tag:joss.theoj.org,2005:/papers/edited_by/@jmschreiJournal of Open Source Software2024-01-22T15:00:12ZJournal of Open Source Softwarehttps://joss.theoj.orgtag:joss.theoj.org,2005:Paper/48382024-01-22T15:00:12Z2024-01-23T11:55:19Zcstag and cstag-cli: tools for manipulating and visualizing cs tagsacceptedv1.0.42023-10-06 03:25:34 UTC932024-01-22 15:00:12 UTC920246066AkihiroKunoDepartment of Anatomy and Embryology, University of Tsukuba, Tsukuba, Ibaraki, Japan, Laboratory Animal Resource Center, Trans-border Medical Research Center, University of Tsukuba, Tsukuba, Ibaraki, Japan.0000-0002-4674-688210.21105/joss.06066https://doi.org/10.5281/zenodo.10544838Pythonhttps://joss.theoj.org/papers/10.21105/joss.06066.pdfpython, genomics, sequencing, bioinformaticstag:joss.theoj.org,2005:Paper/45402024-01-12T22:11:20Z2024-01-15T11:54:18Zcellanneal: A user-friendly deconvolution software for transcriptomics dataacceptedv1.0.02023-06-12 17:35:47 UTC932024-01-12 22:11:20 UTC920245610LisaBuchauerDepartment of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel, Department of Infectious Diseases and Respiratory Medicine, Charité-Universitätsmedizin Berlin, Berlin, Germany0000-0002-4722-8390ShalevItzkovitzDepartment of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel0000-0003-0685-252210.21105/joss.05610https://doi.org/10.5281/zenodo.10405043Pythonhttps://joss.theoj.org/papers/10.21105/joss.05610.pdfbioinformatics, computational biology, mixture deconvolution, bulk deconvolution, transcriptomics, RNA sequencing, omics methodstag:joss.theoj.org,2005:Paper/42862023-10-01T20:53:57Z2023-10-02T07:50:01ZRosalution: Supporting data accessibility, integration, curation, interoperability, and reuse for precision animal modelingaccepted0.6.02023-03-07 19:18:39 UTC902023-10-01 20:53:57 UTC820235443AngelinaE.Uno-AntonisonCenter for Computational Genomics and Data Sciences, Heersink School of Medicine, 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 America, Department of Pediatrics, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America0000-0002-4631-9135RababFatimaCenter for Computational Genomics and Data Sciences, Heersink School of Medicine, 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 America, Department of Pediatrics, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America0000-0002-3739-6331JamesSchererCenter for Computational Genomics and Data Sciences, Heersink School of Medicine, 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 America, Department of Pediatrics, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America0000-0002-4272-2082AlexanderMossCenter for Computational Genomics and Data Sciences, Heersink School of Medicine, 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 America, Department of Pediatrics, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America0000-0001-5112-0270DonnaBrownCenter for Computational Genomics and Data Sciences, Heersink School of Medicine, 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 America, Department of Pediatrics, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America0000-0002-8805-7225AleksandraFoksinskaHugh Kaul Precision Medicine Institute, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America0000-0002-1035-3294ManavalanGajapathyCenter for Computational Genomics and Data Sciences, Heersink School of Medicine, 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 America, Department of Pediatrics, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America0000-0002-8606-0113ElizabethJ.WilkDepartment of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America0000-0002-7078-1215BrittanyN.LasseigneDepartment of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America0000-0002-1642-8904ElizabethWortheyCenter for Computational Genomics and Data Sciences, Heersink School of Medicine, 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 America, Department of Pediatrics, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America0000-0003-4083-776410.21105/joss.05443https://doi.org/10.5281/zenodo.8380641Python, JavaScripthttps://joss.theoj.org/papers/10.21105/joss.05443.pdfanimal modeling, rare disease, diagnosis, genomics, phenotype, python, javascript, web applicationtag:joss.theoj.org,2005:Paper/43162023-09-11T12:58:31Z2023-09-12T00:01:38ZFrESCO: Framework for Exploring Scalable Computational Oncologyacceptedv1.0.02023-03-16 17:23:44 UTC892023-09-11 12:58:31 UTC820235345AdamSpannausOak Ridge National Laboratory, Oak Ridge, TN, United States of America0000-0002-2521-3657JohnGounleyOak Ridge National Laboratory, Oak Ridge, TN, United States of AmericaMayankaChandraShekarOak Ridge National Laboratory, Oak Ridge, TN, United States of AmericaZacharyR.FoxOak Ridge National Laboratory, Oak Ridge, TN, United States of AmericaJamaludinMohd-YusofLos Alamos National Laboratory, Los Alamos, NM, United States of AmericaNoahSchaefferkoetterOak Ridge National Laboratory, Oak Ridge, TN, United States of AmericaHeidiA.HansonOak Ridge National Laboratory, Oak Ridge, TN, United States of America10.21105/joss.05345https://doi.org/10.5281/zenodo.8325993Python, Jupyter Notebookhttps://joss.theoj.org/papers/10.21105/joss.05345.pdfbioinformatics, natural language processing, deep learning, computational oncologytag:joss.theoj.org,2005:Paper/41872023-05-30T10:10:11Z2023-05-31T00:01:19ZproteoDA: