tag:joss.theoj.org,2005:/papers/tagged/computational-biologyJournal of Open Source Software2024-01-12T22:11:20ZJournal of Open Source Softwarehttps://joss.theoj.orgtag: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/43722023-10-15T19:50:50Z2023-10-16T09:42:21ZBASICO: A simplified Python interface to COPASIacceptedv0.482023-03-29 21:23:27 UTC902023-10-15 19:50:50 UTC820235553FrankT.BergmannBioQUANT/COS, Heidelberg University, Heidelberg, Germany0000-0001-5553-470210.21105/joss.05553https://doi.org/10.5281/zenodo.8189386Pythonhttps://joss.theoj.org/papers/10.21105/joss.05553.pdfsystems biology, computational modeling, simulation, COPASItag:joss.theoj.org,2005:Paper/41792023-05-10T21:48:40Z2023-05-11T09:01:03Zmutyper: assigning and summarizing mutation types for analyzing germline mutation spectraacceptedv0.7.02023-01-24 22:40:00 UTC852023-05-10 21:48:40 UTC820235227WilliamS.DeWittDepartment of Electrical Engineering & Computer Sciences, University of California, Berkeley, CA, United States of America0000-0002-6802-9139LukeZhuDepartment of Bioengineering, University of Washington, Seattle, WA, United States of America0000-0002-6324-1464MitchellR.VollgerDepartment of Genome Sciences, University of Washington, Seattle, WA, United States of America0000-0002-8651-1615MichaelE.GoldbergDepartment of Genome Sciences, University of Washington, Seattle, WA, United States of America, Departments of Human Genetics and of Biomedical Informatics, University of Utah, Salt Lake City, UT, United States of America0000-0003-3310-6349AndreaTalentiThe Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom0000-0003-1309-3667AnnabelC.BeichmanDepartment of Genome Sciences, University of Washington, Seattle, WA, United States of America0000-0002-6991-587XKelleyHarrisDepartment of Genome Sciences, University of Washington, Seattle, WA, United States of America0000-0003-0302-252310.21105/joss.05227https://doi.org/10.5281/zenodo.7921769Pythonhttps://joss.theoj.org/papers/10.21105/joss.05227.pdfgenomics, computational biology, bioinformatics, mutation spectrum, pythontag:joss.theoj.org,2005:Paper/38562023-01-09T15:28:55Z2023-01-10T00:01:03Zsimcardems: A FEniCS-based cardiac electro-mechanics solveracceptedv2022.3.02022-09-07 12:28:58 UTC812023-01-09 15:28:55 UTC820234753HenrikNicolay TopnesFinsbergSimula Research Laboratory, Oslo, Norway0000-0003-3766-2393IlsbethGerarda Mariavan HerckSimula Research Laboratory, Oslo, Norway0000-0003-0728-3958CécileDaversin-CattySimula Research Laboratory, Oslo, NorwayHermenegildArevaloSimula Research Laboratory, Oslo, NorwaySamuelWallSimula Research Laboratory, Oslo, Norway10.21105/joss.04753https://doi.org/10.5281/zenodo.7503468Pythonhttps://joss.theoj.org/papers/10.21105/joss.04753.pdfFEniCS, Cardiac Electro-Mechanics, Finite Element Method, Computational Biologytag:joss.theoj.org,2005:Paper/13382020-03-18T19:57:53Z2021-02-15T11:31:21ZOrNet - a Python Toolkit to Model the Diffuse Structure of Organelles as Social Networksacceptedv0.12019-11-19 17:20:50 UTC472020-03-18 19:57:53 UTC520201983MojtabaFazliDepartment of Computer Science, University of Georgia, Athens, GA 30602 USA, The two first authors made equal contributions.0000-0002-6082-2538MarcusHillDepartment of Computer Science, University of Georgia, Athens, GA 30602 USA, The two first authors made equal contributions.0000-0002-9380-3181AndrewDurdenDepartment of Computer Science, University of Georgia, Athens, GA 30602 USARachelMattsonInstitute for Artificial Intelligence, University of Georgia, Athens, GA 30602 USAAllysonT.LoyDepartment of Microbiology, University of Georgia, Athens, GA 30602 USABarbaraReavesDepartment of Infectious Diseases, University of Georgia, Athens, GA 30602 USAAbigailCourtneyDepartment of Microbiology, University of Georgia, Athens, GA 30602 USAFrederickD.QuinnDepartment of Infectious Diseases, University of Georgia, Athens, GA 30602 USAChakraChennubhotlaDepartment of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15232 USAShannonQuinnDepartment of Computer Science, University of Georgia, Athens, GA 30602 USA, Department of Cellular Biology, University of Georgia, Athens, GA 30602 USA0000-0002-8916-633510.21105/joss.01983https://doi.org/10.5281/zenodo.3687340Pythonhttps://joss.theoj.org/papers/10.21105/joss.01983.pdfCellular Biology, Organelles, Computer