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83 results for “web tools”
Grapegenomics.com: a web portal with genomic data and analysis tools for wild and cultivated grapevines
<p><a href="https://grapegenomics.com">Grapegenomics.com</a> is a web portal that provides public access to genome references for grapevine cultivars (<em>Vitis vinifera</em> ssp. <em>vinifera</em>), wild grapevines (<em>Vitis vinifera</em> ssp. <em>sylvestris</em>), various wild grape species (<em>Vitis</em> spp. and <em>Muscadinia</em> spp.), and major fungal pathogens affecting grapes.</p> <p>All genomes are accessible through dedicated genome browsers, and published genomes are available for complete <a href="https://www.grapegenomics.com/download.php">download</a>.</p> <p>The site hosts all genomes produced by the laboratory of Dario Cantù in the Department of Viticulture and Enology at the University of California, Davis, along with published genome references generated by others, such as PN40024 and Pinot noir ENTAV115. Instructions for genome submission are provided <a href="https://www.grapegenomics.com/submit.php">here</a>. The portal is maintained by Noé Cochetel (ndcochetel[at]ucdavis.edu). In this version 2.0, all genome browsers utilize <a href="https://jbrowse.org/jb2/">jbrowse 2</a>. <br><br>Link to the website: <a href="https://www.grapegenomics.com">https://www.grapegenomics.com</a> </p>
Measuring Web Latency and Rendering Performance: Method, Tools & Longitudinal Dataset
<p>The dataset used in the paper entitled "Measuring Web Latency and Rendering Performance: Method, Tools & Longitudinal Dataset" published in IEEE Transactions for Network and Service Management. </p>
IMPACT HTA, WP7 (Methodological tools using multi-criteria value methods for HTA decision-making), Task 2 (Multi-criteria evaluation framework), Results of the 2nd Web-Delphi process to HTA stakeholders, organized in a single panel
<p>IMPACT HTA, WP7 (Methodological tools using multi-criteria value methods for HTA decision-making), Task 2 (Multi-criteria evaluation framework), Results of the 2<sup>nd</sup> Web-Delphi process to HTA stakeholders, organized in a single panel (all stakeholder groups in a single panel, 2 rounds), about the views of stakeholders regarding “This aspect should be considered in the evaluation of new medicines on a common basis” (2019)</p> <p>For details on the Web-Delphi process, see: IMPACT HTA, Work Package 7 (Methodological tools using multi-criteria value methods for HTA decision-making), Task 2, Deliverable 7.2 (Multi-criteria evaluation framework), Advancing knowledge and MCDA tools to assist HTA agencies in evaluating medicines on a common basis (2021) Oliveira, M.D. (IST), Panos Kanavos (LSE), Bana e Costa, C. (IST)</p>
IMPACT HTA, WP7 (Methodological tools using multi-criteria value methods for HTA decision-making), Task 2 (Multi-criteria evaluation framework), Results of the 1st Web-Delphi process to HTA stakeholders, organized into 6 separate parallel panels
<p>IMPACT HTA, WP7 (Methodological tools using multi-criteria value methods for HTA decision-making), Task 2 (Multi-criteria evaluation framework), Results of the 1<sup>st</sup> Web-Delphi process to HTA stakeholders, organized into 6 separate parallel panels (one panel per stakeholder group, 2 rounds), about the views of stakeholders regarding “This aspect should be considered in the evaluation of new medicines on a common basis” (2019)</p> <p>For details on the Web-Delphi process, see: IMPACT HTA, Work Package 7 (Methodological tools using multi-criteria value methods for HTA decision-making), Task 2, Deliverable 7.2 (Multi-criteria evaluation framework), Advancing knowledge and MCDA tools to assist HTA agencies in evaluating medicines on a common basis (2021) Oliveira, M.D. (IST), Panos Kanavos (LSE), Bana e Costa, C. (IST)</p>
Automated prediction of visual complexity of web pages: Tools and evaluations
<p>This dataset includes the screenshots of the web pages used for the evaluation of ViCRAM which is described in the following paper:</p> <p>Eleni Michailidou, Sukru Eraslan, Yeliz Yesilada, and Simon Harper. 2020. Automated Prediction of Visual Complexity of Web Pages: Tools and Evaluations. International Journal of Human-Computer Studies (SCI-E, SSCI), 145, 102523.</p>
