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112 results for “Nexus”
Datasets for paper 'Cabello, V., Renner, A., Giampietro, M. 2019. Relational analysis of the resource nexus in arid land crop production. Advances in Water Resources 130:258-629'
<p>Datasets produced for the paper Cabello, V., Renner, A., Giampietro, M. 2019.<em> </em>Relational analysis of the resource nexus in arid land crop production. <em>Advances in Water Resources </em>130:258-269</p>
68 image lysozyme dataset recorded on the Jungfrau 16M detector at SwissFEL and formatted as a NeXus file
<p>Data provided by Meitian Wang at PSI and master file revised May 2020 for full NXmx compliance.</p> <p>To create a new NeXus master file, assuming DIALS is installed in the folder $DIALS, use this command:</p> <p>libtbx.python $DIALS/modules/cctbx_project/xfel/swissfel/jf16m_cxigeom2nexus.py unassembled_file=lyso009a_0087.JF07T32V01.h5 geom_file=16M_bernina_backview_optimized_adu_quads.geom wavelength=1.368479 detector_distance=97.830 mask_file=lyso009a_0087.JF07T32V01.mask.h5 nexus_details.start_time=2018-01-00T00:00:00.000 nexus_details.end_time=2018-01-00T00:00:02.720Z nexus_details.end_time_estimated=2018-01-00T00:00:02.720Z nexus_details.sample_name=Lysozyme nexus_details.total_flux=1000000000000</p> <p>Some notes about the parameters:<br> - Geometry file is in CrystFEL format but has been realigned to group the modules hierarchically into quadrants.<br> - Wavelength is a single wavelength for the whole dataset, but options exist to do 1 wavelength per image, or a whole spectrum per image.<br> - Start and end times are example timestamps for illustration. End times are estimated for 68 frames using a 25 Hz recording rate.<br> - Total flux of 1e12 photons is an estimate.</p> <p>View the data using DIALS: dials.image_viewer lyso009a_0087.JF07T32V01_master.h5</p> <p>Process the data using DIALS, treating the images as stills, assuming 64 cores available on the system:<br> dials.stills_process mp.nproc=64 lyso009a_0087.JF07T32V01_master.h5 dispersion.gain=10 known_symmetry.space_group=P43212 known_symmetry.unit_cell=77,77,37,90,90,90 refinement_protocol.d_min_start=2.5</p> <p>Download DIALS at dials.github.io.</p>
4 image lysozyme dataset recorded on the Jungfrau 16M detector at SwissFEL and formatted as a NeXus file
<p>This is a 4 image lysozyme datasets derived from https://doi.org/10.5281/zenodo.3352357. The specific 4 images are able to be processed by the software package DIALS using commands in the linked dataset above. The images were rounded to integer and compressed to save file space using this script:</p> <pre><code class="language-python">import shutil, h5py import numpy as np shutil.copyfile('../lyso009a_0087.JF07T32V01_master.h5', 'lyso009a_0087.JF07T32V01_master_4img.h5') h5 = h5py.File('lyso009a_0087.JF07T32V01_master_4img.h5', 'r+') data = h5["entry/data/data"][()] del h5["entry/data/data"] h = h5["entry/data"] subset = data[5:9].astype(np.int32) h.create_dataset("data", subset.shape, subset.dtype, subset, compression="gzip", compression_opts=9) h5.close()</code></pre> <p>The .expt file was created by dials.import and is useful for regression testing in DIALS.</p>
Physical inconsistencies in the representation of the ocean heat-carbon nexus in simple climate models (Ocean and Climate variables from Simple Climate Models)
<p>This dataset provide global ocean and climate variables from 8 Simple Climate Models used in the study "Physical inconsistencies in the representation of the ocean heat-carbon nexus in simple climate models"</p>
gEneSys Project - Systematic Literature on the Nexus between Gender and Energy Transition Database
<p>The present Dataset containes the data collected for the gEneSys Systematic Literature Review on the nexus between gender and energy transition. Data have been collected from 152 papers published between 2000 and 2023. The publications have been identified through an hoc research query and retrieved from the Web of Science Database.</p> <p>The dataset inscludes the following variables:</p> <ol> <li>Title of the publication, category of the categorization of Bell et al., 2020 (Political, Economic, Socio-Ecological, Technological).</li> <li>Cluster in which the publication has been included.</li> <li>Parts of the publication’s results about the nexus between gender and energy.</li> <li>Parts of the publication’s text about the gender gap assessed by the publication.</li> <li>Parts of the publication’s text about the gender gap identified to be bridged by future research.</li> <li>The type of the gender issue/s addressed by the publication. </li> <li>The type of the gender issue/s addressed by the publication. </li> <li>Technology/ies mentioned in the publication.</li> <li>The name of the country or countries studied by the publication.