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Showing 24 results. Use the filters on the left and the search box below to refine the results.
Type: KNIME Tag: knime
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Workflow RetroPath2.0 - a retrosynthesis workflow w... (15)

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The RetroPath2.0 workflow build a reaction network from a set of source compounds to a set of sink compounds.When applied in a retrosynthetic fashion, the source is composed of the target compounds and the sink is composed of the available reactants (for instance in the context of metabolic engineering the sink is the set of native metabolites of a chassis strain). From amongst all the chemical reactions generated using RetroPath2.0 (in the retrosynthetic way), only a subset may effectively l...

Created: 2017-05-24 | Last updated: 2022-02-24

Credits: User Thomas Duigou User Baudoin Delépine Network-member BioRetroSynth

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Workflow Indigo-pains (2)

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If you like this workflow, please reference our paper doi:10.1002/minf.201100076, and check the related workflows Indigo-pains-recursive, and RDKit-pains.*** Update 20151130 - using KNIME 3 nodes and the 'RDKit' version of PAINS queries ***Implementation of the PAINS filters[1] using the Indigo (1.1.1300.201511201230) nodes in KNIME (3.0.1). Original PAINS filters were published in SLN format. his workflow contains the SMARTS form of the filters published by Greg Landrum as part of th...

Created: 2011-06-07 | Last updated: 2015-12-01

Credits: User sauberns

Attributions: Workflow RDKit-pains

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Workflow RDKit-pains (4)

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If you like this workflow, please reference our paper doi:10.1002/minf.201100076, and check the related workflows RDKit-pains-parallel, and Indigo-pains.*** Update 20151119 - using KNIME 3 and RDKit version of PAINS queries ***Implementation of the PAINS filters[1] using the RDKit (3.0.0.201511131320) nodes in KNIME (3.0.1). Original PAINS filters were published in SLN format. This workflow contains the SMARTS form of the filters published by Greg Landrum as part of the RDKit library[2], whic...

Created: 2011-02-07 | Last updated: 2015-11-19

Credits: User sauberns

Attributions: Workflow Indigo-pains

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Workflow RetroPath2.0-Mods-metabolomics (2)

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Set of workflows for the "Metabolome completion and metabolomics" use case:1) Produces a list of molecules using a user defined set of rules (RetroPath2.0 workflow).2) Takes as input the products generated by RetroPath2.0 and prepare the files to be read by OpenMS nodes.3) The last workflow finally searches for each produced compound the corresponding peak in some MS spectra.See [1] for details. How to useSee instructions embedded in the workflow.Usage specificationsThe workflo...

Created: 2017-06-30 | Last updated: 2018-11-14

Credits: User Thomas Duigou Network-member BioRetroSynth

Attributions: Workflow RetroPath2.0 - a retrosynthesis workflow with tutorial and example data

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Workflow RDKit-pains-parallel (2)

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If you like this workflow, please reference our paper doi:10.1002/minf.201100076, and check the related workflows RDKit-pains, and Indigo-pains.*** Update 20151119 - using KNIME 3 and RDKit version of PAINS queries ****** This version contains Parallel processing nodes to take advantage of mutil-core processors ***Implementation of the PAINS filters[1] using the RDKit (3.0.0.201511131320) nodes in KNIME (3.0.1). Original PAINS filters were published in SLN format. This workflow contains the S...

Created: 2011-10-13 | Last updated: 2015-12-01

Credits: User sauberns

Attributions: Workflow RDKit-pains

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Workflow Indigo-pains-recursive (2)

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*** Update 20151130 - using KNIME 3 nodes and the 'RDKit' version of PAINS queries ***The old Indigo library (1.1.13) could not take advantage of the parallelizing nodes in KNIME the way the RDKit library could. One way to speed up the PAINS workflow when using the Indigo library was to use a recursive loop that constantly shrank the list of structures being presented to the next PAINS query as structures were knocked out of the main list.Using the WEHI-10k reference set (embedded in ...

Created: 2013-08-13 | Last updated: 2015-12-01

Credits: User sauberns

Attributions: Workflow Indigo-pains Workflow RDKit-pains-parallel

Workflow Epitope-based Vaccine Design Workflow usin... (3)

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Population-based vaccine design workflow in KNIME. AlleleFrequency is used to specify the geographical region or population of interest and returns a tab-separated list of HLA alleles with their corresponding occurrence probability within the selected population. This file, together with a FASTA file containing protein sequences, or a file containing peptides is used as input to EpitopePrediction, which generates a file containing the predicted binding affinities of the (generated) peptides a...

Created: 2016-11-30 | Last updated: 2017-04-11

Credits: User Benjamin Schubert

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Workflow Metabolic differences in ripening of Solan... (2)

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Updated data processing workflow for metabolomics LC-MS/MS data. This workflow depends on the stable community plug-in MassCascade and KNIME plug-ins Base Chemistry, Chemistry Types & Nodes, Math Expression, and XLS Support. The workflow was run under KNIME version 2.9.2.

Created: 2013-10-16 | Last updated: 2014-07-04

Credits: User SBeisken

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Workflow Deriving factual information from WHO COVI... (1)

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 WHO has posted a CSV that's frequently updated with COVID abstracts. A simple PubMed search reveals thousands of abstracts too. So here's an NLP pipeline to mine these and extract meaningful sentences/facts using Stanford Open Information Extractor and Biological entity tagging. #knime #naturallanguageprocessing #textanalytics #textmining #covid19 #nlp #datascience #WHO 

Created: 2020-04-12

Credits: User Insilicoconsulting

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Workflow Antiviral activity multiclass Predictor (1)

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A simple multi-class antiviral activity predictor based on expanded Pubchem fingerprints and random forest algorithm. Seems to work well to perform quick screens for antiviral molecules.Download training data from CTD (http://ctdbase.org/downloads/) or  use this preprocessed version https://www.myexperiment.org/files/2285.html. Write to me at rajeev.gangal@gmail.com regarding any queries.I make no claim that the predictive model is accurate for clinical hypotheses or that it will find mo...

Created: 2020-03-23 | Last updated: 2020-03-25

Credits: User Insilicoconsulting

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