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9,152 results for “Networking”
Environmental and AIS data collected during the EUMarineRobots Trans-National Access activities experiments using the NATO STO-CMRE Littoral Ocean Observatory Network testbed
<p>Environmental and AIS data collected during the H2020 project EUMarineRobots Trans-National Access activities experiments using the NATO STO-CMRE Littoral Ocean Observatory Network (LOON) testbed. Environmental data consists of temperature measured across the water column; sound velocity measured close to the surface and close to the sea bottom; meteorological data at the surface (i.e., pressure, temperature, wind speed and direction, humidity and rain). The environmental dataset is complemented with Automatic Identification System (AIS) data for the ships transiting close to the LOON area (Gulf of La Spezia, Italy)</p> <p>Temperature measured across the water column in the LOON area (Gulf of La Spezia, Italy). The dataset includes measurements for:<br> i) Nov 12, 19-20, 23-24 - 2020<br> ii) Dec 1-4, 14-20 - 2020<br> iii) Jan 12-13, 15, 18-24, 27-28 - 2021</p> <p><br> Meteorological data at the surface (i.e., pressure, temperature, wind speed and direction, humidity and rain) in the LOON area (Gulf of La Spezia, Italy). The dataset includes measurements for:<br> i) Nov 12, 19-20, 23-24 - 2020<br> ii) Dec 1-4, 14-20 - 2020<br> iii) Jan 12-13, 15, 18-24, 27-28 - 2021</p> <p><br> Sound velocity measured close to the surface (SVP1) and close to the sea bottom (SVP2) in the LOON area (Gulf of La Spezia, Italy). The dataset includes measurements for:<br> i) Nov 12, 19-20, 23-24 - 2020<br> ii) Dec 1-4, 14-20 - 2020<br> iii) Jan 12-13, 15, 18-24, 27-28 - 2021</p> <p>SVP2 data missing for Dec 14-20 (2020) and Jan 24, 27-28 (2021).</p> <p>Automatic Identification System (AIS) data for the ships transiting close to the LOON area (Gulf of La Spezia, Italy). The dataset includes AIS data for:<br> i) Nov 12, 19-20, 23-24 - 2020<br> ii) Dec 1-4, 14-20 - 2020<br> iii) Jan 12-13, 15, 18-24, 27-28 - 2021<br> </p> <p>For reference, see: "Environmental data collected on the CMRE LOON tested during the EUMR project: dataset description", Petroccia, Roberto; Zappa, Giovanni; Cimino, Giampaolo; Grati, Alberto; Alves, João. CMRE-DA-2021-001. July 2021, available at https://www.cmre.nato.int/research/publications/latest-techreports/1638-cmre-da-2021-001</p>
Schools Weather and Air Quality (SWAQ) –Metadata – Urban Network, Sydney (NSW)
<p>Schools Weather and Air Quality (SWAQ) is a citizen science project funded by the Department of Industry, Innovation and Science as part of its Inspiring Australia - Citizen Engagement Program. SWAQ is equipping public schools across Sydney with research-grade meteorology and air quality sensors, enabling students to collect and analyse research quality data through curriculum-aligned classroom activities.</p> <p>The network includes twelve automatic weather stations and seven automatic air quality stations, stretched from -33.5995° to -34.0424° latitude and from 150.6918° to 151.2706° longitude. The average spacing is 10.2 km and the average installation height is 2.5 m above ground level. Six meteorological parameters (dry-bulb temperature, relative humidity, barometric pressure, rain, wind speed, and wind direction) and six air pollutants (SO2, NO2, CO, O3, PM2.5, and PM10) are recorded via Vaisala WXT 536 and Vaisala AQT 420 with a 20 minutes sampling frequency. </p> <p>SWAQ data provides urban canopy layer observations of the intra-urban heterogeneity and inter-parameter dependency of all major urban climate and air quality variables, valuable across diverse urban disciplines. SWAQ stations are located where there are gaps in existing government networks, and focus on Sydney’s western suburbs, where the highest urbanization rate is taking place, to better inform future urban planning. QC procedures are designed to ensure observations of extreme episodes are not excluded. Beyond research purposes, SWAQ is a citizen-centered network, conceived to promote valuable STEM (science, technology, engineering, mathematics) skills among citizens and students.