A web-based tool for automatically linking clinical trials to their publications - example calculation
<p><strong>Objective</strong>: Evidence synthesis teams, physicians, policy makers, and patients and their families all have an interest in following the outcomes of clinical trials and would benefit from being able to evaluate both the results posted in trial registries and in the publications that arise from them. Manual searching for publications arising from a given trial is a laborious and uncertain process. We sought to create a statistical model to automatically identify PubMed articles likely to report clinical outcome results from each registered trial in ClinicalTrials.gov.</p> <p><strong>Materials and Methods</strong>: A machine learning-based model was trained on pairs (publications linked to specific registered trials). Multiple features were constructed based on the degree of matching between the PubMed article metadata and specific fields of the trial registry, as well as matching with the set of publications already known to be linked to that trial.</p> <p><strong>Results</strong>: Evaluation of the model using NCT-linked articles as gold standard showed that they tend to be top ranked (median best rank = 1.0), and 91% of them are ranked in the top ten.</p> <p><strong>Discussion</strong>: Based on this model, we have created a free, public web based tool at http://arrowsmith.psych.uic.edu/cgi-bin/arrowsmith_uic/TrialPubLinking/trial_pub_link_start.cgi that, given any registered trial in ClinicalTrials.gov, presents a ranked list of the PubMed articles in order of estimated probability that they report clinical outcome data from that trial. The tool should greatly facilitate studies of trial outcome results and their relation to the original trial designs.</p>
Prototyping 3D Virtual Learning Environments with X3D-based Content and Visualization Tools-Figure 11. Online accessible repository of digital data on cultural heritage with X3D models (STARC Web Repository, 2017, © Copyright 2017, STARC, Cyprus Institute. Used with permission)
<p>Prototyping can also include the development of toolkits for automatic content generation simulator, but in the case of an architectural environment, the components are too complex to be automatically generated. Furniture elements or the learning artifacts (i.e. content created by learners) can be converted to be viewed in X3D compatible browsers or included in online galleries (Figure 11). After functional and 3D content prototyping, certain components of the virtual campus can be easily modified and adapted as needed.</p>
Figure 4. Phenetic tree with 25 in A web based tool to merge geometric morphometric data from multiple characters
Figure 4. Phenetic tree with 25 dung beetles based on Procrustes distances, which are computed from the merged geometric morphometric data from characters of the epipharynx, right mandible, pronotum, elytra, hind wing, and metendosternite in lateral and dorsal view (totally 649 landmarks). Abbreviations for the tribe names: AT—Ateuchini, CO—Coprini, DE—Deltochilini, GY— Gymnopleurini, ON—Oniticellini, OP—Onthophagini, OT—Onitini, SC—Scarabaeini, SI—Sisyphini.
Figure 2 in A web based tool to merge geometric morphometric data from multiple characters
Figure 2. Description of the landmarks, curves and merged data. a). Epipharynx (Onthophagus (Palaeonthophagus) gibbulus in dorsal view), 14 landmarks and five curves. b). Mandible (right mandible of Synapsis yunnanus in dorsal view), eight landmarks and four curves. c). Pronotum (Euonthophagus amyntas), two landmarks and one curve. d). Elytra (Euonthophagus amyntas), three landmarks and one curve. e). Hind wing (right hind wing of Copris lunaris), 19 landmarks, terminology following Kukalová- Peck and Lawrence (1993). f). Metendosternite (Digitonphagus gazelle in lateral view), nine landmarks and four curves. g). Metendosternite (Digitonphagus gazelle in dorsal view), 14 landmarks and five curves. h). Merged data of all seven characters. All curves were re-sampled in 30 semi-landmarks, except the curves mentioned in different numbers of semi-landmarks, such as all curves in Figs 1a–b, and curve 1 in Fig. 1f.
