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Type: KNIME
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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

Workflow KNIME Workflow for RetroRules and Retropat... (3)

KNIME Workflow for RetroRules and RetroPath2.0This worflow provides an examples of retrieving the RetroRules reaction rules for some given reaction identifiers.1. Input to the workflow: Chemical reactions expressed using public database identifiers.2. Each reaction queries RetroRules and outputs the corresponding reaction rules.3. Resulting list of rulesenzymes is stored in a csv file in RetroPath2.0 format.Installation notesThe workflow runs a Python scrpt that requires pandas: Python Data A...

Created: 2018-07-26 | Last updated: 2018-08-11

Credits: User Pablo Carbonell

Workflow Integrative data mining of chemical compou... (1)

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This workflow downloads ligand data  for hepatic Organic Anion Transporting Polypeptides (OATPs) from five different open sources (CHEMBL, Metrabase, USFC-FDA Transportal, IUPHAR, and Drugbank) in an automatized fashion. This workflow can be adopted to any other ligand data linked to a particular membrane transporter. If missing, structural file format is  mapped via PubChem webservices. Pre-curated data are further unified, activity threshold is set up based on pre-selected cutoff,...

Created: 2018-07-26 | Last updated: 2018-07-27

Credits: User Alžbeta Türková User Barbara Zdrazil

Workflow Substructure querying | R-group decomposit... (1)

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This workflow creates maximum common substructure (MCS) out of the provided structures and then substructure mining using MCS as a structural query is performed. Obtained hits are then subjected to R-group decomposition to explore their functional groups. Optionally, physicochemical descriptors for individual functional groups can be calculated. Requirements:- Knime v3.4- KNIME ‘Trusted Community Contributions (3.4)’:1) RDKit KNIME2) Marvin Chemistry3) KNIME Core Chemisry&nbs...

Created: 2018-07-26 | Last updated: 2018-07-26

Credits: User Alžbeta Türková User Barbara Zdrazil

Workflow Scaffold Analysis | Scaffold overlapping p... (1)

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This workflow performs extraction and statistical analysis of Murcko scaffolds for compounds being active toward (a) different target(s). Specifically, overlapping scaffold profiles across different targets, scaffold clustering (using the Maximum Common Substructure as a measure of similarity), and substructure searching for the sake of 'common' scaffold enrichment is performed via this workflow.  Requirements:- Knime v3.4- KNIME ‘Trusted Community Contributions (3.4)&...

Created: 2018-07-26 | Last updated: 2018-07-26

Credits: User Alžbeta Türková User Barbara Zdrazil

Workflow KNIME Workflow for RetroRules and Selenzyme (4)

KNIME Workflow for RetroRules and SelenzymeThis worflow provides an examples of retrieving the RetroRules reaction rules for some given reaction and selecting enzyme sequences using the Selenzyme tool.1. Input to the workflow: Chemical reactions expressed using public database identifiers.2. Each reaction queries RetroRules and outputs the corresponding reaction rules.3. Each reaction rule queries Selenzyem and outputs the selected Uniprot sequences for each rule.4. Resulting list of selected...

Created: 2018-07-24 | Last updated: 2018-08-11

Credits: User Pablo Carbonell

Workflow Europe PMC searchPublications and getAnnot... (2)

This workflow first conducts a search and downloads the PMIDs for all publications in PubMed and PMC that match a particular query using the Europe PMC Articles API. In a second phase, the workflow fetches the ChEBI annotations for all these publications using the Europe PMC Annotations API.

Created: 2018-02-09 | Last updated: 2018-02-12

Credits: User Magnus Palmblad User Aswin Verhoeven

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Workflow zetasizer2excel (2)

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Arrrgh! The exported data file format for the Malvern Zetasizer is insane!Row1, x1,x2,x3,x4,....,y1,y2,y3,y4,....Row2, x1,x2,x3,x4,....,y1,y2,y3,y4,....Row3, x1,x2,x3,x4,....,y1,y2,y3,y4,....This workflow imports the txt file, takes each row and reformats as table with 3 columns: Size, Intensity, Volume. Then exports the data for each row to a new tab in Excel. Or you can just use KNIME to plot and prepare reports (to do).The TableRow2Variable node allows you to name the tabs in Excel from a ...

Created: 2017-11-20 | Last updated: 2017-11-20

Credits: User sauberns

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Workflow RetroPath2.0-Mods-isomer-transformation-queue (2)

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The workflow allows one to enumerate isomers of chemical structure(s) using the isomer transformation algorithm. It is a modified version of "RetroPath2.0-Mods-isomer-transformation". It illustrates how to introduce a FIFO data structure for the source set and use it for iteratively firing rules on small chunks of structures. See [1] for details. How to useSee instructions embedded in the workflow.Usage specificationsThe workflow is compatible starting from version 3.4.1 of Kni...

Created: 2017-10-12 | Last updated: 2017-12-19

Credits: User Thomas Duigou Network-member BioRetroSynth

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

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Workflow QSAR-model-aminoglycosides (2)

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The workflow build a QSAR model with LOO cross-validation for antibacterial activities of aminoglycosides structures using RDKit fingerprints and random forest. See [1] for details. Antibacterial activities were compiled from Setny et al, JCIM, 2009. How to useSee instructions embedded in the workflow.Usage specificationsThe workflow is compatible starting from version 3.3.2 of Knime Analytics Platform.Licence: CC BY-NC-SAThis work is licensed under the Creative Commons Attribution-NonCo...

Created: 2017-06-30 | Last updated: 2017-12-19

Credits: User Thomas Duigou Network-member BioRetroSynth

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