tag:joss.theoj.org,2005:/papers/tagged/PDFJournal of Open Source Software2024-03-10T12:27:59ZJournal of Open Source Softwarehttps://joss.theoj.orgtag:joss.theoj.org,2005:Paper/50672024-03-10T12:27:59Z2024-03-12T10:21:48ZProject RACCOON: Automated construction of PDB files for polymers and polymer peptide conjugatesacceptedv1.0.12024-01-10 16:52:37 UTC952024-03-10 12:27:59 UTC920246293MoritzL.ObenauerDepartment of Chemistry, Johannes Gutenberg-University Mainz, Duesbergweg 10-14, D-55128 Mainz, Germany0009-0003-8140-9907KaiN.SpauszusDepartment of Chemistry, Johannes Gutenberg-University Mainz, Duesbergweg 10-14, D-55128 Mainz, Germany0009-0006-0650-2273PolBeseniusDepartment of Chemistry, Johannes Gutenberg-University Mainz, Duesbergweg 10-14, D-55128 Mainz, Germany0000-0001-7478-4459FriederikeSchmidInstitute of Physics, Johannes Gutenberg University, Staudingerweg 9, 55128 Mainz, Germany0000-0002-5536-671810.21105/joss.06293https://doi.org/10.5281/zenodo.10776652Jupyter Notebook, Python, Bikeshedhttps://joss.theoj.org/papers/10.21105/joss.06293.pdfcheminformatics, molecular-dynamics-simulatiom, pdb-files, molecular-modelingtag:joss.theoj.org,2005:Paper/39102023-05-10T21:56:30Z2023-05-11T09:10:10ZSPyCi-PDB: A modular command-line interface for back-calculating experimental datatypes of protein structures.acceptedv0.1.102022-09-21 16:08:40 UTC852023-05-10 21:56:30 UTC820234861ZiHaoLiuMolecular Medicine Program, Hospital for Sick Children, Toronto, Ontario, Canada, Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada0000-0002-8357-8507OufanZhangPitzer Center for Theoretical Chemistry, University of California, Berkeley, California, United States of America, Department of Chemistry, University of California, Berkeley, California, United States of AmericaJoãoM.c.TeixeiraDepartment of Biomedical Sciences, University of Padua, Padova, Italy0000-0002-9113-0622JieLiPitzer Center for Theoretical Chemistry, University of California, Berkeley, California, United States of America, Department of Chemistry, University of California, Berkeley, California, United States of America0000-0002-4727-1786TeresaHead-GordonPitzer Center for Theoretical Chemistry, University of California, Berkeley, California, United States of America, Department of Chemistry, University of California, Berkeley, California, United States of America, Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California, United States of America, Department of Bioengineering, University of California, Berkeley, California, United States of America0000-0003-0025-8987JulieD.Forman-KayMolecular Medicine Program, Hospital for Sick Children, Toronto, Ontario, Canada, Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada0000-0001-8265-972X10.21105/joss.04861https://doi.org/10.5281/zenodo.7887039Pythonhttps://joss.theoj.org/papers/10.21105/joss.04861.pdfNMR, SAXS, smFRET, Back-calculator, PDB, Structural Biology, Proteins, Biochemistrytag:joss.theoj.org,2005:Paper/38502022-12-16T19:00:02Z2022-12-17T00:01:07ZPDENLPModels.jl: An NLPModel API for Optimization Problems with PDE-Constraintsacceptedv0.3.22022-08-31 15:04:48 UTC802022-12-16 19:00:02 UTC720224736TangiMigotGERAD and Department of Mathematics and Industrial Engineering, Polytechnique Montréal, QC, Canada.0000-0001-7729-2513DominiqueOrbanGERAD and Department of Mathematics and Industrial Engineering, Polytechnique Montréal, QC, Canada.0000-0002-8017-7687AbelSoaresSiqueiraNetherlands eScience Center, Amsterdam, NL0000-0003-4451-281X10.21105/joss.04736https://doi.org/10.5281/zenodo.7447623Juliahttps://joss.theoj.org/papers/10.21105/joss.04736.pdfnonlinear optimization, large-scale optimization, constrained optimization, nonlinear programming, PDE-constrained optimizationtag:joss.theoj.org,2005:Paper/14702021-08-16T22:08:41Z2021-08-17T04:22:13ZSARAS: A general-purpose PDE solver for fluid dynamicsacceptedv1.02020-02-06 08:18:10 UTC642021-08-16 22:08:41 UTC620212095RoshanSamuelDepartment of Mechanical Engineering, Indian Institute of Technology - Kanpur, Uttar Pradesh - 208016, India0000-0002-1280-9881ShashwatBhattacharyaDepartment of Mechanical Engineering, Indian Institute of Technology - Kanpur, Uttar Pradesh - 208016, India0000-0001-7462-7680AliAsadDepartment of Physics, Indian Institute of Technology - Kanpur, Uttar Pradesh - 208016, India0000-0001-9704-6686SoumyadeepChatterjeeDepartment of Physics, Indian Institute of Technology - Kanpur, Uttar Pradesh - 208016, India0000-0001-7957-1727MahendraK.VermaDepartment of Physics, Indian Institute of Technology - Kanpur, Uttar Pradesh - 208016, India0000-0002-3380-4561RaviSamtaneyMechanical