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481
datasets available to search
ShareScore release 0.9.0
Dataset results
481 results for “network modeling”
Newly constructed network models of different WNT signaling cascades applied to breast cancer expression data
GEO Series GSE73857. Homo sapiens. 5 samples. Type: Expression profiling by high throughput sequencing.
Transcriptome-based network analysis reveals a spectrum model of human macrophage activation [miRNA-seq]
GEO Series GSE51307. Homo sapiens. 20 samples. Type: Non-coding RNA profiling by high throughput sequencing.
REST and Neural Gene Network Dysregulation in iPS Cell Models of Alzheimer’s Disease (RNA-seq data set)
GEO Series GSE117588. Homo sapiens. 6 samples. Type: Expression profiling by high throughput sequencing.
Environmental cadmium-induced circRNA-miRNA-mRNA network regulatory mechanism in human normal liver cell model [circRNA]
GEO Series GSE246129. Homo sapiens. 6 samples. Type: Non-coding RNA profiling by array.
A functional genomics predictive network model identifies regulators of inflammatory bowel disease: Ribo-zero RNAseq mouse distal colon DSS Colitis model of genetically engineered mice
GEO Series GSE83550. Mus musculus. 194 samples. Type: Expression profiling by high throughput sequencing.
Comprehensive circRNA expression profile and construction of circRNAs-related ceRNA network in a mouse model of autism
GEO Series GSE163904. Mus musculus. 6 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Genome-Scale Transcriptional Regulatory Network Models of Psychiatric and Neurodegenerative Disorders
GEO Series GSE102122. Homo sapiens. 16 samples. Type: Expression profiling by array.
Integrated metabolic modelling reveals cell-type specific epigenetic control points of the macrophage metabolic network
GEO Series GSE68798. Homo sapiens. 6 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Data for manuscript: Sediment Routing and Floodplain Exchange (SeRFE): A spatially explicit model of sediment balance and connectivity through river networks
<p>Data used to calibrate and run the SeRFE model in the applications presented in the manuscript "Sediment Routing and Floodplain Exchange (SeRFE): A spatially explicit model of sediment balance and connectivity through river networks."</p>
Analysis of the model of integration of multicultural media in the network's space of public opinion
<p>Supplementary data of the manuscript published on Transinformação, which title is Analysis of the model of integration of multicultural media in the network’s space of public opinion.</p>
Cross-Node Federated Graph Neural Network for Spatio-Temporal Data Modeling
<p>Dataset for ICLR 2021 submission "Cross-Node Federated Graph Neural Network for Spatio-Temporal Data Modeling".</p>
On Broadcast in Generalized Network and Adversarial Models
Full video presentation of the paper: On Broadcast in Generalized Network and Adversarial Models.<br><br>Appears in Session 1 of the 24th International Conference on Principles of Distributed Systems OPODIS 2020<br><a href="https://opodis2020.unistra.fr">https://opodis2020.unistra.fr</a>
Data from: Modeling of kidney hemodynamics: probability-based topology of an arterial network
Through regulation of the extracellular fluid volume, the kidneys provide important long-term regulation of blood pressure. At the level of the individual functional unit (the nephron), pressure and flow control involves two different mechanisms that both produce oscillations. The nephrons are arranged in a complex branching structure that delivers blood to each nephron and, at the same time, provides a basis for an interaction between adjacent nephrons. The functional consequences of this interaction are not understood, and at present it is not possible to address this question experimentally. We provide experimental data and a new modeling approach to clarify this problem. To resolve details of microvascular structure, we collected 3D data from more than 150 afferent arterioles in an optically cleared rat kidney. Using these results together with published micro-computed tomography (μCT) data we develop an algorithm for generating the renal arterial network. We then introduce a mathematical model describing blood flow dynamics and nephron to nephron interaction in the network. The model includes an implementation of electrical signal propagation along a vascular wall. Simulation results show that the renal arterial architecture plays an important role in maintaining adequate pressure levels and the self-sustained dynamics of nephrons.
