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1,855 results for “Framework”
Example configurations and test cases for the Python HDF5Translator framework.
<p>This is a set of use examples for the <a href="https://github.com/BAMresearch/HDF5Translator">HDF5Translator framework</a>. This framework lets you translate measurement files into a different (e.g. NeXus-compatible) structure, with some optional checks and conversions on the way. For an in-depth look at what it does<a href="https://lookingatnothing.com/?p=4087">, there is a blog post here. </a></p> <p>The use examples provided herein are each accompanied by the measurement data necessary to test and replicate the conversion. The README.md files in each example show the steps necessary to do the conversion for each. </p> <p>We encourage those who have used or adapted one or more of these exampes to create their own conversion, to get in touch with us so we may add your example to the set. </p>
PathoEye: a deep learning framework for histopathological image analysis of skin tissue
<p>This dataset comprises two parts: one consisting of skin pathology slices near the epidermal layer of elderly individuals under sunlight exposure conditions, and the other comprising skin pathology slices near the epidermal layer of young individuals under the same conditions. Each type of image comes in two sizes: one is 128×128 pixels, and the other is 512×512 pixels.</p>
MetaVision3D: Automated Framework for the Generation of Spatial Metabolome Atlas in 3D | MALDI Data
<p>This repository contains MALDI data related to the Ma et al. study "<strong>MetaVision3D: Automated Framework for the Generation of Spatial Metabolome Atlas in 3D</strong>". Processed MALDI pixel-by-pixel .csv files for both metabolomics and lipidomics for two Wild-type samples, one 5xFAD sample and one GAA sample. If you use this dataset in your research, please consider citing the above study.</p> <p>The content of the files are:<br>wt.zip - pixel-by-pixel .csv files of metabolomics and lipidomics for wild-type sample.</p> <p>5x.zip - pixel-by-pixel .csv files of metabolomics and lipidomics for 5xFAD sample.</p> <p>gaa.zip - pixel-by-pixel .csv files of metabolomics and lipidomics for GAA sample.</p> <p>wt2.zip - pixel-by-pixel .csv files of metabolomics and lipidomics for wild-type2 sample.</p>
Transformer-based graphical neural network with expert experience multimodal learning (TGEML) framework: a nanocomposite performance predictor
<p>TGEML is a novel multimodal nanocomposite processing framework consists of a polymer multimodal featurizer called TGEML-polymer and a nanoparticle expert experience featurizer called TGEML-nano.</p>
Predictive Maintenance Literature Review Framework
<p>This dataset contains information collected during a literature review in the domain of Predictive Maintenance in Industry 4.0. It consists of Two Tables:</p><ol><li>Paper references and their contribution to individual topics</li><li>Types of Neural Networks that have been used in the Papers</li></ol>
A Comprehensive Review of Techniques, Methods, Processes, Frameworks, and Tools for Privacy Requirements
<p> Context: Requirements Engineering (RE) relies on the collaboration of various roles—such as requirements engineers, stakeholders, and developers—and various techniques, methods, processes, frameworks, and tools. This makes RE a highly human-dependent process that benefits greatly from tool support. Understanding how these techniques, methods, processes, frameworks, and tools are applied across RE phases could provide valuable insights into ways to enhance the RE process, contributing to more successful outcomes. Objective: The primary objective of this study is to identify the techniques, methods, processes, frameworks, and tools applied across different requirements engineering phases—such as elicitation, analysis, specification, validation, and management—to address privacy requirements. Method: We conducted a systematic literature review (SLR) and identified 125 primary studies, and we also conducted a survey with 37 practitioners. Results: Our review identified a range of techniques, methods, processes, frameworks, and tools for addressing privacy requirements. Most studies were conducted in academic contexts, with the most frequently used tools being: PriS Method, Secure Tropos, LINDDUN, i* (i-star), STRAP (Structured Analysis for Privacy), Privacy by Design (PbD), and SQUARE. Additionally, over 75% of the studies applied these tools in the privacy requirements elicitation phase. In the industry, most of the techniques identified in the literature are not known or used by practitioners. Conclusion: This study provides a comprehensive analysis of techniques and tools for privacy requirements in RE, revealing a strong focus on academic contexts with limited industry application. Future research should explore the scalability and effectiveness of these tools in real-world environments, as well as the reasons why practitioners do not use them.</p>
WOMBAT: A fully Bayesian global flux-inversion framework, version 1 (intermediate files)
<p>Code for reproducing the results of the <a href="https://arxiv.org/abs/2102.04004">WOMBAT v1 paper</a> is available on <a href="https://github.com/mbertolacci/wombat-paper">Github</a>. However, fully reproducing the results takes a very long time because of the need to run an atmospheric chemical transport model. To ease this, this dataset contains intermediate files comprising the outputs of the model. These can be used to run the flux inversions; instructions can be found on the code repository.</p>