Engineering, Physical Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal - 23955, Saudi Arabia0000-0002-4702-6473SyedFahadAnwerDepartment of Mechanical Engineering, ZHCET, Aligarh Muslim University, Uttar Pradesh - 202002, India0000-0003-3602-117210.21105/joss.02095https://doi.org/10.5281/zenodo.5205320C++, Pythonhttps://joss.theoj.org/papers/10.21105/joss.02095.pdfPDE, turbulence, fluid dynamicstag:joss.theoj.org,2005:Paper/14542020-05-28T12:25:52Z2021-02-15T11:31:06ZThe pdb2sql Python Package: Parsing, Manipulation and Analysis of PDB Files Using SQL Queriesaccepted0.2.22020-01-27 14:32:28 UTC492020-05-28 12:25:52 UTC520202077NicolasRenaudNetherlands eScience Center, Science Park 140 1098 XG Amsterdam, the Netherlands0000-0001-9589-2694CunliangGengNetherlands eScience Center, Science Park 140 1098 XG Amsterdam, the Netherlands0000-0002-1409-835810.21105/joss.02077https://doi.org/10.5281/zenodo.3860329Pythonhttps://joss.theoj.org/papers/10.21105/joss.02077.pdfBioinformatics, PDB filestag:joss.theoj.org,2005:Paper/15362020-04-03T17:59:33Z2021-02-15T11:30:55Zpy-pde: A Python package for solving partial differential equationsacceptedv0.22020-03-02 13:30:45 UTC482020-04-03 17:59:33 UTC520202158DavidZwickerMax Planck Institute for Dynamics and Self-Organization, Göttingen, Germany0000-0002-3909-333410.21105/joss.02158https://doi.org/10.5281/zenodo.3739300Pythonhttps://joss.theoj.org/papers/10.21105/joss.02158.pdfpartial differential equation, dynamical systems, finite-difference, just-in-time compilationtag:joss.theoj.org,2005:Paper/9272019-11-14T17:49:35Z2021-02-15T11:32:24ZPDFIO: PDF Reader Library for native Juliaacceptedv0.1.12019-03-15 03:14:23 UTC432019-11-14 17:49:35 UTC420191453SambitKumarDashDirector, Lenatics Solutions Pvt. Ltd.0000-0003-4856-724410.21105/joss.01453https://doi.org/10.5281/zenodo.3541938Juliahttps://joss.theoj.org/papers/10.21105/joss.01453.pdfPDF, document archive, data extraction, text extraction, data mining, data managementtag:joss.theoj.org,2005:Paper/13112019-11-01T14:57:54Z2021-02-15T11:31:26ZworkloopR: Analysis of work loops and other data from muscle physiology experiments in Raccepted1.1.02019-10-30 20:46:36 UTC432019-11-01 14:57:54 UTC420191856VikramB.BaligaDepartment of Zoology, University of British Columbia, Vancouver, British Colombia, Canada V6T 1Z40000-0002-9367-8974ShreeramSenthivasanDepartment of Zoology, University of British Columbia, Vancouver, British Colombia, Canada V6T 1Z40000-0002-7118-954710.21105/joss.01856https://doi.org/10.5281/zenodo.3523384R, Rebolhttps://joss.theoj.org/papers/10.21105/joss.01856.pdfmuscle physiology, work loop, twitch, tetanus, ddftag:joss.theoj.org,2005:Paper/9212019-06-10T11:52:03Z2021-02-15T11:32:25ZMPIFiles.jl: A Julia Package for Magnetic Particle Imaging Filesacceptedv0.5.02019-03-09 21:12:24 UTC382019-06-10 11:52:03 UTC420191331TobiasKnoppSection for Biomedical Imaging, University Medical Center Hamburg-Eppendorf, Institute for Biomedical Imaging, Hamburg University of Technology0000-0002-1589-8517MartinMöddelSection for Biomedical Imaging, University Medical Center Hamburg-Eppendorf, Institute for Biomedical Imaging, Hamburg University of Technology0000-0002-4737-7863FlorianGrieseSection for Biomedical Imaging, University Medical Center Hamburg-Eppendorf, Institute for Biomedical Imaging, Hamburg University of Technology0000-0003-3309-9783FranziskaWernerSection for Biomedical Imaging, University Medical Center Hamburg-Eppendorf, Institute for Biomedical Imaging, Hamburg University of TechnologyPatrykSzwargulskiSection for Biomedical Imaging, University Medical Center Hamburg-Eppendorf, Institute for Biomedical Imaging, Hamburg University of Technology0000-0003-2563-9006NadineGdaniecSection for Biomedical Imaging, University Medical Center Hamburg-Eppendorf, Institute for Biomedical Imaging, Hamburg University of Technology0000-0002-5060-0683MarijaBobergSection for Biomedical Imaging, University Medical Center Hamburg-Eppendorf, Institute for Biomedical Imaging, Hamburg University of Technology0000-0003-3419-748110.21105/joss.01331https://doi.org/10.5281/zenodo.3242352Juliahttps://joss.theoj.org/papers/10.21105/joss.01331.pdfMagnetic Particle Imaging, HDF5, MDFtag:joss.theoj.org,2005:Paper/9322019-06-03T10:36:55Z2021-02-15T11:32:23Zscikit-finite-diff, a new tool for PDE solvingacceptedv0.6.0rc12019-03-18 22:46:42 UTC382019-06-03 10:36:55 UTC420191356NicolasCellierUniversité Savoie Mont-Blanc0000-0002-3759-3546ChristianRuyer-QuilUniversité Savoie Mont-Blanc10.21105/joss.01356https://doi.org/10.5281/zenodo.3236970Pythonhttps://joss.theoj.org/papers/10.21105/joss.01356.pdfpython, pde, physical modelling