-15T11:32:25ZMPIFiles.jl: A Julia Package for Magnetic Particle Imaging Filesacceptedv0.5.02019-03-09 21:12:24 UTC382019-06-10 11:52:03 UTC420191331TobiasKnoppSection for Biomedical Imaging, University Medical Center Hamburg-Eppendorf, Institute for Biomedical Imaging, Hamburg University of Technology0000-0002-1589-8517MartinMöddelSection for Biomedical Imaging, University Medical Center Hamburg-Eppendorf, Institute for Biomedical Imaging, Hamburg University of Technology0000-0002-4737-7863FlorianGrieseSection for Biomedical Imaging, University Medical Center Hamburg-Eppendorf, Institute for Biomedical Imaging, Hamburg University of Technology0000-0003-3309-9783FranziskaWernerSection for Biomedical Imaging, University Medical Center Hamburg-Eppendorf, Institute for Biomedical Imaging, Hamburg University of TechnologyPatrykSzwargulskiSection for Biomedical Imaging, University Medical Center Hamburg-Eppendorf, Institute for Biomedical Imaging, Hamburg University of Technology0000-0003-2563-9006NadineGdaniecSection for Biomedical Imaging, University Medical Center Hamburg-Eppendorf, Institute for Biomedical Imaging, Hamburg University of Technology0000-0002-5060-0683MarijaBobergSection for Biomedical Imaging, University Medical Center Hamburg-Eppendorf, Institute for Biomedical Imaging, Hamburg University of Technology0000-0003-3419-748110.21105/joss.01331https://doi.org/10.5281/zenodo.3242352Juliahttps://joss.theoj.org/papers/10.21105/joss.01331.pdfMagnetic Particle Imaging, HDF5, MDFtag:joss.theoj.org,2005:Paper/10022019-06-06T14:47:49Z2021-02-15T11:32:10ZA reproducible Snakemake pipeline to analyse Illumina paired-end data from ChiP-Seq experimentsacceptedv1.2.02019-05-17 15:30:39 UTC382019-06-06 14:47:49 UTC420191465JihedChouarefSwammerdam Institute for Life Sciences, University of Amsterdam0000-0003-3865-896XMattijsBliekSwammerdam Institute for Life Sciences, University of Amsterdam0000-0002-0488-4873MarcGallandSwammerdam Institute for Life Sciences, University of Amsterdam0000-0003-2161-868910.21105/joss.01465https://doi.org/10.5281/zenodo.3240026Pythonhttps://joss.theoj.org/papers/10.21105/joss.01465.pdfSnakemake, ChIP-seq, Deeptools, Biocondatag:joss.theoj.org,2005:Paper/9362019-05-19T20:32:55Z2021-02-15T11:32:23ZContainer Tree: Software to Model Container Filesystems, Packages, and Inheritanceaccepted0.0.482019-03-21 21:29:59 UTC372019-05-19 20:32:55 UTC420191418VanessaSochatStanford University Research Computing0000-0002-4387-381910.21105/joss.01418https://doi.org/10.5281/zenodo.2853983Pythonhttps://joss.theoj.org/papers/10.21105/joss.01418.pdfcontainers, docker, reproducibilitytag:joss.theoj.org,2005:Paper/9512019-05-09T13:23:46Z2021-02-15T11:32:19ZWatchMe: Software for Reproducible Monitoring and Data Collectionaccepted0.0.132019-04-08 14:57:09 UTC372019-05-09 13:23:46 UTC420191388VanessaSochatStanford University Research Computing0000-0002-4387-381910.21105/joss.01388https://doi.org/10.5281/zenodo.2633142Pythonhttps://joss.theoj.org/papers/10.21105/joss.01388.pdfmonitoring, data, reproducibilitytag:joss.theoj.org,2005:Paper/9092019-04-04T03:07:41Z2021-02-15T11:32:28ZBadread: simulation of error-prone long readsacceptedv0.1.32019-03-01 11:22:17 UTC362019-04-04 03:07:41 UTC420191316RyanR.WickDepartment of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria 3004, Australia0000-0001-8349-077810.21105/joss.01316https://doi.org/10.5281/zenodo.2622997Pythonhttps://joss.theoj.org/papers/10.21105/joss.01316.pdflong-read sequencing, oxford nanopore, ont, pacific biosciences, pacbiotag:joss.theoj.org,2005:Paper/8252019-02-28T04:47:11Z2021-02-15T11:32:37ZBedparse: feature extraction from BED filesacceptedv0.2.02019-01-22 15:47:36 UTC342019-02-28 04:47:11 UTC420191228TommasoLeonardiThe Gurdon Institute, University of Cambridge, Cambridge, UK, Center for Genomic Science IIT\@SEMM, Istituto Italiano di Tecnologia (IIT), Milan, Italy0000-0002-4449-186310.21105/joss.01228https://doi.org/10.5281/zenodo.2578820Pythonhttps://joss.theoj.org/papers/10.21105/joss.01228.pdfBioinformatics, Genomics, BED formattag:joss.theoj.org,2005:Paper/7542019-02-12T18:40:24Z2022-01-18T11:19:56ZRSeqAn: Headers and wrappers for the SeqAn library in Racceptedv1.02018-12-17 20:52:53 UTC342019-02-12 18:40:24 UTC420191160AugustGuangCenter for Computation and Visualization, Brown University, Providence, Rhode Island, United States of America, Center for Computational Biology of Human Disease, Brown University, Providence, Rhode Island, United States of America10.21105/joss.01160https://doi.org/10.5281/zenodo.2558617R, C++, Chttps://joss.theoj.org/papers/10.21105/joss.01160.pdfSeqAn, bioinformatics, Rcpp