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10 results for “KNIME”
BRAIN Journal-Prediction of Thyroid Disease Using Data Mining Techniques-Figure 3. KNIME Diagram
<p>The proposed KNIME diagram representing the data mining models is given in Figure 3. The nodes that constitute the model diagram are: ARFF Reader – the input node used to load the data set in arff format, Partitioning – the node with the role of data set partition (for training and for the validation of the classification model), Naive Bayes Learner and Decision Tree Learner – the nodes used to build the classification model, Naive Bayes Predictor and Decision Tree Predictor – the nodes used to validate the model, Scorer – the node reports a confusion matrix and the accompanying quality measures in its view, Normalizer – the data set are normalized to be able to apply the neural network models, Multilayer Perceptron and RBFNetwork – the nodes corresponding to the neural network classification models, Weka Predictor – a node implemented in Weka to validate the models. </p>
Video tutorial for Multi-Template-Matching implementation in Fiji and KNIME
<p>Set of tutorial videos on how to use Multi-Template-Matching as implemented in Fiji and KNIME by Thomas LSV and Gehrig J.</p> <p>Test datasets are also available on Zenodo</p> <p>Contact: l.thomas(at)acquifer.de, j.gehrig(at)acquifer.de</p>
PPARδ dataset curated and enriched using the Enalos tools and Enalos KNIME nodes for machine learning analysis (SCENARIOS project)
<p><span>A curated and enriched dataset for PPAR</span>δ<span>, suitable for in silico model development, was obtained from PubChem BioAssay under the numeric identifier AID 469785 using Enalos tools and Enalos KNIME nodes. This dataset comprises 136 compounds that induce luciferase activity, serving as an indicator of agonist activity against the human PPAR</span>δ<span> ligand-binding domain. These molecules were tested in a human embryonic kidney cell line (293T), co-transfected with a chimeric plasmid containing the yeast GAL4 DNA-binding domain (DBD). All 136 oxazole-based compounds retrieved from the dataset are accompanied by their half-maximal effective concentration (EC50) and enriched with 777 molecular descriptors extracted from their 2D structure using EnalosMold2 KNIME nodes</span></p>
Retropath2_wrapper_Knime_4.6.4
<p>Dependencies needed by <a href="https://github.com/brsynth/RetroPath2-wrapper">Retropath2_wrapper</a></p> <p>Related to:</p> <p>Delépine B, Duigou T, Carbonell P, Faulon JL. RetroPath2.0: A retrosynthesis workflow for metabolic engineers. Metabolic Engineering, 45: 158-170, 2018. DOI: <a href="https://doi.org/10.1016/j.ymben.2017.12.002">https://doi.org/10.1016/j.ymben.2017.12.002</a></p> <p>Embedded Knime v4.6.4 (linux, mac, windows) and the associated dependencies.</p> <p>Visit also <a href="https://www.knime.com/">KNIME</a> website</p>
Knime workflow and data files to calculate a lead-likeness evaluation function 'Λ' for small molecule compounds
<p class="RSCB01COMAbstract"><span class="06CHeading"><span>A simple and rational method to rank molecules' lead-likeness using continuous evaluation functions was developed to support epigenetic drug discovery. This strategy proved to be highly effective on model chemical libraries and finally helped driving synthetic efforts towards candidates of interest for epigenetic applications towards HDAC6, BRD4 and EZH2.</span></span></p> <p>Here we provide sample data and the knime workflow for generatating lead-like chemical probes for epigenetics. This tool and example data set will enable researchers to establish this workflow in their own laboratories and apply it to new synthetic scaffolds for medicinal chemistry.</p>
Knime workflow and data files to calculate a lead-likeness evaluation function 'Λ' for small molecule compounds
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Example workflow using KLIFS nodes in KNIME - identifying structures with similar molecules
<p>This is KNIME workflow created during the recording of the following <a href="https://www.youtube.com/channel/UCzSo1G_wyTv1vp42AhFDT8A">YouTube demonstration video</a>.</p> <p>Using this workflow, the user can draw a molecule and compare this molecule to all ligands from the KLIFS database (<a href="https://klifs.net">https://klifs.net</a>) to identify structures with molecules that are similar to the drawn molecule.</p> <p>In this workflow the follow steps are performed:</p> <ul> <li>Draw a molecule</li> <li>Collect all kinase ligands with a known structures from KLIFS</li> <li>Compare all KLIFS ligands to the drawn molecule using the ECFP-4 fingerprint and calculate a Tanimoto score </li> <li>Select the highest scoring three ligands and search for their PDB structures</li> <li>Collect the MOL2 files of the ligands as observed while binding in the PDB structures (note: all the PDB structures were first aligned by KLIFS)</li> </ul>
Retropath2_wrapper_Knime_4.7.0
<p>Dependencies needed by <a href="https://github.com/brsynth/RetroPath2-wrapper">Retropath2_wrapper</a></p> <p>Related to:</p> <p>Delépine B, Duigou T, Carbonell P, Faulon JL. RetroPath2.0: A retrosynthesis workflow for metabolic engineers. Metabolic Engineering, 45: 158-170, 2018. DOI: <a href="https://doi.org/10.1016/j.ymben.2017.12.002">https://doi.org/10.1016/j.ymben.2017.12.002</a></p> <p>Embedded Knime v4.7.0 (linux, mac, windows) and the associated dependencies.</p> <p>Visit also <a href="https://www.knime.com/">KNIME</a> website</p>
KNIME workflows for the evaluation of neurotoxic effects in zebrafish embryos by automatic measurement of early motor behaviours
<p>Zebrafish (<em>Danio rerio</em>) has rapidly become a popular model species for behavioural studies that may be relevant to drug screening and safety toxicology. Zebrafish embryos show a complex behavioural repertoire already a few hours after fertilization. Particularly, early stage zebrafish show characteristic behavioural features such as spontaneous tail coiling (STC) or induced movements when exposed to a short and bright light flash (called photomotor response -PMR-). In this chapter, we provide the methods for assessing STC and PMR in zebrafish embryos and to detect changes provoked by chemicals. One of the protocols uses video analysis suitable for automated high-throughput screening. Moreover, both protocols describe the use of automated video analysis by using an open-source integration platform (KNIME analytics platform), providing a flexible workflow system that can be adapted to a diversity of video recordings. We also provide a toxicological validation of this assay and show that these protocols can be used to provide an automated, high data-content readout for zebrafish behavioural responses. </p>
PPARγ-bla dataset curated and enriched using the Enalos tools and Enalos KNIME nodes for machine learning analysis (SCENARIOS project)
<p>A curated and enriched dataset for PPARγ-bla, intended for in silico model development, was obtained from PubChem BioAssay under the numeric identifier AID 743194 using Enalos tools and Enalos KNIME nodes. This dataset specifically utilizes compounds from the Tox21 10K chemical library that underwent screening against the PPARγ-bla HEK293H cell line. The cell line contains a beta-lactamase reporter gene, and all the information was extracted from PubChem Bioassay ID 743194 using Enalos tools and Enalos KNIME nodes. The original bioassay, consisting of 6587 compounds, assessed the antagonist activity of small molecules and classified them as 'active', 'inactive' or 'inconsistent' based on their AC50 (potency) score. The curated PPARγ dataset comprises 1230 compounds selected from the original bioassay and enriched with 777 molecular descriptors extracted from their 2D structure using EnalosMold2 KNIME nodes.</p>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
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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.