Visiontag:joss.theoj.org,2005:Paper/14572020-02-25T00:42:46Z2021-02-15T11:31:05ZscPCA: A toolbox for sparse contrastive principal component analysis in Racceptedv1.1.62020-01-28 17:27:57 UTC462020-02-25 00:42:46 UTC520202079PhilippeBoileauGraduate Group in Biostatistics, University of California, Berkeley0000-0002-4850-2507NimaS.HejaziGraduate Group in Biostatistics, University of California, Berkeley, Center for Computational Biology, University of California, Berkeley0000-0002-7127-2789SandrineDudoitCenter for Computational Biology, University of California, Berkeley, Department of Statistics, University of California, Berkeley, Division of Epidemiology and Biostatistics, School of Public Health, University of California, Berkeley0000-0002-6069-862910.21105/joss.02079https://doi.org/10.5281/zenodo.3686201Rhttps://joss.theoj.org/papers/10.21105/joss.02079.pdfdimensionality reduction, principal component analysis, computational biology, unwanted variation, sparsitytag:joss.theoj.org,2005:Paper/12982019-11-22T22:00:17Z2021-02-15T11:31:29ZBioSimSpace: An interoperable Python framework for biomolecular simulationaccepted2019.2.02019-10-21 14:47:05 UTC432019-11-22 22:00:17 UTC420191831LesterO.HedgesAdvanced Computing Research Centre, University of Bristol, UK0000-0002-5624-0500AntoniaS.j.s.MeyEaStCHEM School of Chemistry, University of Edinburgh, UK0000-0001-7512-5252CharlesA.LaughtonSchool of Pharmacy, University of Nottingham, UK0000-0003-4090-3960FrancescoL.GervasioDepartment of Chemistry and Institute of Structural and Molecular Biology, University College London, UK0000-0003-4831-5039AdrianJ.MulhollandCentre for Computational Chemistry, School of Chemistry, University of Bristol, UK0000-0003-1015-4567ChristopherJ.WoodsAdvanced Computing Research Centre, University of Bristol, UK0000-0001-6563-9903JulienMichelEaStCHEM School of Chemistry, University of Edinburgh, UK0000-0003-0360-176010.21105/joss.01831https://doi.org/10.5281/zenodo.3551030Python, Jupyter Notebookhttps://joss.theoj.org/papers/10.21105/joss.01831.pdfbiomolecular-simulation, computational-chemistry, computational-physics, computational-biology, interoperability, molecular dynamics, reproducibilitytag:joss.theoj.org,2005:Paper/9402019-04-19T23:35:39Z2021-02-15T11:32:22ZWGS2NCBI - Toolkit for preparing genomes for submission to NCBIacceptedv1.0.02019-03-28 14:48:56 UTC362019-04-19 23:35:39 UTC420191364RutgerAldoVosResearch Group 'Understanding Evolution', Naturalis Biodiversity Center, Leiden, The Netherlands0000-0001-9254-7318NnadiNnaemekaEmmanuelDepartment of Microbiology, Faculty of Natural and Applied Science, Plateau State University, Bokkos, Plateau State, NigeriaJohnChinyereO'LearyAfrican Centre of Excellence on Phytomedicine Research and Development (ACEPRD), University of Jos, Jos, Plateau State, Nigeria, Department of Pharmacology, Faculty of Pharmaceutical Sciences, University of Jos, Jos, Plateau State, Nigeria10.21105/joss.01364https://doi.org/10.5281/zenodo.2645762Perl, Scalahttps://joss.theoj.org/papers/10.21105/joss.01364.pdfbioinformatics, computational biology, genomestag:joss.theoj.org,2005:Paper/1202018-10-19T00:30:17Z2021-02-15T11:34:21Zadaptest: Data-Adaptive Statistics for High-Dimensional Testing in Raccepted0.2.02016-11-22 00:17:26 UTC302018-10-19 00:30:17 UTC32018161WeixinCaiGroup in Biostatistics, University of California, Berkeley0000-0003-2680-3066AlanHubbardGroup in Biostatistics, University of California, Berkeley0000-0002-3769-0127NimaHejaziGroup in Biostatistics, University of California, Berkeley0000-0002-7127-278910.21105/joss.00161https://doi.org/10.5281/zenodo.1466019Rhttps://joss.theoj.org/papers/10.21105/joss.00161.pdfR language, data-adaptive statistics, data mining, multiple testing, computational biology, bioinformatics, targeted learningtag:joss.theoj.org,2005:Paper/5142018-10-04T00:35:10Z2021-02-15T11:33:19ZPython Implementation of Codon Adaptation Indexacceptedv1.0.02018-06-06 18:15:02 UTC302018-10-04 00:35:10 UTC32018905BenjaminD.LeeSchool of Engineering and Applied Sciences, Harvard University0000-0002-7133-839710.21105/joss.00905https://doi.org/10.5281/zenodo.1439494Python, Jupyter Notebookhttps://joss.theoj.org/papers/10.21105/joss.00905.pdfbioinformatics, computational biology, codon adaptation index, molecular biology