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    Atmospheric dust modeling from meso to global scales with the online NMMB/BSC-Dust model – Part 2: Experimental campaigns in Northern Africa
    (München : European Geopyhsical Union, 2012) Haustein, K.; Pérez, C.; Baldasano, J.M.; Jorba, O.; Basart, S.; Miller, R.L.; Janjic, Z.; Black, T.; Nickovic, S.; Todd, M.C.; Washington, R.; Müller, D.; Tesche, M.; Weinzierl, B.; Esselborn, M.; Schladitz, A.
    The new NMMB/BSC-Dust model is intended to provide short to medium-range weather and dust forecasts from regional to global scales. It is an online model in which the dust aerosol dynamics and physics are solved at each model time step. The companion paper (Pérez et al., 2011) develops the dust model parameterizations and provides daily to annual evaluations of the model for its global and regional configurations. Modeled aerosol optical depth (AOD) was evaluated against AERONET Sun photometers over Northern Africa, Middle East and Europe with correlations around 0.6–0.7 on average without dust data assimilation. In this paper we analyze in detail the behavior of the model using data from the Saharan Mineral dUst experiment (SAMUM-1) in 2006 and the Bodélé Dust Experiment (BoDEx) in 2005. AOD from satellites and Sun photometers, vertically resolved extinction coefficients from lidars and particle size distributions at the ground and in the troposphere are used, complemented by wind profile data and surface meteorological measurements. All simulations were performed at the regional scale for the Northern African domain at the expected operational horizontal resolution of 25 km. Model results for SAMUM-1 generally show good agreement with satellite data over the most active Saharan dust sources. The model reproduces the AOD from Sun photometers close to sources and after long-range transport, and the dust size spectra at different height levels. At this resolution, the model is not able to reproduce a large haboob that occurred during the campaign. Some deficiencies are found concerning the vertical dust distribution related to the representation of the mixing height in the atmospheric part of the model. For the BoDEx episode, we found the diurnal temperature cycle to be strongly dependant on the soil moisture, which is underestimated in the NCEP analysis used for model initialization. The low level jet (LLJ) and the dust AOD over the Bodélé are well reproduced. The remaining negative AOD bias (due to underestimated surface wind speeds) can be substantially reduced by decreasing the threshold friction velocity in the model.
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    Data publication in the open access initiative
    (London : Ubiquity Press, 2006) Klump, J.; Bertelmann, R.; Brase, J.; Diepenbroek, M.; Grobe, H.; Höck, H.; Lautenschlager, M.; Schindler, U.; Sens, I.; Wächter, J.
    The 'Berlin Declaration' was published in 2003 as a guideline to policy makers to promote the Internet as a functional instrument for a global scientific knowledge base. Because knowledge is derived from data, the principles of the 'Berlin Declaration ' should apply to data as well. Today, access to scientific data is hampered by structural deficits in the publication process. Data publication needs to offer authors an incentive to publish data through long-term repositories. Data publication also requires an adequate licence model that protects the intellectual property rights of the author while allowing further use of the data by the scientific community.
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    The plant phenological online database (PPODB): An online database for long-term phenological data
    (Heidelberg : Springer Verlag, 2013) Dierenbach, J.; Badeck, F.-W.; Schaber, J.
    We present an online database that provides unrestricted and free access to over 16 million plant phenological observations from over 8,000 stations in Central Europe between the years 1880 and 2009. Unique features are (1) a flexible and unrestricted access to a full-fledged database, allowing for a wide range of individual queries and data retrieval, (2) historical data for Germany before 1951 ranging back to 1880, and (3) more than 480 curated long-term time series covering more than 100 years for individual phenological phases and plants combined over Natural Regions in Germany. Time series for single stations or Natural Regions can be accessed through a user-friendly graphical geo-referenced interface. The joint databases made available with the plant phenological database PPODB render accessible an important data source for further analyses of long-term changes in phenology. The database can be accessed via www.ppodb.de.
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    NCIO 1.0: A simple Fortran NetCDF interface
    (München : European Geopyhsical Union, 2015) Robinson, A.; Perrette, M.
    The NetCDF (Network Common Data Form) library has become an indispensable tool for data and model output management in geoscience. However for simple tasks, particularly in Fortran, the complexity of native NetCDF functionality can be cumbersome. The NCIO (NetCDF Input/Output) module has been designed as an interface to the NetCDF library with simplicity and ease of use in mind. While this implies that some NetCDF functionality is masked from the user, the subroutines provided here are adequate for basic serial reading and writing tasks of up to 6-D data arrays along with corresponding data attributes. The code is available online via a GitHub repository (http://www.github.com/alex-robinson/ncio), which includes an example program to illustrate the approach.
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    IMAGE-IN: Interactive web-based multidimensional 3D visualizer for multi-modal microscopy images
    (San Francisco, California, US : PLOS, 2022) Gupta, Yubraj; Costa, Carlos; Pinho, Eduardo; A. Bastião Silva, Luís; Heintzmann, Rainer
    Advances in microscopy hardware and storage capabilities lead to increasingly larger multidimensional datasets. The multiple dimensions are commonly associated with space, time, and color channels. Since “seeing is believing”, it is important to have easy access to user-friendly visualization software. Here we present IMAGE-IN, an interactive web-based multidimensional (N-D) viewer designed specifically for confocal laser scanning microscopy (CLSM) and focused ion beam scanning electron microscopy (FIB-SEM) data, with the goal of assisting biologists in their visualization and analysis tasks and promoting digital work-flows. This new visualization platform includes intuitive multidimensional opacity fine-tuning, shading on/off, multiple blending modes for volume viewers, and the ability to handle multichannel volumetric data in volume and surface views. The software accepts a sequence of image files or stacked 3D images as input and offers a variety of viewing options ranging from 3D volume/surface rendering to multiplanar reconstruction approaches. We evaluate the performance by comparing the loading and rendering timings of a heterogeneous dataset of multichannel CLSM and FIB-SEM images on two devices with installed graphic cards, as well as comparing rendered image quality between ClearVolume (the ImageJ open-source desktop viewer), Napari (the Python desktop viewer), Imaris (the closed-source desktop viewer), and our proposed IMAGE-IN web viewer.