Figure 3 in A web based tool to merge geometric morphometric data from multiple characters
Figure 3. Morphological variation of 25 dung beetles species based on merged geometric morphometric data from the epipharynx, right mandible, pronotum, elytra, hind wing, and metendosternite in lateral and dorsal view (totally 649 landmarks). Relative warps computed from the landmark data set merged from seven body character complexes. Each tribe is indicated by a different color. The Minimal Spanning Tree is the shortest possible set of lines connecting all points.
Example ScRNAseq Dataset 1 for Learning Web-based Tools
<p>This is one of the three example ScRNAseq datasets used to follow the guided example analyses within "A Guide to Single-Cell RNA Sequencing Analysis Using Web-based Tools for Non-Bioinformaticians" in the FEBS Journal. This dataset can be downloaded and imported into a variety of web-based tools and used as a learning device to gain more familiarity with the tools. As described in the paper, this dataset represents the untreated control. </p>
Example ScRNAseq Dataset 2 for Learning Web-based Tools
<p>This is one of the three example ScRNAseq datasets used to follow the guided example analyses within "A Guide to Single-Cell RNA Sequencing Analysis Using Web-based Tools for Non-Bioinformaticians" in the FEBS Journal. This dataset can be downloaded and imported into a variety of web-based tools and used as a learning device to gain more familiarity with the tools. As described in the paper, this dataset represents the negative control (carrier only). </p>
A web-based tool for automatically linking clinical trials to their publications - example calculation
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Reorient. A Web tool for reorienting and cropping MRI data.
<p>Having a properly oriented MRI dataset is a fundamental step in any neuroimaging workflow. Reorient (<a href="https://neuroanatomy.github.io/reorient">https://neuroanatomy.github.io/reorient</a>) is an open source Web application for the manual alignment and cropping of MRI nifti volumes using an intuitive graphic interface. Even for completely arbitrarily oriented brains, with different data encodings and anisotropic voxels, the tool provides a fast and precise method to include manual alignment in a reproducible workflow.</p> <p>This figure shows the interface, the reorientation process, and the final result.</p> <p> </p>
Animal Diversity Web: ADW Traits & image objects from Quaardvark Tool
This morphometry and life history dataset for size characteristics of birds is from undergraduate students who contributed to the Animal Diversity Web. Traits and images are harvested using ADW__s Quaardvark data download tool.<p></p>
User evaluation results for a Wikidata-centric tool for temporal data in Humanities and Cultural Heritage (June 2024): raw tabular result data and web forms for two questionnaires from five online focus group workshops
<p><strong>Introduction</strong></p> <p>This resource is created for the article: "Wikidata Visualization for Event and Temporal Data Exploration in Digital Humanities and Cultural Heritage" in Semantic Web Journal Special issue on the Semantic Web and Ontology Design for Cultural Heritage. It contains materials use for the user evaluation (June 2024) of a Wikidata visualization tool (<a title="ReKisstory" href="https://rekisstory.labs.vu.nl/" target="_blank" rel="noopener">ReKisstory</a>) described in the article. </p> <p><strong>Summary of the user evaluation</strong></p> <p>The structrue of the user evalution is summarized in the table below:</p> <table style="border-collapse: collapse; width: 99.9708%;"><colgroup><col style="width: 28.0622%;"><col style="width: 26.893%;"><col style="width: 27.0309%;"><col style="width: 17.9856%;"></colgroup> <tbody> <tr> <td> </td> <td>Objectives</td> <td>Setup </td> <td># of people participating</td> </tr> <tr> <td>Pre-workshop survey</td> <td>Understanding potential user profiles before workshop</td> <td>Online questionnaire (Q1)</td> <td>51</td> </tr> <tr> <td>Workshop (Focus Group)</td> <td>Introducing and testing the tool. Obtaining feedback about it</td> <td>Online