tag:joss.theoj.org,2005:/papers/in/M4Journal of Open Source Software2024-03-16T22:48:59ZJournal of Open Source Softwarehttps://joss.theoj.orgtag:joss.theoj.org,2005:Paper/46292024-03-16T22:48:59Z2024-03-17T00:00:58ZFeenoX: a cloud-first finite-element(ish) computational engineering toolacceptedv0.32023-07-27 16:01:35 UTC952024-03-16 22:48:59 UTC920245846JeremyThelerSeamplex, Argentina, Instituto Balseiro, Argentina0000-0002-4142-498010.21105/joss.05846https://doi.org/10.5281/zenodo.10819606M4, C, GLSLhttps://joss.theoj.org/papers/10.21105/joss.05846.pdfengineering, partial differential equations, differential algebraic equationstag:joss.theoj.org,2005:Paper/46862024-01-22T16:32:03Z2024-01-23T00:01:01ZThe Kestrel software for simulations of morphodynamic Earth-surface flowsaccepted1.02023-08-09 17:30:12 UTC932024-01-22 16:32:03 UTC920246079JakeLanghamSchool of Mathematics, Fry Building, University of Bristol, Bristol, BS8 1UG, UK0000-0001-9857-7016MarkJ.WoodhouseSchool of Earth Sciences, Wills Memorial Building, University of Bristol, Bristol, BS8 1RJ, UK0000-0002-2198-679110.21105/joss.06079https://doi.org/10.5281/zenodo.10477693M4, Fortran, C++https://joss.theoj.org/papers/10.21105/joss.06079.pdfgeophysics, shallow water, debris flow, morphodynamicstag:joss.theoj.org,2005:Paper/46002023-10-03T20:23:42Z2023-10-04T10:38:48ZepiworldR: Fast Agent-Based Epi Modelsaccepted0.0-22023-07-13 15:39:41 UTC902023-10-03 20:23:42 UTC820235781DerekMeyerDivision of Epidemiology, University of Utah, Salt Lake City, UT, United States of America0009-0005-1350-6988GeorgeG VegaYonDivision of Epidemiology, University of Utah, Salt Lake City, UT, United States of America0000-0002-3171-084410.21105/joss.05781https://doi.org/10.5281/zenodo.8327345R, M4, C++https://joss.theoj.org/papers/10.21105/joss.05781.pdfABM, epiworldR, parallel computingtag:joss.theoj.org,2005:Paper/33412022-12-28T08:58:46Z2022-12-29T00:01:19ZRedOak: a reference-free and alignment-free structure for indexing a collection of similar genomesaccepted0.1.42022-02-15 13:53:48 UTC802022-12-28 08:58:46 UTC720224363ClémentAgretLIRMM, Univ Montpellier, CNRS, Montpellier, France, Cirad, UMR AGAP, Avenue Agropolis, Montpellier, France, CRIStAL, Centre de Recherche en Informatique Signal et Automatique de Lille, Lille, France0000-0002-7404-7253AnnieChateauLIRMM, Univ Montpellier, CNRS, Montpellier, France, Institut de Biologie Computationnelle, Montpellier, France0000-0003-4760-8171GaetanDrocCirad, UMR AGAP, Avenue Agropolis, Montpellier, France0000-0003-1849-1269GautierSarahINRA, UMR AGAP, 2 Place Pierre Viala, Montpellier, France0000-0001-5179-972XManuelRuizCirad, UMR AGAP, Avenue Agropolis, Montpellier, France, Institut de Biologie Computationnelle, Montpellier, France0000-0001-8153-276XAlbanMancheronLIRMM, Univ Montpellier, CNRS, Montpellier, France, Institut de Biologie Computationnelle, Montpellier, France0000-0001-9249-759210.21105/joss.04363https://doi.org/10.6084/m9.figshare.21711767M4, Chttps://joss.theoj.org/papers/10.21105/joss.04363.pdfC/C++, Bioinformatic, k-mers, Genomes, Indextag:joss.theoj.org,2005:Paper/30062022-05-07T21:21:13Z2022-05-08T00:01:23ZROCK: digital normalization of whole genome sequencing dataacceptedv_1.9.42021-09-01 12:54:20 UTC732022-05-07 21:21:13 UTC720223790VéroniqueNbspLegrandInstitut Pasteur, Université Paris Cité, Plateforme HPC, F-75015 Paris, FranceThomasNbspKergrohenPrédicteurs moléculaires et nouvelles cibles en oncologie, INSERM, Gustave Roussy, Université Paris-Saclay, Villejuif, France, Département de Cancérologie de l'Enfant et de l'Adolescent, Gustave Roussy, Université Paris-Saclay, Villejuif, FranceNicolasNbspJolyInstitut Pasteur, Université Paris Cité, Plateforme HPC, F-75015 Paris, FranceAlexisNbspCriscuoloInstitut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, F-75015 