</p> <p>This collection includes the metadata files for all SWAQ stations, in pdf. Metadata describe the site (type, geographic coordinates, elevation, orographic setting, representativeness, local climatic zone, dominant land use, percent land cover, mean tree and building heights, proximity to water/heat and pollutants sources/sinks, estimation of Davenport Roughness, traffic density, sky view factor), and the instrumentation (variables, models, manufacturers, calibration and installation dates). Site characteristics are described at three radial scales: 20 km, 500 m, and 50 m. Graphical representations include: satellite images, street-view maps, cardinal direction photographs, panoramic photos, and close-up photos of sensors, solar panels, and connections. Optimum site allocation was determined by undertaking a multi-criteria weighted overlay analysis to ensure data representativeness and quality. All SWAQ sensors are installed:</p> <ul> <li>in homogenous urban regions, without sections of anomalous variation in the regional urban makeup and aspect-ratio, and without large, concentrated heat/pollution sources or sinks;</li> <li>in areas falling into the WMO Class 4 with no electromagnetic sources that could have distorted the transmission;</li> <li>at a constant height of 2 - 3.5 m above ground level.</li> </ul> <p>The actual data is available from the Australian Terrestrial Ecosystem Research Network (TERN) <a href="https://https://portal.tern.org.au/schools-weather-air-sydney-nsw/22077">data portal</a> and is regularly updated. The data available from TERN has undergone a rigorous quality check routine before upload.</p> <ul> <li>Calibration: Sensors and gateways are calibrated and tested by Vaisalain controlled conditions </li> <li>Quality Assurance: Annual maintenance log</li> <li>Quality control: continuity tests, fixed range tests (on both physical and instrumental limits), dynamic range and step tests (both performed on a monthly basis), internal consistency tests (on known atmospheric relations) and persistence tests. </li> </ul> <p>The files are in csv format. On the <a href="https://www.swaq.org.au">SWAQ website</a> a non quality controlled subset is available for educational purposes only.</p> <p>This project was funded by an Australian Government Department of Industry, Innovation and Science, Inspiring Australia – Science Engagement Program: Citizen Science Grants (CSG56028).</p> <p>It was also part of the Centre of Excellence for Climate Extremes research project "Attribution & Risk".</p> <p>More information is available in the readme file, in particular a full list of the variables and a legend for the quality flags used.</p>
Supplementary material for "Learning Boolean controls in regulated metabolic networks: a case-study"
<p>This record contains notebooks and Docker image for reproducing the learning of Boolean controls in regulated metabolic networks, and the case study presented in the CMSB 2021 conference proceeding article "Learning Boolean controls in regulated metabolic networks: a case-study".</p> <p>Visualize notebooks online:</p> <ul> <li><a href="https://nbviewer.jupyter.org/urls/zenodo.org/record/5060985/files/CaseStudy-Simulations.ipynb">CaseStudy-Simulations.ipynb</a></li> <li><a href="https://nbviewer.jupyter.org/urls/zenodo.org/record/5060985/files/CaseStudy-SearchSpace.ipynb">CaseStudy-SearchSpace.ipynb</a></li> <li><a href="https://nbviewer.jupyter.org/urls/zenodo.org/record/5060985/files/CaseStudy-Inference.ipynb">CaseStudy-Inference.ipynb</a></li> </ul> <p>Notebooks can be executed interactively within the Docker image <code>bioasp/boolean-caspo-flux:cmsb2021 </code>which extends the <a href="http://colomoto.org/notebook">CoLoMoTo Docker</a> version <code>2021-02-01.</code></p> <p>Alternatively, they can be executed without any installation at <a href="https://mybinder.org/v2/zenodo/10.5281/zenodo.5070151/">https://mybinder.org/v2/zenodo/10.5281/zenodo.5070151/</a>.</p> <p>The Docker image can be executed as follows:</p> <pre><code class="language-bash">docker pull bioasp/boolean-caspo-flux:cmsb2021 docker run -it --rm -p 8888:8888 bioasp/boolean-caspo-flux:cmsb2021 </code></pre> <p>then point your browser to <a href="http://127.0.0.1:8888">http://127.0.0.1:8888</a>.</p> <p>The image can be imported using the command <code>docker load</code> with the image file provided in this record:</p> <pre><code>docker load -i image.tar.gz</code></pre> <p>or with the <code>donodo</code> command available at <a href="https://github.com/pauleve/donodo">https://github.com/pauleve/donodo</a>:</p> <pre><code>pip install -U donodo donodo pull 10.5281/zenodo.5070151</code></pre>
Urban bicycle networks, existing and synthetically grown