</li> <li>World Bank classification of the level of income of the country or countries studied by the publication.</li> <li>World Bank classification of the region of the country or countries studied by the publication.</li> <li>Spatial Context (e.g. international, national, inner-country, peri-urban, rural) of the country or countries studied by the publication.</li> <li>Research method employed in the publication (qualitative, quantitative, mixed).</li> <li>Specific qualitative, quantitative or mixed method or methods employed in the publication.</li> <li>Number of observations for the methods used.</li> <li>Parts of the publication’s text about the policy recommendations elaborated in the publication.</li> <li>If the publication mentions a pathway.</li> <li>Year of publication.</li> <li>Author/s surname and name initial. </li> <li>Author/s full surnames and names. </li> <li>Keywords chosen by the author/s. </li> <li>Abstract of the publication. </li> <li>Name of the source or journal. </li> <li>Type of publication. </li> <li>Category/ies identified by Web of Science. </li> <li>Publication’s language. </li> <li>Keywords identified by Web of Science. </li> <li>Number of references cited by the publication. </li> <li>Number of times the publication has been cited in Web of Science Core Database. </li> <li>Number of times the publication has been cited in Web of Science All Databases. </li> <li>Name of the publisher. </li> <li>Digital Object Identifier. </li> <li>Digital Object Identifier link. </li> <li>Publication’s number of pages. </li> <li>Web of Science citation index. </li> <li>Research area or areas of the publication. </li> <li>Web of Science Unique Identifier.</li> </ol>
Example data set from Diamond Light Source VMXi beamline (Eiger 4M data, NeXus format)
<p>Data set recorded from Thermolysin crystal record <em>in situ</em> with Eiger 4M detector, to demonstrate file format used for this instrument at Diamond Light Source. Processing results using xia2 / DIALS:</p> <p> </p> <pre>For AUTOMATIC/DEFAULT/SAD Overall Low High High resolution limit 1.97 5.35 1.97 Low resolution limit 46.86 46.87 2.01 Completeness 59.8 73.2 6.0 Multiplicity 5.8 8.0 1.1 I/sigma 13.6 24.4 1.8 Rmerge(I) 0.072 0.050 0.308 Rmerge(I+/-) 0.067 0.048 0.000 Rmeas(I) 0.078 0.054 0.436 Rmeas(I+/-) 0.076 0.054 0.000 Rpim(I) 0.028 0.018 0.308 Rpim(I+/-) 0.035 0.023 0.000 CC half 0.997 0.998 0.450 Wilson B factor 13.401 Anomalous completeness 51.3 78.8 0.8 Anomalous multiplicity 3.3 4.8 1.0 Anomalous correlation 0.039 -0.006 0.000 Anomalous slope 0.987 dF/F 0.103 dI/s(dI) 1.086 Total observations 85069 8229 82 Total unique 14747 1031 73 Assuming spacegroup: P 6 2 2 Other likely alternatives are: P 61 2 2 P 65 2 2 P 62 2 2 P 64 2 2 P 63 2 2 Unit cell (with estimated std devs): 93.7184(3) 93.7184(3) 130.864(2) 90.0 90.0 120.0 </pre> <p> </p>
Dataset for "An alternative to market-oriented energy models: nexus patterns across hierarchical levels"
<p>Dataset used for the publication "Di Felice, Louisa Jane, Maddalena Ripa, and Mario Giampietro. "An alternative to market-oriented energy models: Nexus patterns across hierarchical levels." <em>Energy Policy</em> 126 (2019): 431-443.". The dataset follows the distinction across hierarchical levels as specified in the publication.</p> <p>The same dataset was also used for a case study developed for the MAGIC project, available <a href="http://magic-nexus.eu/case_study/electric-grid-catalonia-illustrations-musiasem">here</a>. </p>
Zambezi dataset to "WHAT-IF: an open-source decision support tool for water infrastructure investment planning within the Water-Energy-Food-Climate Nexus"
<p>This is the dataset used in the HESS publication "<a href="https://www.hydrol-earth-syst-sci-discuss.net/hess-2019-167/">WHAT-IF: an open-source decision support tool for water infrastructure investment planning within the Water-Energy-Food-Climate Nexus</a>"</p> <p>The dataset describes the water-energy-food nexus of the Zambezi River Basin used as input to the <a href="https://github.com/RaphaelPB/WHAT-IF">WHAT-IF model</a>.</p> <p>The file Data_Organization.pdf, summarizes the available data. For more info look at the <a href="https://www.hydrol-earth-syst-sci-discuss.net/hess-2019-167/">publication</a> and/or <a href="https://github.com/RaphaelPB/WHAT-IF">Github</a>.</p>
Sub-national Water-Food-Labour Nexus in Colombia