Paris, France, Institut Pasteur, Université Paris Cité, Plateforme de Microbiologie Mutualisée (P2M), F-75015 Paris, France0000-0002-8212-521510.21105/joss.03790https://doi.org/10.5281/zenodo.6527091M4, C++https://joss.theoj.org/papers/10.21105/joss.03790.pdfhigh-throughput sequencing, digital normalization, _k_-mertag:joss.theoj.org,2005:Paper/28392021-11-23T21:49:31Z2021-11-24T00:00:20Zsacio: A library for Seismic Analysis Code data filesaccepted1.0.22021-07-08 19:59:06 UTC672021-11-23 21:49:31 UTC620213619BrianSavageUniversity of Rhode Island0000-0002-9252-628210.21105/joss.03619https://doi.org/10.5281/zenodo.5722418C, M4https://joss.theoj.org/papers/10.21105/joss.03619.pdfFortran, seismology, earth science, geophysicstag:joss.theoj.org,2005:Paper/22302021-09-19T14:35:35Z2021-09-20T00:01:25ZCorrelation: An Analysis Tool for Liquids and for Amorphous Solidsacceptedv1.0.02020-12-10 19:12:39 UTC652021-09-19 14:35:35 UTC620212976IsaíasRodríguezDepartamento de Materia Condensada, Instituto de Investigaciones en Materiales, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México, México.0000-0002-4359-2742RenelaM.ValladaresDepartamento de Física, Facultad de Ciencias, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México, México.0000-0002-3819-2226AlexanderValladaresDepartamento de Física, Facultad de Ciencias, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México, México.DavidHinojosa-RomeroDepartamento de Materia Condensada, Instituto de Investigaciones en Materiales, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México, México.0000-0002-8686-965XUlisesSantiagoDepartment of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.0000-0003-2259-5984ArielA.ValladaresDepartamento de Materia Condensada, Instituto de Investigaciones en Materiales, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México, México.0000-0003-1505-224410.21105/joss.02976https://doi.org/10.5281/zenodo.5514113M4, C++https://joss.theoj.org/papers/10.21105/joss.02976.pdfMaterials, Molecular dynamics, Pair Correlation Function, Plane Angle Distributiontag:joss.theoj.org,2005:Paper/24752021-05-30T19:37:17Z2021-05-31T00:00:47ZExaFMM: a high-performance fast multipole method library with C++ and Python interfacesacceptedv0.1.12021-03-05 22:10:19 UTC612021-05-30 19:37:17 UTC620213145TingyuWangThe George Washington University0000-0003-2520-0511RioYokotaTokyo Institute of Technology0000-0001-7573-7873LorenaA.BarbaThe George Washington University0000-0001-5812-271110.21105/joss.03145https://doi.org/10.5281/zenodo.4874663M4, C++https://joss.theoj.org/papers/10.21105/joss.03145.pdfPython, fast multipole method, low-rank approximation, high performance computingtag:joss.theoj.org,2005:Paper/25522021-05-02T08:50:41Z2021-05-03T00:02:41Zdatasailr - An R Package for Row by Row Data Processing, Using DataSailr Scriptaccepted0.8.72021-04-03 12:02:51 UTC612021-05-02 08:50:41 UTC620213166ToshihiroUmeharaIndependent Researcher0000-0001-7015-621X10.21105/joss.03166https://doi.org/10.5281/zenodo.4732788R, M4, C++https://joss.theoj.org/papers/10.21105/joss.03166.pdfstatistics, data processingtag:joss.theoj.org,2005:Paper/20042021-01-20T16:18:01Z2021-02-15T11:30:01Znap: A molecular dynamics package with parameter-optimization programs for classical and machine-learning potentialsacceptedv0.9.22020-09-01 06:14:38 UTC572021-01-20 16:18:01 UTC620212768RyoKobayashiDepartment of Physical Science and Engineering, Nagoya Institute of Technology, Gokiso, Showa, Nagoya 466-8555, Japan0000-0001-8244-584410.21105/joss.02768https://doi.org/10.5281/zenodo.4451790M4, Python, Fortranhttps://joss.theoj.org/papers/10.21105/joss.02768.pdfmaterials science, molecular dynamics, interatomic potential, neural-network potential, meta-heuristics