<p>This data set contains all data used and generated in the study Growing Urban Bicycle Networks. The data contain, for 62 cities: original data of bicycle and street networks acquired from OpenStreetMap using OSMnx, processed simplified and merged data of these networks and snapped points of interests of rail and metro stations and grids, results and metrics of simulated synthetic bicycle networks, plots of results, plots of existing and synthetic networks, videos of simulated growing synthetic bicycle networks.</p>
ZIRFs: zero-inflated random forests for estimating gene regulatory networks from single cell RNA-seq data (assessment of predictive accuracy and VIM stability)
<p>We developed a zero-inflated random forests (ZIRFs) algorithm to produce a metric of connection strength between regulator genes and target genes. This file contains SCENIC results for the aorta and diaphragm tissue data sets from the Tabula Muris Consortium results. SCENIC is a genetic regulatory network analysis published by Aibar et al. (2017). The purpose of the data sets and R source code are described by README files in each directory.</p>
Dataset defining representative route network for GLOWOPT market segments
<p>For calculating the GLOWOPT representative route network, a forecast model chain was used. The model was calibrated with 2019 flight movement data (unimpeded by COVID-19) and provided forecasted aircraft movements from the year 2019 (~2020) to 2050 in 5 years intervals.</p> <p>Two formats of datasets are generated with the results of the forecast model chain, a csv file format and 4-dimensional array supported with MATLAB (.mat).</p> <p><strong>CSV Datasets</strong></p> <p>For each forecasted year a csv file is generated with the information on the origin-destination (OD) airports IATA codes, region, latitude and longitude of OD pair, representative aircraft type along with the aircraft category , the average load factor and finally, the distance between the OD pair. The airports worldwide are sub-dived into nine regions namely Africa, Asia, Caribbean, Central America, Europe, Middle East, North America, Oceania and South America. There are total of seven datasets, one for each forecasted year i.e. for years 2019 (~2020), 2025, 2030, 2035, 2040, 2045 and 2050.</p> <p><strong>Description of the data labels:</strong></p> <p><strong>Origin-</strong> Origin airport IATA code</p> <p><strong>Origin_Region-</strong> Region of the Origin Airport</p> <p><strong>Origin_Latitude-</strong> Latitude of the Origin Airport</p> <p><strong>Origin_Longitude-</strong> Longitude of the Origin Airport</p> <p><strong>Destination-</strong> Destination airport IATA code</p> <p><strong>Destination_Region-</strong> Region of the Destination Airport</p> <p><strong>Destination_Latitude-</strong> Latitude of the Destination Airport</p> <p><strong>Destination_Longitude-</strong> Longitude of the Destination Airport</p> <p><strong>AcType- </strong>Representative aircraft type</p> <p><strong>Load_Factor- </strong>Average load factor per flight</p> <p><strong>Yearly_Frequency-</strong> Total aircraft movements per annum</p> <p><strong>RefACType-</strong> Aircraft Category based on number of seats (Category 6 represents aircraft with seats 252-301 and category 7 represents aircraft with seats greater than 302.)</p> <p><strong>Distance-</strong> Great circle distance between Origin and Destination in Km.</p> <p> </p> <p><strong>MATLAB Datasets</strong></p> <p>The dataset generated with MATLAB is a 4-dimensional array with the extension *.mat. The first dimension is the region of the origin airport and subsequently the second dimensions contains the region of the destination airport. The third and fourth dimension are the aircraft category based on seat numbers and the categorized great circle distances. The information received therein is a 1X1 cell with the IATA codes of the OD pairs, frequency and great circle distance in Km.</p> <p>The 4D array is categorised such that the user can select the route segment specific to a region or a combination of regions. The range categorisation in combination with an aircraft category additionally offers the user the possibility to select routes depending on their great circle distances. The ranges are categorised to represent very short range (0-2000 km), short range (2000-6000 km), medium range (6000-10000 km) and long range (10000 – 15000 km).</p> <p><strong>Indexing based on the categorisation of the 4D array dataset</strong> - Refer to file 'Indexing_MAT_Dataset.PNG'</p> <p>For example:</p> <p>To derive the OD pairs and yearly frequency of aircraft movements for routes which originate from Europe and are destined to Asia, operated with category 6 aircraft type and are separated by distances between 10,000 to 15,000 km:</p> <p><strong>In MATLAB (Indexing based on file </strong> 'Indexing_MAT_Dataset.PNG' <strong>): </strong></p> <p><strong>Route_Network (5,2,1,4), </strong></p> <p>Description on Index:</p> <p>5 – Europe: Origin Region </p> <p>2 – Asia: Destination Region</p> <p>1– Category 6: Aircraft Type</p> <p>4 – 10000-15000 km: Range</p>