MetaComNet: A random forest-based framework for making spatial prediction of plant-pollinator interactions
<p>1. Predicting plant-pollinator interaction networks over space and time will improve our understanding of how environmental change is likely to impact the functioning of ecosystems. Here we propose a framework for producing spatially explicit predictions of the occurrence and number of pairwise plant-pollinator interactions and of the species richness, diversity, and abundance of pollinators visiting flowers. We call the framework 'MetaComNet' because it aims to link metacommunity dynamics to the assembly of ecological networks.</p> <p>2. To illustrate the MetaComNet functionality, we used a dataset on bee-flower networks sampled at 16 sites in southeast Norway along with random forest models to predict bee-flower interactions. We included variables associated with climatic conditions (elevation) and habitat availability within a 250m radius of each site. Regional commonness, site-specific distance to conspecifics, social guild, and floral preference were included as bee traits. Each plant species was assigned a score reflecting its site-specific abundance, and four scores reflecting the bee species that the plant family is known to attract. We used leave-one-out cross-validations to assess the models' ability to predict pairwise plant-bee interactions across the landscape.</p> <p>3. The relationship between observed occurrence or absence of interactions and the predicted probability of interactions was nearly proportional (GLMlogistic regression slope = 1.09), matching the data well (AUC = 0.88), and explained 30% of the variation. Predicted probability of interactions was also correlated with the number of observed pairwise interactions (r = 0.32). The sum of predicted probabilities of bee-flower interactions were positively correlated with observed species richness (r = 0.50), diversity (r = 0.48), and abundance (r = 0.42) of wild bees interacting with plant species within sites.</p> <p>4. Our findings show that the MetaComNet framework can be a useful approach for making spatially explicit predictions and mapping plant-pollinator interactions. Such predictions have the potential to identify areas where the pollination potential for wild plants is particularly high, and where conservation action should be directed to preserve this ecosystem function.</p>
Quality Evaluation Models or Frameworks for Open Source Software: A Systematic Literature Review (Matching articles with categories)
<p>This document includes which primary study falls into which category with respect to the RQs in the following study: “Quality Evaluation Models or Frameworks for Open Source Software: A Systematic Literature Review”</p>
Quality Evaluation Models or Frameworks for Open Source Software: A Systematic Literature Review (Matching articles with categories)
<p>This document includes which primary study falls into which category with respect to the RQs in the following study: “Quality Evaluation Models or Frameworks for Open Source Software: A Systematic Literature Review”</p>
Quality Evaluation Models or Frameworks for Open Source Software: A Systematic Literature Review (Matching articles with categories)
<p>This document includes which primary study falls into which category with respect to the RQs in the following study: “Quality Evaluation Models or Frameworks for Open Source Software: A Systematic Literature Review”</p>
Dataset for AlphaDesign: A de novo protein design framework based on AlphaFold
<p>This dataset consists of output data from the work reported in: </p> <p>Jendrusch, M., Korbel, J. O., & Sadiq, S. K. (2021). AlphaDesign: A de novo protein design framework based on AlphaFold. bioRxiv.</p> <p> </p> <p> </p>
Epistemic Insight Framework
<p>This is the new updated Epistemic Insight framework</p>
Data on plant health stakeholder priorities for tests and general prioritisation framework
<p>Data collected in the framework of work package 4 of the Valitest project. They correspond to a qualitative assessment of plant health stakeholder requirements, have been collected using online surveys supplemented by desk-based research, as well as impact assessments</p>
The Regional Coupled Suite (RCS): application of a flexible regional coupled modelling framework to the Indian region at km-scale
<p>Supporting data for figures in GMD draft paper: The Regional Coupled Suite (RCS): application of a flexible regional coupled modelling framework to the Indian region at km-scale.</p>
Project files provided as supporting information to the manuscript "Coarse-grained Mori-Zwanzig dynamics in a time-non-local stationary-action framework"
<p><strong>Project files provided as supporting information to the manuscript "Coarse-grained Mori-Zwanzig dynamics in a time-non-local stationary-action framework"</strong></p> <p><br> GLE Optimization: Optimizator of GLE parameters. Uses Matlab</p> <p>MD_GLE: CG GLE and LE simulator. Uses Matlab</p> <p>Water_simulation: Folders for atomistic water system simulation with GROMACS. It requires to be run on Linux with GROMACS <br> and VOTCA packages installed.</p>
A framework to identify priority wetland habitats and movement corridors for urban amphibian conservation