Metrics of neural network models in 2022 crops in Extremadura, Spain
<p>Characteristics of the 32 neural network models generated through the analysis of Sentinel-2 images in crops in Extremadura in 2022.</p>
Interpretable Deep Convolutional Neural Network-based Surrogates for Complex Urban Hydrodynamic Modeling using Random Chaotic Rainfall
<p>This data is part of the article "Interpretable Deep Convolutional Neural Network-based Surrogates for Complex Urban Hydrodynamic Modeling using. Random Chaotic Rainfall "data for model training and validation, as well as a dynamic runoff range generated by DHMUrban</p>
urbisphere_gb-london_UR-3: Transport database derived from UK road networks, OSM, and TfL public transport timetables, for modelling in London, UK
<h2><strong>Files included in this archive</strong></h2> <p><strong>Documentation</strong></p> <ul> <li> urbisphere_London_transport_database.pdf</li> </ul> <p><strong>JSON Database files</strong> (JSON: <a href="https://www.loc.gov/preservation/digital/formats/fdd/fdd000381.shtml">https://www.loc.gov/preservation/digital/formats/fdd/fdd000381.shtml</a> (<em>last accessed: 30/3/2024</em>))</p> <ul> <li>driving_transport.json <ul> <li>Database of driving routes</li> </ul> </li> <li>cycling_transport.json <ul> <li>Database of cycling routes</li> </ul> </li> <li>walking_transport.json <ul> <li>Database of walking routes</li> </ul> </li> <li>public_transport.json <ul> <li>Database of public transport routes</li> </ul> </li> </ul> <p><strong>Python 3.9 Code</strong></p> <ul> <li>London_travel_dictionaries.py <ul> <li>to create databases</li> </ul> </li> <li>assign_speed_limits.py <ul> <li> to assign OSM speed limits to each road in GLA</li> </ul> </li> <li>reduce_sub_services.py <ul> <li> to group transport routes within the TfL timetables</li> </ul> </li> </ul> <h2>Data purpose</h2> <p>This dataset contains transport routes for walking, driving, cycling, and public transport (train, tube, and bus) within the Greater London (GLA), which can be used for simulations of human behaviour and movement, for example using agent-based models (e.g. Capel-Timms et al. 2021, McGrory et al. 2024b).</p> <h3><em>Associated publications</em></h3> <ul> <li>Hertwig et al. 2024b: urbisphere_presentations_UR-1: Modelling anthropogenic heat emissions from residential buildings-comparison between Berlin and London. EMS Annual Meeting 2023 [Poster]. Zenodo. https://doi.org/10.5281/zenodo.10889863</li> <li>Hertwig et al. 2024c: urbisphere_gb-london_UR-7: Gridded total road lengths by type for London, UK. urbisphere–London Data Release and Technical Documentation [Dataset].. Zenodo. https://doi.org/10.5281/zenodo.10889841</li> <li>McGrory et al. 2024a: urbisphere_presentations_UR-3: Dynamic Anthropogenic actiVities and feedback to Emissions (DAVE): An agent-based model for heat and exposure to other anthropogenic emissions. EMS Annual Meeting 2023 [Presentation].. Zenodo. https://doi.org/10.5281/zenodo.10889900</li> </ul> <div> <div> </div> <div> <p> </p> </div> </div>
Effective Molecular Dynamics from Neural-Network Based Structure Prediction Models
<p>Molecular dynamics simulation (61.5 us) data of 28 one- and two-domain proteins from Jussupow & Kaila: Effective Molecular Dynamics from Neural-Network Based Structure Prediction Models</p>
Using a real-world network to model the trade-off between stay-at-home restriction, vaccination, social distancing and working hours on COVID-19 dynamics
<p>These datasets have been obtained through thousands of well-carried simulations by using the agent-based model based on a time-dynamic graph with stochastic transmission events. </p> <p>These simulations have been conducted on MATLAB 2019a.</p>
Evolving geometries, topologies, and apertures in fracture networks: Quantitative insights from lattice modeling
<p>Fracture networks are crucial in controlling rock mass permeability. Some of the important features of the fracture networks like the density, interconnectivity, spatial distribution, and fracture apertures determine the success of the subsurface operations. Fracture networks can be studied with analogue studies, physical experiments, and numerical modeling. In this study, we analyse the evolution of a two-dimensional fracture network under gravitational and shear loads using the lattice modeling capabilities of the microstructural modeling environment “Elle”. The simulation cases include varying gravitational loads and Young’s moduli of the formations. The topological progression of the modeled fracture network from isolated to interconnected nodes depicts a realistic network evolution process. The study shows that the rock stiffness exhibits a direct correlation with the number of fractures influencing the average aperture size of the network. A higher gravity load resulted in the development of a sparse fracture network. Stiffer rock models also showed an early onset of fracturing.</p>
Rewired SSCx network model with 5th-order simplified connectome
<p>This dataset is an accompanying dataset to the article with the title "A connectome manipulation framework for the systematic and reproducible study of structure-function relationships through simulations" (DOI: <a href="https://doi.org/10.1162/netn_a_00429" target="_blank" rel="noopener">10.1162/netn_a_00429</a>). The dataset is part of the main accompanying dataset (DOI: <a href="https://doi.org/10.5281/zenodo.11402579" target="_blank" rel="noopener">10.5281/zenodo.11402579</a>) and contains the rewired SSCx network model with simplified E-to-E connectivity within the central column based on a 5th-order simplified model of connectivity which had been fit against the original connectome beforehand.</p> <p>The corresponding repository with code, configuration files, and detailed instructions for reproducing the results in this dataset as well as generating the results figures in the accompanying article is available here: <a href="https://github.com/BlueBrain/sscx-connectome-manipulations" target="_blank" rel="noopener">https://github.com/BlueBrain/sscx-connectome-manipulations</a></p> <p>The underlying <em>Connectome-Manipulator</em> software is available here: <a href="https://github.com/BlueBrain/connectome-manipulator" target="_blank" rel="noopener">https://github.com/BlueBrain/connectome-manipulator</a></p> <p>Additional requirement: Original SSCx network model (DOI: <a href="https://doi.org/10.5281/zenodo.8026353" target="_blank" rel="noopener">10.5281/zenodo.8026353</a>)</p> <p>ℹ️ Disclaimer: Some results may have been produced with an older version of <em>Connectome-Manipulator</em>, so slight differences might be possible when re-running with the latest version.</p> <blockquote> <p><strong><em>Funding</em></strong></p> <p><em>Funding provided by the Swiss government’s ETH Board to the Blue Brain Project, a research center of the École polytechnique fédérale de Lausanne (EPFL).</em></p> </blockquote>
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.