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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: Bosia, Francesco; Husch, Tamara; Müller, Charlotte H.; Polonius, Severin; +7 Authors

    This is development version 7b41c57 of SCINE Sparrow.

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    ZENODO
    Software . 2022
    Data sources: ZENODO
    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/
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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/ 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
      Software . 2022
      Data sources: ZENODO
      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/
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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: Akhlaghi, Mohammad; Bacon, Roland; Inami, Hanae;

    Reproduction pipeline and necessary data for Sections 7.3 and 3.4 of Bacon et al., (2017) and Inami et al., (2017) respectively (papers I and II of the series of papers on "The MUSE Hubble Ultra Deep Field Survey", published in Astronomy & Astrophysics, 608, A1 and A2). This pipeline will estimate the Hubble Space Telescope (HST) segmentation maps (for paper 1) and make the necessary measurements (for paper 2) for objects that were detected in the MUSE 3D cubes, but didn't correspond to any detection in the Rafelski et al. (2015) catalog. This repository on Zenodo contains all the necessary input data, software and reproduction pipeline (containing the scripts, configuration files and settings to exactly reproduce the results in Sections 7.3 and 3.4 of the papers above). Below is a description of the contents: gnuastro-0.2.51-bc64-bugfix.tar.gz: Gnuastro version 0.2.51 with a small bug fix only relevant to this analysis. The base Gnuastro 0.2.51 was used for this pipeline when it was written, similar to zenodo.1163746. However, a bug relating to estimation of upper-limit magnitudes was later found. This bug was fixed, but along with many other changes that made the whole Gnuastro package incompatible with this pipeline. Hence, this bug-fixed copy of Gnuastro 0.2.51 was used in the catalog of Inami et al. (2017). The reproduction pipeline below contains the fixed file and instructions on how to make this version from version 0.2.51 that is available in the official Gnuastro version controlled history. The library dependencies of this version of Gnuastro can be downloaded from zenodo.1163746 (gnuastro-dependencies.tar.gz). IMPORTANT NOTE: Since version 0.2.51 of Gnuastro was released, CFITSIO (one of Gnuastro's dependencies) has added a dependency for the cURL library (to read https URLs). Therefore, to install Gnuastro 0.2.51, please install CFITSIO version 3.41 or earlier. hst-uvudf.tar.gz: images and weight maps in 0.06 arcsec/pixel resolution from the HST-UVUDF survey. These images are not necessary to run the reproduction pipeline (they will be downloaded from the HST archives if not present). They are stored here for the self-sufficiency of this repository and faster download: in this lossless compressed format, they are roughly 1/4th the volume of the same files in HST archives. hst-xdf.tar.gz: images and weight maps in 0.06 arcsec/pixel resolution from the HST-XDF survey. These are also available from the HST archives and are kept here with similar reasons to above (with a compression ratio of almost 1/3rd). output-v4-2-gf97e.tar.gz: output of the reproduction pipeline. reproduce-v4-2-gf97e.tar.gz: The reproduction pipeline (version 4-2-gf97e) that produces the results (tables) plotted in the paper. The full Git version controlled history of this repository is available on git-cral.univ-lyon1.fr or gitlab.com. We recommend cloning from the Git repository if it is available. This tarball is kept here in case those servers don't work or Git is no longer in common use. Please see the README file in this repository for instructions on how to run the reproduction pipeline and exactly reproduce the results. This pipeline will download all the necessary data if they aren't already present on the system (it is probably just necessary to install the required version of Gnuastro). The Creative Commons Attribution-NonCommercial 4.0 copyright mentioned in the Zenodo webpage is only applicable to files that don't have an explicit copyright within them. The copyright of other files (mainly scripts and software) is mentioned within them (all are free licenses). For any issues with the pipeline/processing, please contact Mohammad Akhlaghi. {"references": ["Illingworth et al. (2013), Astrophysical Journal Supplement, Volume 209, Issue 1, article id. 6", "Rafelski et al. (2015), Astronomical Journal, Volume 150, Issue 1, article id. 31"]}

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    ZENODO
    Software . 2018
    License: CC BY NC
    Data sources: ZENODO
    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
    Software . 2018
    License: CC BY NC
    Data sources: Datacite
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      ZENODO
      Software . 2018
      License: CC BY NC
      Data sources: ZENODO
      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
      Software . 2018
      License: CC BY NC
      Data sources: Datacite
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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: Eggenhofer, Florian; Eggenhofer, Florian;

    RNAlien is a tool for automatic construction of RNA family models from a single sequence. Results include a covariance model, structural alignment and consensus secondary structure.

