tag:joss.theoj.org,2005:/papers/tagged/molecular%20biologyJournal of Open Source Software2021-12-01T22:36:48ZJournal of Open Source Softwarehttps://joss.theoj.orgtag:joss.theoj.org,2005:Paper/26782021-12-01T22:36:48Z2021-12-02T00:02:30ZpyrexMD: Workflow-Orientated Python Package for Replica Exchange Molecular Dynamicsaccepted1.02021-05-14 19:14:13 UTC682021-12-01 22:36:48 UTC620213325ArthurVoroninSteinbuch Centre for Computing, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany, Department of Physics, Karlsruhe Institute of Technology, Karlsruhe, Germany0000-0002-5804-5151AlexanderSchugInstitute for Advanced Simulation, Jülich Supercomputing Center, Jülich, Germany, Faculty of Biology, University of Duisburg-Essen, Duisburg, Germany0000-0002-0534-502X10.21105/joss.03325https://doi.org/10.5281/zenodo.5744760Pythonhttps://joss.theoj.org/papers/10.21105/joss.03325.pdfGROMACS, physics, biology, replica exchange, molecular dynamics, contact biastag:joss.theoj.org,2005:Paper/22272021-01-07T14:27:34Z2021-02-15T11:29:38ZAugur: a bioinformatics toolkit for phylogenetic analyses of human pathogensacceptedv10.1.12020-12-09 23:55:20 UTC572021-01-07 14:27:34 UTC620212906JohnHuddlestonMolecular and Cellular Biology Program, University of Washington, Seattle, WA, USA, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA0000-0002-4250-2063JamesHadfieldVaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA0000-0002-4118-6468ThomasR.SibleyVaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA0000-0001-5269-2297JoverLeeVaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA0000-0002-2391-0512KairstenFayVaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA0000-0002-6529-9205MisjaIlcisinVaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA0000-0002-1468-7697EliasHarkinsVaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA0000-0001-6525-9134TrevorBedfordMolecular and Cellular Biology Program, University of Washington, Seattle, WA, USA, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA0000-0002-4039-5794RichardA.NeherBiozentrum, University of Basel, Basel, Switzerland, Swiss Institute of Bioinformatics, Basel, Switzerland0000-0003-2525-1407EmmaB.HodcroftBiozentrum, University of Basel, Basel, Switzerland, Swiss Institute of Bioinformatics, Basel, Switzerland, Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland0000-0002-0078-221210.21105/joss.02906https://doi.org/10.5281/zenodo.4421955Python, Perlhttps://joss.theoj.org/papers/10.21105/joss.02906.pdfbioinformatics, molecular biology, human pathogens, evolutionary biologytag:joss.theoj.org,2005:Paper/17042020-08-17T05:57:27Z2021-02-15T11:30:35Zdms-view: Interactive visualization tool for deep mutational scanning dataacceptedv1.0.02020-06-01 21:39:22 UTC522020-08-17 05:57:27 UTC520202353SarahK.HiltonDivision of Basic Sciences and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA, Department of Genome Sciences, University of Washington, Seattle, WA, USA0000-0001-9278-3644JohnHuddlestonVaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA, Molecular and Cell Biology, University of Washington, Seattle, WA, USA0000-0002-4250-2063AllisonBlackVaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA, Department of Epidemiology, University of Washington, Seattle, WA, USA0000-0002-6618-4127KhrystynaNorthDivision of Basic Sciences and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA, Department of Genome Sciences, University of Washington, Seattle, WA, USAAdamS.DingensDivision of Basic Sciences and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA0000-0001-9603-9409TrevorBedfordVaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA0000-0002-4039-5794JesseD.BloomDivision of Basic Sciences and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA, Department of Genome Sciences, University of Washington, Seattle, WA, USA, Howard Hughes Medical Institute, Seattle, WA, USA0000-0003-1267-340810.21105/joss.02353https://doi.org/10.5281/zenodo.3986155Ruby, JavaScript, Pythonhttps://joss.theoj.org/papers/10.21105/joss.02353.pdfJavascript, D3, molecular biology, protein evolution, data visualizationtag:joss.theoj.org,2005:Paper/15402020-06-03T10:40:49Z2021-02-15T11:30:54Ztaurenmd: A command-line interface for analysis of Molecular Dynamics simulations.acceptedv0.8.92020-03-03 20:18:24 UTC502020-06-03 10:40:49 UTC520202175JoãoM.C.TeixeiraPrevious, Biomolecular NMR Laboratory, Organic Chemistry Section, Inorganic and Organic Chemistry Department, University of Barcelona, Baldiri Reixac 10-12, Barcelona 08028, Spain, Current, Program in Molecular Medicine, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada0000-0002-9113-062210.21105/joss.02175https://doi.org/10.5281/zenodo.3843326Pythonhttps://joss.theoj.org/papers/10.21105/joss.02175.pdfMolecular Dynamics, Structural Biology, Proteins, DNA, RNA, Biochemistrytag: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/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