Data related to: Hippocampal ripples and their coordinated dialogue with the default mode network during recent and remote recollection, Norman et al. (2021)
<p>This dataset contains intra-cranial EEG recordings and analysis code related to the paper: "Hippocampal ripples and their coordinated dialogue with the default mode network during recent and remote recollection" by Norman et al. (https://doi.org/10.1016/j.neuron.2021.06.020)<br> The study investigates the role of hippocampal ripples in the human brain during retrieval of recent and remote autobiographical memories and semantic facts. The intracranial recordings underwent standard preprocessing as described in the paper and were stored in EEGLAB datasets. The analysis code that accompanies the dataset implements the main analyses described in the paper.</p> <p>The dataset includes the following zip files:</p> <ul> <li>iEEG data and main analysis code: <ul> <li>“Norman_et_al_2021_iEEG_data_and_code_1.zip" </li> <li>“Norman_et_al_2021_iEEG_data_and_code_2.zip" </li> </ul> </li> <li>Patients' anatomical data: <ul> <li>“Norman_et_al_2021_Freesurfer.zip”</li> </ul> </li> <li>Additional toolboxes (developed by others): <ul> <li>“MATLAB_toolboxes.zip”</li> </ul> </li> </ul> <p>The code is written primarily in Matlab (version R2018b) and runs on a desktop computer with a 3.4Ghz Intel Core i7-6700 CPU with 64GB RAM. Matlab's Signal Processing Toolbox is required, as well as EEGLAB, Unfold toolbox, and several other open-source toolboxes.</p>
In-network convolution in grid-shaped wired sensor networks
<p>Data about the simulation of the in-network convolution in grid-shaped wired sensor networks. <br> We designed the simulation to examine the communication overhead of the technique applied on a wired sensor network at two different topologies.<br> Data include measurements of traveling time of packets and packet loss at varying of the link bitrate and kernel size. </p>
Tree mortality risks under climate change in Europe: assessment of silviculture practices and genetic conservation networks
<p>General context: Climate change can positively or negatively affect abiotic and biotic drivers of tree mortality. Process-based models integrating these climatic effects are only seldom used at species distribution scale.</p> <p>Objective: The main objective of this study was to investigate the multi-causal mortality risk of five major European forest tree species across their distribution range from an ecophysiological perspective, to quantify the impact of forest management practices on this risk and to identify threats on the genetic conservation network.</p> <p><br> Methods: We used the process-based ecophysiological model CASTANEA to simulate the mortality risk of \textit{Fagus sylvatica}, \textit{Quercus petraea}, \textit{Pinus sylvestris}, \textit{Pinus pinaster} and \textit{Picea abies} under current and future climate conditions, while considering local silviculture practices. The mortality risk was assessed by a composite risk index \textit{(CRIM)} integrating the risks of carbon starvation, hydraulic failure and frost damage. We took into account extreme climatic events with the \textit{CRIM$_{max}$}, computed as the maximum annual value of the \textit{CRIM}.</p> <p><br> Results: The physiological processes' contributions to \textit{CRIM} differed among species: it was mainly driven by hydraulic failure for \textit{P. sylvestris} and \textit{Q. petraea}, by frost damage for \textit{P. abies}, by carbon starvation for \textit{P. pinaster}, and by a combination of hydraulic failure and frost damage for \textit{F. sylvatica}. Under future climate, projection showed an increase of \textit{CRIM} for \textit{P. pinaster} but a decrease for \textit{P. abies}, \textit{Q. petraea} and \textit{F. sylvatica}, and little variation for \textit{P. sylvestris}. Under the harshest future climatic scenario, forest management decreased the mean \textit{CRIM} for \textit{P. sylvestris}, increased it for \textit{P. abies} and \textit{P. pinaster} and had no major impact for the two broadleaved species. By the year 2100, 38\% to 90\% of the conservation units are at extinction threat (\textit{CRIM$_{max}$}=1), depending on the species.