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    bio.tools
    Software . 2017
    License: GPL-3.0
    Data sources: bio.tools
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      bio.tools
      Software . 2017
      License: GPL-3.0
      Data sources: bio.tools
  • Authors: Robinson, Mark;

    Tools for the analysis of enrichment-based epigenomic data. Features include summarization and visualization of epigenomic data across promoters according to gene expression context, finding regions of differential methylation/binding, BayMeth for quantifying methylation etc.

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    bio.tools
    Software . 2017
    License: GPL-2.0
    Data sources: bio.tools
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      bio.tools
      Software . 2017
      License: GPL-2.0
      Data sources: bio.tools
  • 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: Cissé, Ousmane; Cissé, Ousmane;

    Genome completeness assessment tool focused on Fungi

    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/ bio.toolsarrow_drop_down
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    bio.tools
    Software . 2018
    License: MIT
    Data sources: bio.tools
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      bio.tools
      Software . 2018
      License: MIT
      Data sources: bio.tools
  • Authors: Gautier, Romain;

    A bioinformatic tool that performs a topographic analysis of lipid bilayer surfaces from various molecular dynamics simulations.

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    bio.tools
    Software . 2018
    License: Unlicense
    Data sources: bio.tools
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      bio.tools
      Software . 2018
      License: Unlicense
      Data sources: bio.tools
  • Authors: Mailinglist, General;

    Open source library and a collection of tools and interfaces for the analysis of mass spectrometry data. Includes over 200 standalone (TOPP) tools that can be combined to a workflow with the integrated workflow editor TOPPAS. Raw and intermediate mass spectrometry data can be visualised with the included viewer TOPPView.

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    bio.tools
    Software . 2016
    License: BSD-3-Clause
    Data sources: bio.tools
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      bio.tools
      Software . 2016
      License: BSD-3-Clause
      Data sources: bio.tools
  • 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: Schneeweiss, Sean; Fonk, Robin; Simon, Ulrich; Engelhardt, Lucas;

    Initial version with LeapSDK Orion 4.0.0, Python 3.7.

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    ZENODO
    Software . 2020
    Data sources: ZENODO
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      ZENODO
      Software . 2020
      Data sources: ZENODO
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  • Authors: Wüest, Valentin; Jeger, Simon; Feroskhan, Mir; Ajanic, Enrico; +2 Authors

    This repository contains the code and data to reproduce the results of the paper "Agile perching maneuvers in birds and morphing-wing drones" by V. Wüest, S. Jeger, M. Feroskhan, E. Ajanic, F. Bergonit, and D. Floreano. We provide code to reproduce the results of the paper. We provide code to reproduce the trajectory optimization study, the drone flight data analysis, the Harris' hawk flight data analysis, and the trajectory tracking control. If you follow the instructions in the README.md file, you will be able to recreate the data analysis and simulation studies. The data is provided in the data.zip file and will be extracted when following the instructions in the README.md file. It consists of the following: 12 ROS bags of the drone flight data 1 CSV file with the Harris' hawk flight data for perching maneuvers over a distance of 12m, obtained from KleinHeerenbrink et al., Nature, 2022

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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: Ramelli, Fabiola; Henneberger, Jan; David, Robert O.; Bühl, Johannes; +9 Authors

    This repository contains the scripts to produce the figures in the paper: Ramelli, F., Henneberger, J., David, R. O., Bühl, J., Radenz, M., Seifert, P., Wieder, J., Lauber, A., Pasquier, J. T., Engelmann, R., Mignani, C., Hervo, M., and Lohmann, U.: Microphysical investigation of the seeder and feeder region of an Alpine mixed-phase cloud, Atmos. Chem. Phys. Discuss., https://doi.org/10.5194/acp-2020-772, in review, 2020. More information can be found in the README files. Note that the data is to be found in the accompanying package (10.5281/zenodo.4644553).

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    ZENODO
    Software . 2021
    License: CC BY
    Data sources: ZENODO
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      ZENODO
      Software . 2021
      License: CC BY
      Data sources: ZENODO
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91 Research products
  • 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: Bosia, Francesco; Husch, Tamara; Müller, Charlotte H.; Polonius, Severin; +7 Authors

    This is development version 7b41c57 of SCINE Sparrow.

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    ZENODO
    Software . 2022
    Data sources: ZENODO
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      ZENODO
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    Authors: Akhlaghi, Mohammad; Bacon, Roland; Inami, Hanae;