a package for quantitative proteomicsacceptedv1.0.02023-02-02 15:47:05 UTC852023-05-30 10:10:11 UTC820235184TimothyJ.ThurmanDepartment of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA0000-0002-9602-6226CharityL.WashamDepartment of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA0000-0001-5761-9304DuahAlkamDepartment of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA0000-0002-5965-7694JordanT.BirdDepartment of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA0000-0001-5753-6058AllenGiesDepartment of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA0000-0003-2492-0429KalyaniDhusiaDepartment of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA0000-0002-8803-1295MichaelS.RobesonDepartment of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, USA0000-0001-7119-6301StephanieD.ByrumDepartment of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA, Arkansas Children's Research Institute, Little Rock, AR, USA0000-0002-1783-361010.21105/joss.05184https://doi.org/10.5281/zenodo.7962306R, JavaScripthttps://joss.theoj.org/papers/10.21105/joss.05184.pdfmass spectrometry, intensity data, normalization, linear modelstag:joss.theoj.org,2005:Paper/41442023-04-20T14:54:21Z2023-04-21T00:03:22ZRxInfer: A Julia package for reactive real-time Bayesian inferenceacceptedv2.4.12023-01-03 13:07:23 UTC842023-04-20 14:54:21 UTC820235161DmitryBagaevTechnical University of Eindhoven0000-0001-9655-7986AlbertPodusenkoTechnical University of Eindhoven0000-0003-0515-0465Bertde VriesTechnical University of Eindhoven0000-0003-0839-174X10.21105/joss.05161https://doi.org/10.5281/zenodo.7774921Jupyter Notebook, Juliahttps://joss.theoj.org/papers/10.21105/joss.05161.pdfstatistics, Bayesian inference, variational optimization, message passingtag:joss.theoj.org,2005:Paper/40682023-04-06T13:28:10Z2023-04-07T00:03:09ZFitSNAP: Atomistic machine learning with LAMMPSaccepted32022-12-02 19:54:26 UTC842023-04-06 13:28:10 UTC820235118A.RohskopfCenter for Computing Research, Sandia National Laboratories, Albuquerque, NM, United States of America0000-0002-2712-8296C.SieversCenter for Computing Research, Sandia National Laboratories, Albuquerque, NM, United States of America, Boeing, Seattle, WA, United States of AmericaN.LubbersLos Alamos National Laboratory, Los Alamos, NM, United States of America0000-0002-9001-9973M.a.CusentinoMaterial, Physical, and Chemical Sciences Center, Sandia National Laboratories, Albuquerque, NM, United States of America0000-0001-9505-6442J.GoffCenter for Computing Research, Sandia National Laboratories, Albuquerque, NM, United States of America0000-0001-7026-7200J.JanssenLos Alamos National Laboratory, Los Alamos, NM, United States of America0000-0001-9948-7119M.McCarthyCenter for Computing Research, Sandia National Laboratories, Albuquerque, NM, United States of America0000-0003-4388-4953D.Montes Ocade ZapiainCenter for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, NM, United States of America0000-0001-7890-0859S.NikolovCenter for Computing Research, Sandia National Laboratories, Albuquerque, NM, United States of America0000-0002-2907-6629K.SargsyanChemistry, Combustion and Materials Science Center, Sandia National Laboratories, Livermore, CA, United States of America0000-0002-1037-786XD.SemaDepartment of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States of America0000-0002-0160-1743E.SikorskiCenter for Computing Research, Sandia National Laboratories, Albuquerque, NM, United States of America0000-0003-3292-6564L.WilliamsChemistry, Combustion and Materials Science Center, Sandia National Laboratories, Livermore, CA, United States of America0000-0002-9062-8293A.p.ThompsonCenter for Computing Research, Sandia National Laboratories, Albuquerque, NM, United States of America0000-0002-0324-9114M.a.WoodCenter for Computing Research, Sandia National Laboratories, Albuquerque, NM, United States of America0000-0001-5878-409610.21105/joss.05118https://doi.org/10.5281/zenodo.7764752Python, Cython, C, Jupyter Notebookhttps://joss.theoj.org/papers/10.21105/joss.05118.pdfmachine learning, interatomic potentials, neural networkstag: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/40082023-01-22T13:50:18Z2023-01-23T09:46:10ZFuseMedML: a framework for accelerated discovery in machine learning based biomedicineaccepted0.2.82022-11-16 16:29:49 UTC812023-01-22 13:50:18 UTC820234943AlexGoltsIBM Research - Haifa, IsraelMosheRabohIBM Research - Haifa, IsraelYoelShoshanIBM Research - Haifa, IsraelSagiPolaczekIBM Research - Haifa, IsraelSimonaRabinovici-CohenIBM Research - Haifa, IsraelEfratHexterIBM Research - Haifa, Israel10.21105/joss.04943https://doi.org/10.5281/zenodo.7346694Python, Jupyter Notebookhttps://joss.theoj.org/papers/10.21105/joss.04943.pdfDeep Learning, Machine Learning, Artificial Intelligence, Medical imaging, Clinical data, Computational biomedicinetag:joss.theoj.org,2005:Paper/39132022-12-01T09:36:52Z2022-12-02T00:01:00Zkep_solver: A Python package for kidney exchange programme explorationaccepted2.1.02022-09-22 12:32:22 UTC802022-12-01 09:36:52 UTC720224881WilliamPetterssonSchool of Computing Science, University of Glasgow, United Kingdom0000-0003-0040-208810.21105/joss.04881https://doi.org/10.5281/zenodo.7369472Python, Jupyter Notebookhttps://joss.theoj.org/papers/10.21105/joss.04881.pdfkidney exchange, operations research