</p> <p><br> Conclusions: Using a process-based ecophysiological model allowed us to disentangle the multiple drivers of tree mortality under current and future climate. Taking into account the positive effect of increased CO$_2$ on fertilization and water use efficiency, the average risks may increase or decrease in the future depending on species and sites. However, considering extreme climatic events, future projections are as pessimistic than those obtained with bioclimatic niche models.</p> <p> </p> <p>Abbreviation for column:</p> <p>X Longitude<br> Y Latitude<br> LAImax Leaf area index max reach<br> Nha Density per hectar<br> Vha Volume per hectar<br> NEE Net ecosystem exchange<br> NPP net primary production<br> Reco Respiration ecosystem<br> GPP Gross primary production<br> Etveg Evapotranspiration canopy<br> Etsol Evapotranspiration sol<br> TR tree transpiration<br> ETP evapotranspiration potentiel<br> BiomassOfReserves Biomass of reserve<br> rw ring width<br> dbh diameter at breast heast<br> height height<br> BBday Budburst date<br> rFD risk of frost<br> CRIM_max Maximum combined risk index of mortality reach<br> rNSC risk of carbon starvation<br> rPLC risk of embolism<br> rPLC_max Maximum risk of embolism reach<br> CRIM combined risk index of mortality<br> Climate Climatic model<br> rNSC_max maximum risk of carbon starvation reach<br> rFD_max Maximum risk of frost reach<br> Scenario_Sylvicol null means no silvulcture simulated<br> species species<br> Country Country<br> alt_watch altitude of climate simulated<br> grid_watch number of the pixel point of WATCH<br> grid_eurocordex number of the pixel point of Eurocordex<br> Pinus_sylvestris 0 abscence ; 1 presence<br> Fagus_sylvatica 0 abscence ; 1 presence<br> Quercus_petraea 0 abscence ; 1 presence<br> Picea_abies 0 abscence ; 1 presence<br> Pinus_pinaster 0 abscence ; 1 presence</p> <p> </p>
Predicting continuous ground reaction forces from accelerometers during uphill and downhill running: A recurrent neural network solution
<p>Data and model files supporting the manuscript: </p> <p>Predicting continuous ground reaction forces from accelerometers during uphill and downhill running: A recurrent neural network solution.</p> <p>Repository: https://github.com/alcantarar/Recurrent_GRF_Prediction</p>
Dataset for "A Bayesian neural network predicts the dissolution of compact planetary systems"
<p>The dataset used for training and evaluating the models in the paper "A Bayesian neural network predicts the dissolution of compact planetary systems": https://arxiv.org/abs/2101.04117. </p> <p>The code for working with this dataset, and other links, can be found at: https://github.com/MilesCranmer/bnn_chaos_model.</p>
Gene Regulatory Network inference in long lived C.elegans reveals modular properties that are predictive of novel ageing genes - Supplementary Tables
<p>This repository contains the Supplementary Tables for Suriyalaksh et al. Gene Regulatory Network inference in long lived C.elegans reveals modular properties that are predictive of novel ageing genes.</p> <p>The list of table files can be found in <a href="https://zenodo.org/api/files/431155b3-c2b2-4fff-92bb-e93cad8bf5c2/Supplementary%20table%20guide.pdf">Supplementary Tables guide.pdf</a></p> <p>Tables S1, S2 and S3 corresponding to physical gene-gene interaction data are in a separate repository doi:10.5281/zenodo.4382337</p> <p>Details about some of the Supplementary tables:</p> <p>TableS4_inferred_networks.csv - list of inferred GRNs for specified input combinations (set of input regulators, length of the time sequence, NI tool and prior used).</p> <p><a href="https://zenodo.org/api/files/431155b3-c2b2-4fff-92bb-e93cad8bf5c2/TableS5_consensus_network_member.xlsx">TableS5_consensus_network_member.xlsx</a> - list of groups of topologically similar GRNs (from Table S4)</p> <p>Table S6: edge lists (source,target) for each one of the three consensus networks selected according to the GS validation metrics: middle PFE/AUFE, max AUFE, max PFE.