tag:joss.theoj.org,2005:/papers/tagged/RESTJournal of Open Source Software2023-10-23T10:25:02ZJournal of Open Source Softwarehttps://joss.theoj.orgtag: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/36232022-07-07T14:13:07Z2022-07-08T00:00:34Z`pygetpapers`: a Python library for automated retrieval of scientific literatureacceptedv1.2.32022-05-24 09:56:22 UTC752022-07-07 14:13:07 UTC720224451AyushGargUniversity of Richmond, Richmond, VA 23173, United States0000-0001-7016-747XRichardD.Smith-UnnaLabDAO, https://www.labdao.com/0000-0001-8721-7197PeterMurray-RustYusuf-Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK0000-0003-3386-397210.21105/joss.04451https://doi.org/10.5281/zenodo.6805842Python, Jupyter Notebookhttps://joss.theoj.org/papers/10.21105/joss.04451.pdfREST APItag:joss.theoj.org,2005:Paper/27612021-09-22T22:01:52Z2021-09-23T00:02:13Zoptimade-python-tools: a Python library for serving and consuming materials data via OPTIMADE APIsacceptedv0.15.32021-06-14 12:39:30 UTC652021-09-22 22:01:52 UTC620213458MatthewL.EvansInstitut de la Matière Condensée et des Nanosciences, Université catholique de Louvain, Chemin des Étoiles 8, Louvain-la-Neuve 1348, Belgium, Theory of Condensed Matter Group, Cavendish Laboratory, University of Cambridge, J. J. Thomson Avenue, Cambridge, CB3 0HE, United Kingdom0000-0002-1182-9098CasperW.AndersenTheory and Simulation of Materials (THEOS), Faculté des Sciences et Techniques de l'Ingénieur, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland0000-0002-2547-155XShyamDwaraknathLawrence Berkeley National Laboratory, Berkeley, CA, USA0000-0003-0289-2607MarkusScheidgenFritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195, Berlin, Germany, Humboldt-Universität zu Berlin, Institut für Physik and IRIS Adlershof, 12489 Berlin, Germany0000-0002-8038-2277ÁdámFeketeInstitut de la Matière Condensée et des Nanosciences, Université catholique de Louvain, Chemin des Étoiles 8, Louvain-la-Neuve 1348, Belgium, Department of Physics, King's College London, Strand, London WC2R 2LS, United Kingdom, Department of Physics and Namur Institute of Structured Materials, University of Namur, Rue de Bruxelles 51, 5000 Namur, Belgium0000-0002-6263-897XDonaldWinstonLawrence Berkeley National Laboratory, Berkeley, CA, USA, Polyneme LLC, New York, NY, USA0000-0002-8424-060410.21105/joss.03458https://doi.org/10.5281/zenodo.5517803Pythonhttps://joss.theoj.org/papers/10.21105/joss.03458.pdfREST API, JSON:API, OPTIMADE API, crystallography, density-functional theory, ab initio, materials discovery, databasestag:joss.theoj.org,2005:Paper/24882021-08-23T15:44:51Z2021-08-24T00:01:09Zbwsample: Processing Best-Worst Scaling dataaccepted0.6.02021-03-13 21:50:25 UTC642021-08-23 15:44:51 UTC620213324UlfA.HamsterBerlin-Brandenburgische Akademie der Wissenschaften, Berlin, Germany0000-0002-0440-486810.21105/joss.03324https://doi.org/10.5281/zenodo.5233945Pythonhttps://joss.theoj.org/papers/10.21105/joss.03324.pdfSampling, Best-Worst Scaling, Pairwise Comparison, Dictionary of Keys, Open-sourcetag:joss.theoj.org,2005:Paper/23522021-05-01T07:41:15Z2021-05-05T18:39:45ZBayesian X-ray Analysis (BXA) v4.0acceptedv4.0.22021-01-24 00:44:17 UTC612021-05-01 07:41:15 UTC620213045JohannesBuchnerMax Planck Institute for Extraterrestrial Physics, Giessenbachstrasse, 85741 Garching, Germany, Millenium Institute of Astrophysics, Vicuña MacKenna 4860, 7820436 Macul, Santiago, Chile, Pontificia Universidad Católica de Chile, Instituto de Astrofísica, Casilla 306, Santiago 22, Chile, Excellence Cluster Universe, Boltzmannstr. 