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  • European Marine Science
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Trouche, Blandine;

    Anvi'o databases of the 47 ammonia-oxidizing archaea MAGs from abyssal and hadal surface sediments presented in Trouche et al, 2023 (https://doi.org/10.1038/s43705-023-00341-6). 

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ ZENODOarrow_drop_down
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    ZENODO
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    ZENODO
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      ZENODO
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    Authors: Delaporte, Baptiste; Arsouze, Thomas; Keppel, Gunnar; Jullien, Swen; +2 Authors

    Version reviewed for software paper in "The Journal of Open Source Software". You can find the article here

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    ZENODO
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      ZENODO
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    Authors: Athanase, Marylou; Wang, Qiang; Danilov, Sergey; Sidorenko, Dmitry; +5 Authors

    Source code of the Finite Element Sea ice-Ocean Model version 1.4 (FESOM v1.4) used in the coupled climate model AWI-CM-1-1-MR to produce the nudged storyline simulations presented in the paper entitled "Projected amplification of summer marine heatwaves in a warming Northeast Pacific Ocean", Athanase et al. (Communications Earth & Environment). For the source code of ECHAM6, registration on the MPI-ESM user page is required (http://www.mpimet.mpg.de/en/science/models/license/).

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    ZENODO
    Model . 2023
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    Model . 2023
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    Authors: Sun, Xiaoyu; Ritter, Christoph;

    Algorithms for retrieving cirrus cloud geometrical and optical properties from COMCAL (Raman lidar located in Koror, Palau 7.3°N, 134.5°E).

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    ZENODO
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      ZENODO
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Bruggeman, Jorn; Bolding, Karsten; Nerger, Lars;

    EAT is a flexible and extensible software package that enables data assimilation of physical and biogeochemical variables in a one-dimensional water column. EAT builds on established open-source components for hydrodynamics (GOTM), biogeochemistry (FABM) and data assimilation (PDAF). It is easy to install and operate, and flexible through support for user-written plugins. EAT is well suited to explore and advance the state-of-the-art in DA in natural waters thanks to its support for: strongly and weakly coupled data assimilation observations describing any prognostic and diagnostic element of the physical-biogeochemical model estimation of biogeochemical parameters. On Windows, Mac and Linux systems with Anaconda or Miniconda, EAT can be installed with conda create -n eat -c bolding-bruggeman -c conda-forge eatpy. It is then not necessary to download and compile the source code. This record contains the EAT source code. It can be compiled and installed as described on the wiki.

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    Authors: Wang, Siyuan; Zhang, Futing; Koedooder, Coco; Qafoku, Odeta; +8 Authors

    The uploaded file contains three separate Python scripts aimed at modeling the sinking velocity of natural Trichodesmium colonies loaded with dust particles. Two scripts have been developed to calculate the dust influencing factor (K), and one script is dedicated to calculating the sinking velocity of particle-free Trichodesmium colonies (v0). All Python scripts are available on GitHub (https://github.com/Zhanzhu1110/Trichobuoyancy.git) and can be processed using the "Codespaces" function on GitHub. The file 'K given values' is a specialized script designed to simulate the dust factor (K), assuming seawater and dust densities of 1028 kg/m3 and 2500 kg/m3, respectively, with a colony radius of 1 mm.

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    ZENODO
    Model . 2023
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    Model . 2023
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    Authors: Gentili, Bernard; Gattuso, Jean-Pierre; Schlegel, Robert William;

    Satellite data collected between 2003 and 2022, in conjunction with gridded bathymetric data (50-150 m resolution), are used to estimate the irradiance reaching the bottom of a series of representative EU Arctic fjords. An Earth System Science Data (ESSD) manuscript, Schlegel et al. (2023, in review), that provides a detailed explanation of the methodology is currently in review.