<br> TableS6a_max_AUFE_GRN.txt - max AUFE; largest network - this is the one we used in the main analysis and discussion<br> TableS6b_max_PFE_GRN.xt - max PFE<br> TableS6c_middle_AUFE_PFE_GRN.txt - middle PFE/AUFE</p> <p><a href="https://zenodo.org/api/files/431155b3-c2b2-4fff-92bb-e93cad8bf5c2/TableS7_qRTPCR_ddCt_network_accuracy.csv">TableS7_qRTPCR_ddCt_network_accuracy.csv</a> - gene expression count differences for RNAi knockdown GRN validation experiments. </p> <p>Table S8: Group membership for each one of the nodes in each one of the selected networks according to the SBM that best describes the observed network topology. Each column shows the group membership for each level in a SBM block hierarchy. Our analysis is in the second most coarse-grained level (level 1).</p> <p>TableS8a_max_AUFE_SBM.csv<br> TableS8b_max_PFE_SBM.csv<br> TableS8c_middle_AUFE_PFE_SBM.csv</p> <p><a href="https://zenodo.org/api/files/431155b3-c2b2-4fff-92bb-e93cad8bf5c2/TableS9_glp_gs_datasets.pdf">TableS9_glp_gs_datasets.pdf</a> - list of datasets used for defining functional clusters.</p> <p>TableS14a_glp_l1_vs_fem_l1_lifespan_assay.xlsx - Day13 survival of fem-3(q20)ts vs day 19 survival of glp-1(e2144)ts;rrf-3(pk1426) RNAi from L1</p> <p>TableS14b_glp_l1_vs_glp_l4_lifespan_assay.xlsx - Day 19 survival of glp-1(e2144)ts;rrf-3(pk1426) RNAi from L4 vs day 19 survival of glp-1(e2144)ts;rrf-3(pk1426) RNAi from L1</p> <p>TableS15a_glp1_in_vivo_fluorescence_data.xlsx - in vivo fluorescent reporter data of glp-1(e2144)ts;rrf-3(pk1426)</p> <p>TableS15b_fem3_in_vivo_fluorescence_data.xlsx - in vivo fluorescent reporter data of fem-3(q20)ts</p> <p>TableS17_input_regulators_annotated.csv - list input regulators used as input for Network Inference Tools annotated by source type (2nd column): GenAge, known transcription factors (TF) and gene with high variability in the gene expression time series (HV). The third column lists whether that regulator has an orthologue in human (y) according to WormBase (v 278).</p> <p>TableS20_epistasis_lifespan_data.xlsx - Epistasis lifespan data of glp-1(e2144)ts</p> <p>All the image (TIF) files represent representative images in the following genetic backgrounds (below) that have been treated </p> <p>with empty vector (EV) or RNAi against the gene highlighted in the title of the image. See methods section for details. </p> <p><strong>femliu1: </strong></p> <p><em>fem-3(q20)ts.; dhs-3p::dhs-3::gfp</em></p> <p><strong>femsod3:</strong></p> <p><em>fem-3(q20)ts.; sod-3p::gfp</em></p> <p><strong>glp1lgg1:</strong></p> <p><em>glp-1(e2144); lgg-1p:lgg-1:gfp</em></p>
Synthetic bus validation of Rennes public transportation network focus on Beaulieu campus
<p>Synthetic data based on the STAR/Keolis open data version GTFS_2021.1.0.3_20210830_20211017 for regular weeks and GTFS_2020.10.1_20210705_20210829 for holidays. This dataset contains the generation of bus validations for 3500 individuals during 14 weeks with an average of 15 travels per week. It also contains GPS information of the bus stops associated to the validation.</p>
Photometric Redshifts for Cosmology: Improving accuracy and uncertainty estimates using Bayesian Neural Networks
<p><strong>This data consists of 286,401 with broad-band g,r,i,z,y photometry from the HSC DR2 survey and spectroscopic redshifts. The majority of galaxies in our sample lies between redshift of 0.01 and 2.5</strong></p>
Seasonal trajectories of plant-pollinator interaction networks differ following phenological mismatches along an urbanization gradient - Data and code
<p>Dataset and code used in the article "Seasonal trajectories of plant-pollinator interaction networks differ following phenological mismatches along an urbanization gradient", by A. Fisogni et al., published in Landscape and Urban Planning (2022, 226:104512, <a href="https://www.sciencedirect.com/science/article/pii/S016920462200161X?via%3Dihub">https://doi.org/10.1016/j.landurbplan.2022.104512</a>)</p>
Database from: Orthometric, Normal and Geoid Heights In the Context of the Brazilian Altimetric Network
<p>This dataset is part of an article entitled "ORTHOMETRIC, NORMAL AND GEOID HEIGHTS IN THE CONTEXT OF THE BRAZILIAN ALTIMETRIC NETWORK" (https://doi.org/10.1590/s1982-21702022000100003), published in the Bulletin of Geodesic Sciences.</p> <p>This dataset includes 569 stations whose values for geodetic and normal height, gravity and geopotential numbers are provided by the IBGE (Brazilian Institute of Geography and Statistics). In addition, we included orthometric height data and differences between orthometric and normal height data calculated from the Hemlert and Mader methods, using constant and variable density data provided by Medeiros et al. (2021) (https://doi.org/10.1016/j.jsames.2021.103425) and Sheng et al. (2019) (https://doi.org/10.1016/j.tecto.2019.04.005).</p> <p> </p>
