tag:joss.theoj.org,2005:/papers/tagged/databaseJournal of Open Source Software2024-02-17T07:07:40ZJournal of Open Source Softwarehttps://joss.theoj.orgtag:joss.theoj.org,2005:Paper/49802024-02-17T07:07:40Z2024-02-18T00:01:01ZREDCapTidieR: Extracting complex REDCap databases into tidy tablesacceptedv1.0.02023-12-05 18:25:20 UTC942024-02-17 07:07:40 UTC920246277RichardHannaDivision of Oncology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania0009-0005-6496-8154EzraPorterDivision of Oncology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania0000-0002-4690-8343StephanyRomeroDivision of Oncology, Children's Hospital of Philadelphia, Philadelphia, PennsylvaniaPaulWildenhainDivision of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PennsylvaniaWilliamBeasleyDepartment of Pediatrics, The University of Oklahoma Health Sciences Center, College of Medicine, Oklahoma City, Oklahoma, USA0000-0002-5613-5006StephanKadaukeDepartment of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, Division of Transfusion Medicine, Children's Hospital of Philadelphia, Pennsylvania, Division of Pathology Informatics, Children's Hospital of Philadelphia, Pennsylvania0000-0003-2996-803410.21105/joss.06277https://doi.org/10.5281/zenodo.10658773Rhttps://joss.theoj.org/papers/10.21105/joss.06277.pdfREDCap, data managementtag:joss.theoj.org,2005:Paper/48252024-01-19T21:37:47Z2024-01-20T00:00:44Zpymatgen-analysis-defects: A Python package for analyzing point defects in crystalline materialsacceptedv2023.08.222023-10-02 01:54:09 UTC932024-01-19 21:37:47 UTC920245941Jimmy-XuanShenLawrence Livermore National Laboratory, Livermore, California 94550, United States0000-0002-2743-7531JoelVarleyLawrence Livermore National Laboratory, Livermore, California 94550, United States0000-0002-5384-524810.21105/joss.05941https://doi.org/10.5281/zenodo.6994437Python, Jupyter Notebookhttps://joss.theoj.org/papers/10.21105/joss.05941.pdfpython, materials science, point defects, finite-size corrections, database buildingtag:joss.theoj.org,2005:Paper/44712023-11-28T15:38:26Z2023-11-29T00:00:34Zneotoma2: An R package to access data from the Neotoma Paleoecology Databaseacceptedv1.0.02023-05-03 21:32:36 UTC912023-11-28 15:38:26 UTC820235561SocorroDominguezVidañaHT Data0000-0002-7926-4935SimonJ.GoringDepartment of Geography, University of Wisconsin -- Madison, Center for Climatic Research, University of Wisconsin -- Madison0000-0002-2700-460510.21105/joss.05561https://doi.org/10.5281/zenodo.10198238Rhttps://joss.theoj.org/papers/10.21105/joss.05561.pdfpaleoecology, databases, paleoenvironment, Holocene, Pleistocenetag:joss.theoj.org,2005:Paper/43632023-10-15T06:24:40Z2023-10-16T10:44:49ZNOMAD: A distributed web-based platform for managing materials science research dataacceptedv1.1.82023-03-24 09:37:47 UTC902023-10-15 06:24:40 UTC820235388MarkusScheidgenDepartment of Physics, Humboldt-Universität zu Berlin, Berlin, Germany0000-0002-8038-2277LauriHimanenDepartment of Physics, Humboldt-Universität zu Berlin, Berlin, Germany0000-0002-3130-8193AlvinNoeLadinesDepartment of Physics, Humboldt-Universität zu Berlin, Berlin, Germany0000-0003-0077-2097DavidSikterDepartment of Physics, Humboldt-Universität zu Berlin, Berlin, Germany0000-0002-2102-7160MohammadNakhaeeDepartment of Physics, Humboldt-Universität