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    Authors: Rackow, Thomas; Hegewald, Jan; Koldunov, Nikolay V.; Mogensen, Kristian; +3 Authors

    Version of the 'Finite Volume Sea ice - Ocean Model' (FESOM2) that was used in the coupled model IFS-FESOM for nextGEMS Cycle 3 simulations. It includes all changes from FESOM2.5 plus modifications for better stability on DKRZ Levante. This is the source code used in the study Rackow, Pedruzo-Bagazgoitia, Becker, Milinski, Sandu et al. : Multi-year simulations at kilometre scale with the Integrated Forecasting System coupled to FESOM2.5/NEMOV3.4 This work was supported by the European Union's Horizon 2020 collaborative project NextGEMS (grant number 101003470). For more infos about the nextGEMS project, see https://nextgems-h2020.eu (last access: 30.11.2023) 

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    Authors: Daniel Moreno-Parada; Alexander Robinson; Marisa Montoya; Jorge Alvarez-Solas;

    We present the ice-sheet model Nix, an open-source project intended for collaborative development. Nix is a 2D thermomechanical model written in C/C++ that simultaneously solves for the momentum balance equations, mass conservation and temperature evolution.

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    Authors: Reese, Lloyd; Gräwe, Ulf; Klingbeil, Knut; Li, Xiangyu; +2 Authors

    Supporting Python scripts used for data processing for Reese et al. (2023): "Local Mixing Determines Spatial Structure of Diahaline Exchange Flow in a Mesotidal Estuary: A Study of Extreme Runoff Conditions" [1]. River discharge information and topography as used for the numerical tidal Elbe setup applied in the same study. Contains: riverinfo.dat -- river and tributary freshwater input grid locations as grid cell indices rivers.nc -- freshwater forcing used in setup, contains sources from all included tributaries and Geesthacht. Data retrieved from [2,3,4] in combination with personal communication via the Bundesanstalt für Wasserbau (BAW). topo_smoothed_v20_z0.nc -- setup topography and curvilinear grid. Topography created from datasets [5,6], for the latter see also [7]. Python scripts used for the creation of the figures, namely: fig2: Figure 2 fig3: Figure 3 fig4: Figure 4 and Table 1 data fig5: Figure 5 and Table 2 salt data fig6: Figure 6 fig7-8: Figures 7,8 fig9: Figure 9 fig10: Figure 10 fig11: Figure 11 plot_salt_tidally-resolved: Tidally resolved stratification, not shown in paper plot_temperature_correlation_section2e: Correlation of observed and simulated temperature at same stations as Figure 5 (not shown) and Table 2 temperature data The model data used for the figures and loaded within the Python scripts is available from the corresponding author of the study [1]. Note that *paper_plot_forcing_validation.py, *paper_plot_tidal_analysis.py, and *paper_plot_salinity_correlation.py require observational data that is freely available via portal-tideelbe.de; for in-depth documentation see [1]. *paper_plot_forcing_validation.py additionally requires meteorological forcing data for the first figure panel, which cannot be made public due to its proprietary nature. The use of shapefiles to colour landmasses and plot the coastline in Figures 2, 6, and 11 has to be commented out in the respective Python scripts due to unclear copyright regarding the underlying data. However, omission of these shapefiles does not change the interpretation of the model results. ---- [1] L. Reese, U. Graewe, K. Klingbeil, X. Li, M. Lorenz, H. Burchard, 2023: Local mixing determines spatial structure of diahaline exchange flow in a mesotidal estuary – a study of extreme runoff conditions. J. Phys. Oceanogr., submitted. [2] Wasserstraßen- und Schifffahrtsamt Magdeburg, 2021: Abflussstation Neu Darchau. Wasserstraßen- und Schifffahrtsverwaltung des Bundes, accessed 10 March 2021, http://www.portal-tideelbe.de. [3] Landesamt für Landwirtschaft, Umwelt und ländliche Räume Schleswig-Holstein, 2022: Daily averaged freshwater runoff at Kellinghusen-Parkplatz and Kölln-Reisiek A23, 2012–2014. Hochwasser- und Sturmflutinformation Schleswig-Holstein, accessed 2 February 2022, https://www.umweltdaten.landsh.de/pegel/jsp/pegel.jsp?gui=ganglinie&thema=q&mstnr=114377;https://www.umweltdaten.landsh.de/pegel/jsp/pegel.jsp?mstnr=114527&wsize=free. [4] Niedersächsicher Landesbetrieb für Wasserwirtschaft, Küsten- und Naturschutz, 2022: Daily averaged freshwater runoff at gauges no. 5963101 (Oersdorf), 5945125 (Bienenbüttel), 5983110 (Rockstedt), and 5972105 (Schwinge), 2012–2014. Niedersächsische Landesdatenbank für wasserwirtschaftliche Daten, accessed 27 April 2022, http://www.wasserdaten.niedersachsen.de/cadenza/pages/home/welcome.xhtml. [5] Wasserstraßen- und Schifffahrtsamt Hamburg, 2011: DGM-W 2010 Unter- und Außenelbe (Digitales Geländemodell des Wasserlaufes - Multifunktionsmodell). Wasserstraßen- und Schifffahrtsverwaltung des Bundes, accessed 12 January 2021, https://www.kuestendaten.de/Tideelbe/DE/Service/Kartenthemen/Kartenthemen_node.html [6] Bundesamt für Seeschifffahrt und Hydrographie, 2019: AufMod Bathymetries German Bight 1982-2012 - WMS. Wasserstraßen- und Schifffahrtsverwaltung des Bundes, accessed 28 May 2013, https://gdk.gdi-de.org/geonetwork/srv/api/records/3543c490-d251-4948-830c-1da723a1a8eb. [7] Heyer, H., and K. Schrottke, 2015: Einführung, Aufgabenstellung und Bearbeitungsstruktur im KFKI-Projekt AufMod. Die Küste, 83, 1–18, ISBN: 978-3-939230-40-3.