Dataset: Environmental Impact on the Long-Term Connectivity and Link Quality of an Outdoor LoRa Network
<p>This repository contains the long-term connectivity and link quality dataset collected on <a href="https://chirpbox.github.io/">ChirpBox</a> over 4 months (May -- September 2021) in the city of Shanghai, China. </p> <p>In addition to the dataset itself, we provide evaluation scripts for data analysis and visualization, in order to facilitate data exploration and re-use. To make it clear how to use the scripts, we provide a <em>Jupyter notebook -- </em> <strong>dataset.ipynb</strong> for dataset visualization.</p> <p><strong>List of files:</strong></p> <ol> <li><em>dataset_03052021_15092021.csv</em> <ul> <li>The dataset includes LoRa connectivity and link quality, as well as environmental information, collected from May 3 to September 15, 2021.</li> </ul> </li> <li><em>data_analysis.py</em> <ul> <li>The script for dataset analysis and visualization. One can use the functions in this script to derive network-level statistics (e.g., in terms of average number of correctly-exchanged packets), link-level statistics (e.g., in terms of SNR, RSS, and PRR), and node-level statistics(e.g., in terms of number of neighbours and temperature evolution over time).</li> </ul> </li> <li><em>metadata_processing.py</em> <ul> <li>The script for pre-processing metadata into CSV files. One can use the functions in this script to convert metadata for each measurement saved in TXT and JSON formats to CSV files that include attributes such as link quality, connectivity, and environmental information, an example of which is <strong>dataset_03052021_15092021.csv</strong>.</li> </ul> </li> <li><em>dataset.ipynb </em> <ul> <li>The Jupiter notebook contains examples of visualization and metadata pre-processing of datasets with functions in <strong>data_analysis.py</strong> and <strong>metadata_processing.py</strong>.</li> </ul> </li> <li><em>topology_map.png</em> <ul> <li>The node deployment map used to create topology figures. A usage example is <strong>Figure 1</strong> shown in the notebook <strong>dataset.ipynb</strong>.</li> </ul> </li> <li><em>dataset_metadata.zip</em> <ul> <li>The dataset metadata is stored in TXT and JSON formats. Among them, link quality, connectivity and on-board sensor data are stored in TXT files and weather information are stored in JOSN files.</li> </ul> </li> <li><em>README.md</em> <ul> <li>The README.md explains all the files in this repository and gives some examples of how to use the provided scripts to analyze the dataset.</li> </ul> </li> </ol>
Traffic network routing index for the Czech Republic
<p><strong>Graph representation of road network of the Czech Republic</strong></p> <p>This dataset contains graph of the entire Czech road network. The data are derived from the Open Street Map project and stored in a HDF5 file. The file contains graph topology and metadata for edges and vertices. </p> <p>Spatial index is also included for the purpose of point snapping and other spatial queries. The spatial index is stored in a SQLite file with SpatiaLite extension.</p> <p>Creation of this dataset has been supported by the <a href="http://antarex-project.eu">Antarex project</a>.</p> <p><strong>Routing Index in HDF5</strong></p> <p><strong>File: </strong><a href="/api/files/f1fb6db8-a2e2-425b-b15e-8e401eb22d44/CZE-1528295206-proc-20180724134457.hdf?versionId=3294ae0b-c3b2-4155-ad36-311d2bb06ed9">CZE-1528295206-proc-20180724134457.hdf</a></p> <p>The index is divided into parts according to geographical boundaries defined by country borders. In this case it contains only single part - CZE. This information along with the creation time is stored as an attribute in the root group of the file.</p> <p>The graph topology is stored in the following way. Nodes have assigned a row index in the edges dataset which points to an outbound edge plus a number of the subsequent edges which are also output to this node. The edge metadata are stored in the EdgeData dataset to avoid redundancy. NodeMap dataset provides a convenient way to query nodes based on their uniqe identifiers.