demo, testing, discussion</td> <td>16</td> </tr> <tr> <td>Post-workshop survey</td> <td>Understanding user needs after testing</td> <td>Online questionnaire (Q2)</td> <td>11</td> </tr> </tbody> </table> <p> </p> <p><strong>The structure of the data is as follows:</strong></p> <p>1. The PDF and PPTX files, containing materials prepared for the pre-workshop survey, workshop, and post-workshop survey:</p> <ul> <li>Pre-workshop survey: Questionnaire (Q1) screenshot from GoogleForms <a href="https://zenodo.org/records/14960584/files/1stQuestionnaire.pdf?download=1&preview=1">1stQuestionnaire.pdf</a></li> <li>Post-workshop survey: Questionnaire (Q2) screenshot from GoogleForms <a href="https://zenodo.org/records/14960584/files/2ndQuestionnaire.pdf?download=1&preview=1">2ndQuestionnaire.pdf</a></li> <li>Documents distributed to the participants of the Focus Group Workshop: <ul> <li>ReKisstory Compare section manual <a href="https://zenodo.org/records/14960584/files/rekisstory_compare_manual.pdf?download=1&preview=1">rekisstory_compare_manual.pdf</a></li> <li>ReKisstory Find section manual <a href="https://zenodo.org/records/14960584/files/rekisstory_find_manual.pdf?download=1&preview=1">rekisstory_find_manual.pdf</a></li> <li>ReKisstory Find example search patterns <a href="https://zenodo.org/records/14960584/files/rekisstory_group_search_example_search_patterns.pdf?download=1&preview=1">rekisstory_group_search_example_search_patterns.pdf</a></li> <li>Workshop slides <a href="https://zenodo.org/records/14960584/files/Focus_Group_Workshop_slides.pptx?download=1&preview=1">Focus_Group_Workshop_slides.pptx</a></li> </ul> </li> </ul> <p>2. The Excel spreadsheets consists of the results of two questionnaires (Q1 and Q2) (<a href="https://zenodo.org/records/14960584/files/Two_questionnaires_online_workshops.xlsx?download=1&preview=1">Two_questionnaires_online_workshops.xlsx</a>): </p> <ul> <li>Pre-workshop survey: Questionnaire (Q1), containing information about potential users: <ul> <li>Demographics</li> <li>Experience of <ul> <li>Time-related data</li> <li>Wikidata</li> <li>SPARQL</li> </ul> </li> </ul> </li> <li>Post-workshop survey: Questionnaire (Q2), containing information about feedback from the Workshop participants : <ul> <li>Comparison with Q1</li> <li>Questions about time-related functionalities</li> <li>Questions about Compare and Find searches</li> <li>Overall comment</li> </ul> </li> </ul> <p><em>Please see "Wikidata Visualization for Event and Temporal Data Exploration in Digital Humanities and Cultural Heritage" for more details</em></p>
Evaluation of the Prototyping of a Web Tool for Customization and Management of Rubrics: A Focus Group Study
<p>Files containing the focus group chat and audio transcripted, the questionnaire used, the questionnaire answers sheet and the Figma prototypes applied on the evaluation of the prototyping of a web information system for rubric customization and management: RubricPro</p>
Results of Salinicola genome mining using the antiSMASH web tool.
<p>A collection of GenBank files (.gbk) and html files obtained from 14 <em>Salinicola</em> genomes.<br>Biosynthetic Gene Clusters searched and detected using antiSMASH v7.1.</p> <p>List of strains:</p> <p><em>S. tamaricis</em> CSA4-1, <em>S. tamaricis</em> F01, <em>S. endophyticus</em> CPA92, <em>S. aestuarinus</em> CP62, <em>S. halophilus</em> CECT 5903,<em> S. acroporae</em> LMG 28587, <em>S. lusitanus</em> CR50, <em>S. corii </em>L3, <em>S. salarius</em> DSM 18044, <em>S. socius</em> DSM 19940, <em>S. halimionae</em> CPA60, <em>S. halophyticus</em> CR45, <em>S. peritrichatus </em>JCM 18795 and <em>S. rhizosphaerae </em>KCTC 32998.</p> <pre>-. .-. .-. .-. .-. .-. . ||\|||\ /|||\|||\ /|||\|||\ /| |/ \|||\|||/ \|||\|||/ \|||\|| ~ `-~ `-` `-~ `-` `-~ `- </pre> <p><br> </p>
Supplementary Material to SBIE 2024:Achieving Project Management Educational Web-Tool Evolution Using Service-based Software
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Figure 1. A in A web based tool to merge geometric morphometric data from multiple characters
Figure 1. A workflow for the method.
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.