zu Berlin, Berlin, Germany0000-0003-4146-0129ÁdámFeketeDepartment of Physics, Humboldt-Universität zu Berlin, Berlin, Germany0000-0002-6263-897XTheodoreChangDepartment of Physics, Humboldt-Universität zu Berlin, Berlin, Germany0000-0002-4911-0230AmirGolparvarDepartment of Physics, Humboldt-Universität zu Berlin, Berlin, Germany0000-0002-2412-6615JoséA.MárquezDepartment of Physics, Humboldt-Universität zu Berlin, Berlin, Germany0000-0002-8173-2566SandorBrockhauserDepartment of Physics, Humboldt-Universität zu Berlin, Berlin, Germany0000-0002-9700-4803SebastianBrücknerLeibniz Institut für Kristallzüchtung, Berlin, Germany0000-0002-5969-847XLucaM.GhiringhelliDepartment of Physics, Humboldt-Universität zu Berlin, Berlin, Germany0000-0001-5099-3029FelixDietrichSchool of Computation, Information and Technology, Technical University of Munich, Munich, Germany0000-0002-2906-1769DanielLehmbergSchool of Computation, Information and Technology, Technical University of Munich, Munich, Germany0000-0002-4012-5014TheaDenellDepartment of Physics, Humboldt-Universität zu Berlin, Berlin, Germany0009-0000-7185-9363AndreaAlbinoDepartment of Physics, Humboldt-Universität zu Berlin, Berlin, Germany0000-0001-9280-7431HampusNäsströmDepartment of Physics, Humboldt-Universität zu Berlin, Berlin, Germany0000-0002-3264-1692SherjeelShabihDepartment of Physics, Humboldt-Universität zu Berlin, Berlin, Germany0009-0008-6635-4465FlorianDobenerDepartment of Physics, Humboldt-Universität zu Berlin, Berlin, Germany0000-0003-1987-6224MarkusKühbachDepartment of Physics, Humboldt-Universität zu Berlin, Berlin, Germany0000-0002-7117-5196RubelMozumderDepartment of Physics, Humboldt-Universität zu Berlin, Berlin, Germany0009-0007-5926-6646JosephF.RudzinskiDepartment of Physics, Humboldt-Universität zu Berlin, Berlin, Germany0000-0003-3403-640XNathanDaelmanDepartment of Physics, Humboldt-Universität zu Berlin, Berlin, Germany0000-0002-7647-1816JoséM.PizarroDepartment of Physics, Humboldt-Universität zu Berlin, Berlin, Germany0000-0002-6751-8192MartinKubanDepartment of Physics, Humboldt-Universität zu Berlin, Berlin, Germany0000-0002-1619-2460CuauhtemocSalazarDepartment of Physics, Humboldt-Universität zu Berlin, Berlin, Germany0000-0002-9635-5062PavelOndračkaDepartment of Plasma Physics and Technology, Masaryk University, Brno, Czech Republic0000-0003-0729-629XHans-JoachimBungartzSchool of Computation, Information and Technology, Technical University of Munich, Munich, Germany0000-0002-0171-0712ClaudiaDraxlDepartment of Physics, Humboldt-Universität zu Berlin, Berlin, Germany0000-0003-3523-665710.21105/joss.05388https://doi.org/10.5281/zenodo.8366163https://joss.theoj.org/papers/10.21105/joss.05388.pdfPython, javascript, database, materials science, data management, electronic lab notebook, FAIRtag:joss.theoj.org,2005:Paper/40192023-04-20T13:55:20Z2023-04-21T00:03:24ZPyExperimenter: Easily distribute experiments and track resultsaccepted1.1.02022-11-22 12:16:00 UTC842023-04-20 13:55:20 UTC820235149TanjaTornedeDepartment of Computer Science, Paderborn University, Germany0000-0001-9954-462XAlexanderTornedeDepartment of Computer Science, Paderborn University, Germany0000-0002-2415-2186LukasFehringDepartment of Computer Science, Paderborn University, Germany0000-0001-8057-4650LukasGehringDepartment