<p>Poorer countries often face a severe trade-off: the need to improve socio-economic conditions is hard to balance with the maintenance of key ecological processes. As a case study, we select Colombia, a Latin American country with almost 10% of its inhabitants living in extreme poverty. We elaborate a<strong> water-food-labour (WFL) nexus</strong> grounded on a sub-national Environmentally Extended Input-Output (EEIO) analysis to assess the virtual water trade (VWT) and virtual informal labour (VIL) flows across administrative departments and economic sectors related to domestic trade.</p> <p>The main results are the following: high cross-departmental resource interdependence both in terms of VWT and VIL, rich departments highly depend on the resources of their neighbouring trading partners, extreme poverty conditions are shown by economically isolated departments, and considerable income inequality in the food production sectors. Moreover, departments that are net exporters of virtual water suffer from water stress that might be exacerbated by future high rainfall variability due to climate change. </p> <p>These results suggest that strategies to attain sustainable development goals (SDGs) must deal with the biophysical constraints and the economic and political feasibility of the proposed solutions. In this vein, we argue that a holistic framework, grounded on quantitative analyses, is necessary to support informed policy decisions for the simultaneous achievement of multiple (possibly contrasting) goals. Moreover, severe spatial imbalances call for local policy responses coordinated at the national level.</p>
Nexus database
<p>Nexus database associated with the forthcoming publication "<strong>Modelling energy systems across functional scales: an embodied nexus perspective"</strong></p>
NEXUS file describing the taxonomic relationships of the 466 species for which genome sequencing was underway at Tree of Life, Wellcome Sanger Institute, at 31 December 2020
<p>This NEXUS file shows the taxonomic relationships of 466 species of eukaryote. The taxonomy derives from the NCBI TaxonomyDB. The species are those for which genome sequencing is underway at the Tree of Life programme, Wellcome Sanger Institute, as of 31st Decemnber 2020. The NEXUS file includes a figtree block generated in FigTree [<strong><a href="https://github.com/rambaut/figtree">https://github.com/rambaut/figtree</a>] </strong>that informs display of the data as a circular tree with species coloured by taxonomic Family, and Families with more than one species represented as triangles. The figure is used in publications and presentations describing the activities of the Tree of Life programme and the projects in which Tree of Life is involved, especially the Darwin Tree of Life project [https://darwintreeoflife.org].</p>
Nexus and data files for Pokemon Evolutionary Phylogeny
<p>Data files associated with the following publication:</p> <p>Matan Shelomi, Andrew Richards, Ivana Li, Yukinari Okido. (2012) “A Phylogeny and Evolutionary History of the Pokémon.” Annals of Improbable Research, 18(4): 15-17.</p> <p>Free to use for educators and researchers hoping to use the Pokémon to teach evolution, phylogenetics, etc. Cite in publications as you see fit.<br /> These datasets contain Pokémon up to the 5th generation. Researchers are welcome to produce new, updated datasets so long as they cite our original work, either this dataset and/or the Annals of Improbable Research paper.</p>
Data for the paper: Water-Food-Energy nexus: Learning from global cities using machine learning algorithms
<p>This data respository contains the datasets used to produce the "<strong>Water-Food-Energy nexus: Learning from global cities using machine learning algorithms" </strong>article. </p>
4 image cytochrome dataset with per-shot spectra recorded on the Jungfrau 16M detector at SwissFEL in NeXus format
<p>Cytochrome data recorded in 2019 on the Jungfrau 16M detector recorded at SwissFEL including per-shot spectra measure each SASE pulse.</p> <p>First a NeXus master file was created using scripts in cctbx.xfel:</p> <p>libtbx.python `libtbx.find_in_repositories xfel`/swissfel/jf16m_cxigeom2nexus.py unassembled_file=run_000795.JF07T32V01.h5 geom_file=16M_bernina_backview_optimized_adu_quads.geom wavelength=1.3038 detector_distance=163.9 output_file=./run_000795.JF07T32V01_master_spectrum.h5 beam_file=run_000795.BSREAD.h5 include_spectra=True</p> <p>Then it was sliced down to 4 images that successfully index using the attached script, sliceit.py</p> <p>The file can be processed by DIALS using this command:</p> <p>dials.stills_process run_000795.JF07T32V01_master_spectrum_4img.h5 indexing.phil </p> <p>Where the indexing phil refers to the attached mask and refined geometry file, both produced by DIALS.</p>
Dataset: Dada Nexus Limited (DADA) Stock Performance
This dataset provides historical stock market performance data for specific companies. It enables users to analyze and understand the past trends and fluctuations in stock prices over time. This information can be utilized for various purposes such as investment analysis, financial research, and market trend forecasting.