2, D-85748, Garching, Germany0000-0003-0426-663410.21105/joss.03045https://doi.org/10.5281/zenodo.4721575Pythonhttps://joss.theoj.org/papers/10.21105/joss.03045.pdfX-rays, Bayesian inference, Nested Sampling, Spectroscopy, Bayes factorstag:joss.theoj.org,2005:Paper/23502021-04-02T13:26:55Z2022-01-18T11:55:27ZUltraNest - a robust, general purpose Bayesian inference engineaccepted3.2.02021-01-22 12:59:12 UTC602021-04-02 13:26:55 UTC620213001JohannesBuchnerMax Planck Institute for Extraterrestrial Physics, Giessenbachstrasse, 85741 Garching, Germany., Millenium Institute of Astrophysics, Vicuña MacKenna 4860, 7820436 Macul, Santiago, Chile, Pontificia Universidad Católica de Chile, Instituto de Astrofísica, Casilla 306, Santiago 22, Chile., Excellence Cluster Universe, Boltzmannstr. 2, D-85748, Garching, Germany10.21105/joss.03001https://doi.org/10.5281/zenodo.4653423Python, C++, C, Fortranhttps://joss.theoj.org/papers/10.21105/joss.03001.pdfBayesian inference, Nested Sampling, Monte Carlo, Bayes factorstag:joss.theoj.org,2005:Paper/14322021-01-03T20:17:51Z2021-02-15T11:31:10ZEvoMaster: A Search-Based System Test Generation Toolacceptedv1.0.02020-01-07 09:28:09 UTC572021-01-03 20:17:51 UTC620212153AndreaArcuriKristiania University College, Department of Technology, Oslo, Norway0000-0003-0799-2930JuanPabloGaleottiFCEyN-UBA, and ICC, CONICET-UBA, Depto. de Computaci\'on, Buenos Aires, Argentina0000-0002-0747-8205BogdanMarculescuKristiania University College, Department of Technology, Oslo, Norway0000-0002-1393-4123ManZhangKristiania University College, Department of Technology, Oslo, Norway0000-0003-1204-932210.21105/joss.02153https://doi.org/10.5281/zenodo.4300745C#, Java, TypeScript, JavaScripthttps://joss.theoj.org/papers/10.21105/joss.02153.pdfKotlin, SBST, search-based software engineering, test generation, system testing, REST, evolutionary computationtag:joss.theoj.org,2005:Paper/16882020-11-15T18:30:52Z2021-02-15T11:30:38ZCRBHits: From Conditional Reciprocal Best Hits to Codon Alignments and Ka/Ks in Racceptedv0.0.12020-05-26 15:41:11 UTC552020-11-15 18:30:52 UTC520202424KristianK.UllrichMax Planck Institute for Evolutionary Biology, Scientific IT group, August Thienemann Str. 2, 24306 Plön0000-0003-4308-962610.21105/joss.02424https://doi.org/10.5281/zenodo.4247942R, JavaScripthttps://joss.theoj.org/papers/10.21105/joss.02424.pdfreciprocal best hit, conditional reciprocal best hit, codon alignment, Ka/Ks, dN/dS, tandem duplicated genes, syntenytag:joss.theoj.org,2005:Paper/20682020-10-26T13:52:18Z2021-02-15T11:29:52Zmcbette: model comparison using babetteacceptedv1.8.32020-10-09 10:15:29 UTC542020-10-26 13:52:18 UTC520202762RichèlJ.c.BilderbeekTheoretical & Evolutionary Community Ecology, TRES, GELIFES, University of Groningen0000-0003-1107-704910.21105/joss.02762https://doi.org/10.5281/zenodo.4076183Rhttps://joss.theoj.org/papers/10.21105/joss.02762.pdfphylogenetics, model comparison, nested sampling, babette, BEAST2tag:joss.theoj.org,2005:Paper/15942020-06-05T20:36:59Z2021-02-15T11:30:51Zuravu: Making Bayesian modelling easy(er)acceptedv0.0.72020-05-20 12:20:56 UTC502020-06-05 20:36:59 UTC520202214AndrewR.McCluskeyDiamond Light Source, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK, Department of Chemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK0000-0003-3381-5911TimSnowDiamond Light Source, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK, School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK0000-0001-7146-688510.21105/joss.02214https://doi.org/10.5281/zenodo.3876888Pythonhttps://joss.theoj.org/papers/10.21105/joss.02214.pdfBayesian, analysis, evidence estimation, nested sampling, mcmc