</p> <p><strong>File structure:</strong></p> <pre><code class="language-javascript">HDF5 "CZE-1528295206-proc-20180724134457.hdf" { GROUP "/" { GROUP "Index" { ATTRIBUTE "CreationTime" { DATATYPE H5T_STD_I64LE DATASPACE SCALAR DATA { (0): 1535451896 } } ATTRIBUTE "PartsCount" { DATATYPE H5T_STD_I32LE DATASPACE SCALAR DATA { (0): 1 } } ATTRIBUTE "PartsInfo" { DATATYPE H5T_COMPOUND { H5T_STRING { STRSIZE 4; STRPAD H5T_STR_NULLPAD; CSET H5T_CSET_ASCII; CTYPE H5T_C_S1; } "id"; H5T_STD_I64LE "nodeCount"; H5T_STD_I64LE "edgeCount"; } DATASPACE SIMPLE { ( 1 ) / ( 1 ) } DATA { (0): { "CZE\000", 904085, 2223222 } } } GROUP "CZE" { ATTRIBUTE "PartInfo" { DATATYPE H5T_STRING { STRSIZE 4; STRPAD H5T_STR_NULLPAD; CSET H5T_CSET_ASCII; CTYPE H5T_C_S1; } DATASPACE SCALAR DATA { (0): "CZE\000" } } DATASET "Edges" { DATATYPE H5T_COMPOUND { H5T_STD_I32LE "edgeId"; H5T_STD_I32LE "nodeIndex"; H5T_STD_I32LE "computed_speed"; H5T_STD_I32LE "length"; H5T_STD_I32LE "edgeDataIndex"; } DATASPACE SIMPLE { ( 2223222, 1 ) / ( H5S_UNLIMITED, H5S_UNLIMITED ) } } DATASET "Nodes" { DATATYPE H5T_COMPOUND { H5T_STD_I32LE "id"; H5T_STD_I32LE "latitudeInt"; H5T_STD_I32LE "longtitudeInt"; H5T_STD_U8LE "edgeOutCount"; H5T_STD_I32LE "edgeOutIndex"; H5T_STD_U8LE "edgeInCount"; } DATASPACE SIMPLE { ( 904085, 1 ) / ( H5S_UNLIMITED, H5S_UNLIMITED ) } } } DATASET "EdgeData" { DATATYPE H5T_COMPOUND { H5T_STD_I32LE "id"; H5T_STD_U8LE "speed"; H5T_STD_U8LE "funcClass"; H5T_STD_U8LE "lanes"; H5T_STD_U8LE "vehicleAccess"; H5T_STD_U16LE "specificInfo"; H5T_STD_U16LE "maxWeight"; H5T_STD_U16LE "maxHeight"; H5T_STD_U8LE "maxAxleLoad"; H5T_STD_U8LE "maxWidth"; H5T_STD_U8LE "maxLength"; H5T_STD_I8LE "incline"; } DATASPACE SIMPLE { ( 2838, 1 ) / ( H5S_UNLIMITED, H5S_UNLIMITED ) } } DATASET "NodeMap" { DATATYPE H5T_COMPOUND { H5T_STD_I32LE "nodeId"; H5T_STRING { STRSIZE 4; STRPAD H5T_STR_NULLPAD; CSET H5T_CSET_ASCII; CTYPE H5T_C_S1; } "partId"; H5T_STD_I32LE "nodeIndex"; } DATASPACE SIMPLE { ( 904085, 1 ) / ( H5S_UNLIMITED, H5S_UNLIMITED ) } } } } }</code></pre> <p><strong>Spatial index</strong></p> <p><strong>File: </strong><a href="https://zenodo.org/api/files/f1fb6db8-a2e2-425b-b15e-8e401eb22d44/CZE-1528295206-proc-20180829135251.sqlite?versionId=56bb1e60-ff7c-407f-8041-3c628ef78db0">CZE-1528295206-proc-20180829135251.sqlite</a><br> </p> <p>SQLite database contains two primary tables. Table <em>nodes</em> and table <em>segments</em>, that resluts of selection and projection from the tables of the same name in primary db. Both tables are suitable for <em>searching nearest lines</em> task and <em>searching closest node of nearest line</em> task. </p> <pre><code class="language-sql">CREATE TABLE nodes ( gid INTEGER, part_gid INTEGER, node_type INTEGER, geom POINT ); CREATE TABLE segments ( gid INTEGER, node_gid_from INTEGER, node_gid_to INTEGER, frc TEXT, transition_time DOUBLE, computed_speed REAL, geom_length DOUBLE, geom LINESTRING ); </code></pre> <p>There are three more tables. Table <em>segments_rt</em> is a copy of table <em>segments</em>, that exclude loops in segments, hence it supports network routing task in SpatiaLite. Next table is <em>rt_network</em> (static graph generated from table <em>segments_rt</em> suitable for routing). The last one is table <em>virtual_rt_network</em>, that is an interface for routing query. </p> <p> </p>
Notary network (Notarissennetwerk)
<p>RDF version of the Notary Network (Notarissennetwerk, https://notarissennetwerk.nl/), a structured version of the Repertorium van Notarissen. The dataset is included in the Golden Agents project (https://www.goldenagents.org/). </p> <p>The repo was forked from <a href="https://gitlab.com/uvacreate/vondel/notarissennetwerk-rdf/">https://gitlab.com/uvacreate/vondel/notarissennetwerk-rdf/</a> and has been updated to fit in the Golden Agents infrastructure:</p> <ul> <li>All schema.org resources now use https</li> <li>The prefix is changed from <a href="https://data.create.humanities.uva.nl/id/">https://data.create.humanities.uva.nl/id/</a> to <a href="https://data.goldenagents.org/datasets/">https://data.goldenagents.org/datasets/</a></li> </ul>
Comprehensive Human PPI Network and TF Network
<p>A public resource for curated and comprehensive high-quality PPI network data.<br> The benefit of such a public data resource allows additional information to be integrated based on research question.<br> Periodic updates of the dataset are planned, please see GitHub page for more details about network construction.</p> <table> <thead> <tr> <th>Network</th> <th>Proteins</th> <th>Interactions</th> </tr> </thead> <tbody> <tr> <td>PPI</td> <td>17,798</td> <td>254,214</td> </tr> <tr> <td>TF</td> <td>1,049</td> <td>3,686</td> </tr> </tbody> </table>
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.