of Computer Science, Paderborn University, GermanyHelenaGrafDepartment of Computer Science, Paderborn University, Germany0000-0001-9447-0609JonasHanselleDepartment of Computer Science, Paderborn University, Germany0000-0002-1231-4985FelixMohrUniversidad de La Sabana, Chia, Cundinamarca, Colombia0000-0002-9293-2424MarcelWeverMCML, Institut for Informatics, LMU Munich, Germany0000-0001-9782-681810.21105/joss.05149https://doi.org/10.5281/zenodo.7838280Pythonhttps://joss.theoj.org/papers/10.21105/joss.05149.pdfExperiments, Executor, Databasetag:joss.theoj.org,2005:Paper/41502023-03-29T11:52:06Z2023-03-30T00:03:07Zunfold: removing the barriers to sharing and reproducing prospective life-cycle assessment databasesaccepted1.0.02023-01-05 17:49:49 UTC832023-03-29 11:52:06 UTC820235198RomainSacchiPaul Scherrer Institute, Villigen, Switzerland0000-0003-1440-090510.21105/joss.05198https://doi.org/10.5281/zenodo.7777717Jupyter Notebook, Pythonhttps://joss.theoj.org/papers/10.21105/joss.05198.pdflife cycle assessment, prospective, database, premise, scenariotag:joss.theoj.org,2005:Paper/43552023-03-22T09:42:42Z2023-03-23T00:03:05ZPynteny: a Python package to perform synteny-aware, profile HMM-based searches in sequence databasesacceptedv1.0.02023-03-20 17:14:26 UTC832023-03-22 09:42:42 UTC820235289SemidánRobaina-EstévezDepartment of Microbiology. University of La Laguna. Spain.0000-0003-0781-1677JoséM.GonzálezDepartment of Microbiology. University of La Laguna. Spain.0000-0002-9926-332310.21105/joss.05289https://doi.org/10.5281/zenodo.7750666Pythonhttps://joss.theoj.org/papers/10.21105/joss.05289.pdfbioinformatics, HMMER, synteny, HMMs, sequencingtag:joss.theoj.org,2005:Paper/36322022-10-25T14:16:05Z2022-10-26T00:00:26Zwdpar: Interface to the World Database on Protected Areasaccepted1.3.22022-05-27 06:31:46 UTC782022-10-25 14:16:05 UTC720224594JeffreyO.HansonDepartment of Biology, Carleton University, Ottawa, Canada0000-0002-4716-613410.21105/joss.04594https://doi.org/10.5281/zenodo.7195676Rhttps://joss.theoj.org/papers/10.21105/joss.04594.pdfconservation planning, protected areas, reserves, marine protected areas, other effective area-based conservation measures, spatial prioritizationtag:joss.theoj.org,2005:Paper/31612022-02-17T13:22:46Z2022-02-18T00:00:31ZOpenCADD-KLIFS: A Python package to fetch kinase data from the KLIFS databaseacceptedv1.0.02021-11-09 10:00:17 UTC702022-02-17 13:22:46 UTC720223951DominiqueSydow_In Silico_ Toxicology and Structural Bioinformatics, Institute of Physiology, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Augustenburger Platz 1, 13353 Berlin, Germany0000-0003-4205-8705JaimeRodríguez-Guerra_In Silico_ Toxicology and Structural Bioinformatics, Institute of Physiology, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Augustenburger Platz 1, 13353 Berlin, Germany0000-0001-8974-1566AndreaVolkamer_In Silico_ Toxicology and Structural Bioinformatics, Institute of Physiology, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Augustenburger Platz 1, 13353 Berlin, Germany0000-0002-3760-580X10.21105/joss.03951https://doi.org/10.5281/zenodo.6065555Python, Jupyter Notebookhttps://joss.theoj.org/papers/10.21105/joss.03951.pdfKLIFS, kinasetag: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, databases