<p>Core corridors: derived from Circuitscape modeling results -top 50% of wood frog, boreal chorus frog and tiger salamander results converted to binary value and summed to produce core corridors (probable movement for 2-3 amphibian species). <br> <br> To derive core corridors, we summed connectivity models for three amphibian species. For each species we derived focal nodes from high habitat value (based on HSI modelling), used three resistance scenarios and summed the three scenarios for each species to represent probable movement pathways between focal nodes. Species connectivity models were then classified to top 50% of the model, and converted to a binary value of 0 to 1. The three species were summed where by values 0-3 represent number of amphibian species the corridor probably supports movement. </p>
A framework to identify priority wetland habitats and movement corridors for urban amphibian conservation - Raw Data
<p>Call of the Wetland Program observation data reported by citizen scientists at wetlands in the City of Calgary during three amphibian seasons from 2017 to 2019. Wetlands were surveyed up to 11 times per season and participants reported observations to a smartphone application – where they documented species, and type of observation (eggs, adult, juvenile, tadpole or call). Participants also recorded when they participated in a survey and there were no observations. Observations associated without a site ID represent opportunistic observations at non-survey wetlands. This data was used to validate habitat suitability models derived from the occupancy modeling results. <br> <br> Survey wetland location shapefile (centroid point of wetland) also included. </p>
Moving beyond the diversity paradox: the limitations of competition-based frameworks in understanding species diversity
<p>Over the last century, ecologists have attempted to understand patterns of species diversity by showing stable coexistence arising from a baseline expectation of competitive exclusion. This expectation stems from an explicit assumption of resource scarcity and implicit assumptions of Malthusian struggle and winner-take-all dynamics. Fidelity to the competitive exclusion principle (CEP) presents species diversity as a paradox: if species compete for limited resources, how can they coexist? In this essay, we investigate the contradiction between the theoretical expectation of competitive exclusion and the empirical prevalence of multispecies communities. We trace the persistence of the CEP in ecological research despite numerous challenges and explore publishing trends suggesting that this framework has resulted in a disproportionate focus on competition and exclusion in contemporary research. From a critical science studies perspective, we analyze the sociopolitical factors that have contributed to these patterns. We argue that we must excavate the ideological foundation upon which competition-based coexistence research has been built to move beyond the current perceived "diversity paradox." To that end, we propose shifting the functional null hypothesis of coexistence research, introducing the notion of a "coexistence principle," which positions the persistence of multispecies communities as the rule rather than the exception in nature.</p>
Global maps of soil water characteristics parameters developed using the random forest in a Covariate-based GeoTransfer Functions (CoGTF) framework at 1 km resolution
<p>The global soil water characteristics parameters (<em>α, n, θ<sub>r</sub>, and θ<sub>s</sub></em>) maps based on van Genuchten (vG) model at 1 km resolution was developed by harnessing the technological advances in machine learning and availability of remotely sensed surrogate information such as terrain, climate, vegetation, and soil covariates. We merge concepts of predictive soil mapping with a large data set of vG parameters and local information (soil, vegetation, climate) into "Covariate-based GeoTransfer Functions'' (CoGTFs) to generate global estimates of vG parameters (to highlight the impact of Geo-referenced covariates including various remote sensing maps, we use the term Geotransfer Function GTF and not pedotransfer function PTF; in the latter case, typically only soil properties are used to predict vG parameters).</p> <p>The vG parameters (<em>α, n, θ<sub>r</sub>, and θ<sub>s</sub></em>) dataset is provided in GeoTIFF format. A total of 16 files that represent different soil depths (0, 30, 60, and 100 cm) are provided for each parameter.</p> <table> <caption>Description of vG parameters and their units</caption> <tbody> <tr> <td>vG Parameters</td> <td>Description</td> <td>units</td> </tr> <tr> <td><em>α</em></td> <td>Inverse air entry pressure</td> <td>Log<sub>10</sub><em>α (m<sup>-1</sup>)</em></td> </tr> <tr> <td><em>n</em></td> <td>Shape parameter</td> <td>Log<sub>10</sub><em>n </em>(dimensionless)</td> </tr> <tr> <td><em>θ<sub>r</sub></em></td> <td>Residual water content</td> <td>m<sup>3</sup>/m<sup>3</sup></td> </tr> <tr> <td><em>θ<sub>s</sub></em></td> <td>Saturated water content</td> <td>m<sup>3</sup>/m<sup>3</sup></td> </tr> </tbody> </table> <p> </p> <p>The Global vG training dataset used for this study is available here:</p> <p><a href="https://doi.org/10.5281/zenodo.5547338">10.5281/zenodo.5547338</a></p> <p>For more details / to cite this dataset please use:</p> <ul> <li>Gupta, S., Papritz, A., Lehmann, P., Hengl, T., Bonetti, S., & Or, D. (2022). Global Mapping of Soil Water Characteristics Parameters—Fusing Curated Data with Machine Learning and Environmental Covariates. <strong><em>Remote Sensing</em></strong>, <em>14</em>(8), 1947.</li> </ul> <p>The study was supported by ETH Zurich (Grant ETH-18 18-1). We thank Zhongwang Wei, Associate professor at Sun Yat-Sen University, for helping to collect the datasets and for insightful discussions. We would like to thank Andrea Carmintai, Professor at ETH Zurich, for the insightful discussions.</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.