Morphological matrix in NEXUS format - from Klopfstein & Spasejovic, Illustrating phylogenetic placement of fossils using RoguePlots: An example from ichneumonid parasitoid wasps (Hymenoptera, Ichneumonidae) and an extensive morphological matrix
<p>Morphological matrix in NEXUS format - from Klopfstein & Spasejovic, Illustrating phylogenetic placement of fossils using RoguePlots: An example from ichneumonid parasitoid wasps (Hymenoptera, Ichneumonidae) and an extensive morphological Matrix. Preprint published in bioRxiv (doi: https://doi.org/10.1101/425090 ).</p>
Wildlife gardening: an urban nexus of social and ecological relationships
<p>Data and R script codes to conduct analysis for:</p> <p>Wildlife gardening: an urban nexus of social and ecological relationships</p> <p>Laura Mumaw and Luis Mata</p> <p>https://ecoevorxiv.org/9rkhm/</p> <p><strong>Abstract</strong></p> <p>Biodiversity in urban environments continues to decline, alongside diminution of human connections with nature and community. An integrated ethic and practice of caring for one’s human and ecological community could help address these issues. Here, we describe how wildlife gardening can be such a pathway. We snapshot related social dynamics and human wellbeing benefits, highlighting a case study that reveals an array of connections and wellbeing facets from wildlife gardening, and their relationship with number of activities and time spent in the garden. We outline how positive biodiversity outcomes can be attained through habitat improvement in gardens. We describe how integration of nature and human community stewardship can work across physical and political boundaries when government and communities work collaboratively. We argue that wildlife gardening carried out in this manner can involve urban residents in crafting and enacting an intertwined ethic and practice of caring for nature and humanity.</p> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p>
Integration of Renewable Energy Sources into the Water-Energy-Food (WEF) Nexus – Modelling a Demand Side Management Approach and Application to a Microgrid Farm in Morocco Dataset
<p>Here you can find the official data used for the publication "Integration of Renewable Energy Sources into the Water-Energy-Food (WEF) Nexus – Modelling a Demand Side Management Approach and Application to a Microgrid Farm in Morocco"</p> <p>If you want to run the model, please update line 11 in the run.jl file, to select the dataset from the scenario you want to look at. It is also recommended to change the result path, to a directory that corresponts to the current model run in order to find the results files quicker.</p> <p> </p> <p>To create a new plot a file called newPlot.jl can be found, that already take care of most data handling, only lines 136 and 141 need to be changed, in order to read in the result files of the results you want to investigate.</p>
Dataset of the Journal article "Energy duty in direct contact membrane distillation of hypersaline brines operating at the water-energy nexus"
<p>This repository contains the Dataset of the Journal article "Energy duty in direct contact membrane distillation of hypersaline brines<br> operating at the water-energy nexus" published on Journal of Membrane Science. </p>
Datasets for the study "Hydro-economic analysis of infrastructure investment options within the Water-Energy-Food nexus in the Niger River basin"
<p>This is the dataset used in the study "Hydro-economic analysis of infrastructure investment options within the Water-Energy-Food nexus in the Niger River basin". This study has been conducted within the Department of Environmental Engineering at the Technical University of Denmark as a Master Thesis project. </p> <p>The dataset describes the water-energy-food nexus of the Niger River basin used as input to the open source single objective hydro-economic optimization model WHAT-IF. Note that the Energy Module is partly filled, but has not been used in the study (except the hydropower sheet).</p> <p>More information on data organization <a href="https://zenodo.org/record/2646476#.XxqORudS93g">here</a>.</p> <p>The model is documented in this <a href="https://hess.copernicus.org/articles/23/4129/2019/hess-23-4129-2019-discussion.html">publication</a>.</p> <p>The code is available on <a href="https://github.com/RaphaelPB/WHAT-IF">Github</a>.</p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.