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    Authors: Trouche, Blandine;

    Anvi'o databases of the 47 ammonia-oxidizing archaea MAGs from abyssal and hadal surface sediments presented in Trouche et al, 2023 (https://doi.org/10.1038/s43705-023-00341-6). 

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    Authors: Delaporte, Baptiste; Arsouze, Thomas; Keppel, Gunnar; Jullien, Swen; +2 Authors

    Version reviewed for software paper in "The Journal of Open Source Software". You can find the article here

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    Authors: Athanase, Marylou; Wang, Qiang; Danilov, Sergey; Sidorenko, Dmitry; +5 Authors

    Source code of the Finite Element Sea ice-Ocean Model version 1.4 (FESOM v1.4) used in the coupled climate model AWI-CM-1-1-MR to produce the nudged storyline simulations presented in the paper entitled "Projected amplification of summer marine heatwaves in a warming Northeast Pacific Ocean", Athanase et al. (Communications Earth & Environment). For the source code of ECHAM6, registration on the MPI-ESM user page is required (http://www.mpimet.mpg.de/en/science/models/license/).

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    Authors: Sun, Xiaoyu; Ritter, Christoph;

    Algorithms for retrieving cirrus cloud geometrical and optical properties from COMCAL (Raman lidar located in Koror, Palau 7.3°N, 134.5°E).

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    Authors: Bruggeman, Jorn; Bolding, Karsten; Nerger, Lars;

    EAT is a flexible and extensible software package that enables data assimilation of physical and biogeochemical variables in a one-dimensional water column. EAT builds on established open-source components for hydrodynamics (GOTM), biogeochemistry (FABM) and data assimilation (PDAF). It is easy to install and operate, and flexible through support for user-written plugins. EAT is well suited to explore and advance the state-of-the-art in DA in natural waters thanks to its support for: strongly and weakly coupled data assimilation observations describing any prognostic and diagnostic element of the physical-biogeochemical model estimation of biogeochemical parameters. On Windows, Mac and Linux systems with Anaconda or Miniconda, EAT can be installed with conda create -n eat -c bolding-bruggeman -c conda-forge eatpy. It is then not necessary to download and compile the source code. This record contains the EAT source code. It can be compiled and installed as described on the wiki.

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