    Reproduction pipeline and necessary data for Sections 7.3 and 3.4 of Bacon et al., (2017) and Inami et al., (2017) respectively (papers I and II of the series of papers on "The MUSE Hubble Ultra Deep Field Survey", published in Astronomy & Astrophysics, 608, A1 and A2). This pipeline will estimate the Hubble Space Telescope (HST) segmentation maps (for paper 1) and make the necessary measurements (for paper 2) for objects that were detected in the MUSE 3D cubes, but didn't correspond to any detection in the Rafelski et al. (2015) catalog. This repository on Zenodo contains all the necessary input data, software and reproduction pipeline (containing the scripts, configuration files and settings to exactly reproduce the results in Sections 7.3 and 3.4 of the papers above). Below is a description of the contents: gnuastro-0.2.51-bc64-bugfix.tar.gz: Gnuastro version 0.2.51 with a small bug fix only relevant to this analysis. The base Gnuastro 0.2.51 was used for this pipeline when it was written, similar to zenodo.1163746. However, a bug relating to estimation of upper-limit magnitudes was later found. This bug was fixed, but along with many other changes that made the whole Gnuastro package incompatible with this pipeline. Hence, this bug-fixed copy of Gnuastro 0.2.51 was used in the catalog of Inami et al. (2017). The reproduction pipeline below contains the fixed file and instructions on how to make this version from version 0.2.51 that is available in the official Gnuastro version controlled history. The library dependencies of this version of Gnuastro can be downloaded from zenodo.1163746 (gnuastro-dependencies.tar.gz). IMPORTANT NOTE: Since version 0.2.51 of Gnuastro was released, CFITSIO (one of Gnuastro's dependencies) has added a dependency for the cURL library (to read https URLs). Therefore, to install Gnuastro 0.2.51, please install CFITSIO version 3.41 or earlier. hst-uvudf.tar.gz: images and weight maps in 0.06 arcsec/pixel resolution from the HST-UVUDF survey. These images are not necessary to run the reproduction pipeline (they will be downloaded from the HST archives if not present). They are stored here for the self-sufficiency of this repository and faster download: in this lossless compressed format, they are roughly 1/4th the volume of the same files in HST archives. hst-xdf.tar.gz: images and weight maps in 0.06 arcsec/pixel resolution from the HST-XDF survey. These are also available from the HST archives and are kept here with similar reasons to above (with a compression ratio of almost 1/3rd). output-v4-2-gf97e.tar.gz: output of the reproduction pipeline. reproduce-v4-2-gf97e.tar.gz: The reproduction pipeline (version 4-2-gf97e) that produces the results (tables) plotted in the paper. The full Git version controlled history of this repository is available on git-cral.univ-lyon1.fr or gitlab.com. We recommend cloning from the Git repository if it is available. This tarball is kept here in case those servers don't work or Git is no longer in common use. Please see the README file in this repository for instructions on how to run the reproduction pipeline and exactly reproduce the results. This pipeline will download all the necessary data if they aren't already present on the system (it is probably just necessary to install the required version of Gnuastro). The Creative Commons Attribution-NonCommercial 4.0 copyright mentioned in the Zenodo webpage is only applicable to files that don't have an explicit copyright within them. The copyright of other files (mainly scripts and software) is mentioned within them (all are free licenses). For any issues with the pipeline/processing, please contact Mohammad Akhlaghi. {"references": ["Illingworth et al. (2013), Astrophysical Journal Supplement, Volume 209, Issue 1, article id. 6", "Rafelski et al. (2015), Astronomical Journal, Volume 150, Issue 1, article id. 31"]}

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    ZENODO
    Software . 2018
    License: CC BY NC
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    ZENODO
    Software . 2018
    License: CC BY NC
    Data sources: Datacite
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    Authors: Eggenhofer, Florian; Eggenhofer, Florian;

    RNAlien is a tool for automatic construction of RNA family models from a single sequence. Results include a covariance model, structural alignment and consensus secondary structure.

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    bio.tools
    Software . 2017
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      bio.tools
      Software . 2017
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  • Authors: Robinson, Mark;

    Tools for the analysis of enrichment-based epigenomic data. Features include summarization and visualization of epigenomic data across promoters according to gene expression context, finding regions of differential methylation/binding, BayMeth for quantifying methylation etc.

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    Software . 2017
    License: GPL-2.0
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      License: GPL-2.0
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    Authors: Cissé, Ousmane; Cissé, Ousmane;

    Genome completeness assessment tool focused on Fungi

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    bio.tools
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  • Authors: Gautier, Romain;

    A bioinformatic tool that performs a topographic analysis of lipid bilayer surfaces from various molecular dynamics simulations.

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    Software . 2018
    License: Unlicense
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  • Authors: Mailinglist, General;

    Open source library and a collection of tools and interfaces for the analysis of mass spectrometry data. Includes over 200 standalone (TOPP) tools that can be combined to a workflow with the integrated workflow editor TOPPAS. Raw and intermediate mass spectrometry data can be visualised with the included viewer TOPPView.

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    Software . 2016
    License: BSD-3-Clause
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    Authors: Schneeweiss, Sean; Fonk, Robin; Simon, Ulrich; Engelhardt, Lucas;

    Initial version with LeapSDK Orion 4.0.0, Python 3.7.

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    ZENODO
    Software . 2020
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