Workflows

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Showing 15 results. Use the filters on the left and the search box below to refine the results.
Type: KNIME Tag: workflow

Workflow RetroPath2.0 - a retrosynthesis workflow w... (5)

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: 2018-02-16

Credits: User Baudoin Delépine Network-member BioRetroSynth

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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 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 Texture classification: Knime Image Analytics (1)

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A workflow including image pre-processing and descriptor calculation for building a texture classification model. The workflow can really be used for any kind of image classification task for which has labelled training data.There is significant scope of improvement, both on the image processing , descriptor selection and model building phases..Happy image analytics !

Created: 2015-11-10

Credits: User Insilicoconsulting

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Workflow Pubmed -Google Tag Cloud (1)

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A simple workflow to query PubMed, Google and build a Tag Cloud after some preprocessing.

Created: 2015-11-01

Credits: User Insilicoconsulting

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Workflow Drug-Drug Networks using Matador-DrugBank ... (1)

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These days, Networks of all kinds are all the rage! So here's a trickle contributing to the flood.The workflow generates a network based on Similarity between known drugs based on commonality of their "direct" drug target interactions.The workflow does not provide a comparison between Chemical similarity based network and one based on shared drug targets. It only provides the latter.Other nodes and interfaces to Cytoscape and exported csv can be used to further the network analy...

Created: 2015-09-17 | Last updated: 2015-09-17

Credits: User Insilicoconsulting

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Workflow SAR by Rgroup decomposition (1)

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This workflow showcases a simple way to use Rgroup decomposition for SAR analysis.Once R-groups are obtained for several sites on the Scaffold, molecular properties like logP, TPSA, number of heavy/hetero-atoms, various kinds of ring counts are calculated.While medicinal chemistry purists may decry calculating properties for fragments/R-groups, correlating these at each site with Ki (or activity) shows up interesting trends.It's immediately apparent if increasing logP at a given site incr...

Created: 2015-09-15

Credits: User Insilicoconsulting

Workflow Use Case C, Worflow 4 (1)

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Workflow used to obtain data for the research paper ‘The application of the Open Pharmacological Concepts Triple Store (Open PHACTS) to support Drug Discovery Research’, currently submitted to PLOS ONE.  Requirements:- Knime v2.9- Open PHACTS Knime nodes 1.0.0 (DON'T use any later version!): https://github.com/openphacts/OPS-KnimeInstallation:- Download "org.openphacts.utils.json_1.0.0.zip" and unzip it in the plugins folder of your KNIME installation- Download ...

Created: 2014-05-27 | Last updated: 2014-11-25

Credits: User Emiliano Cuadrado User Joseline Ratnam User Daniela Digles Network-member Open PHACTS

Workflow Use Case C, Worflow 3 (1)

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Workflow used to obtain data for the research paper ‘The application of the Open Pharmacological Concepts Triple Store (Open PHACTS) to support Drug Discovery Research’, currently submitted to PLOS ONE.  Requirements:- Knime v2.9- Open PHACTS Knime nodes 1.0.0 (DON'T use any later version!): https://github.com/openphacts/OPS-KnimeInstallation:- Download "org.openphacts.utils.json_1.0.0.zip" and unzip it in the plugins folder of your KNIME installation- Download ...

Created: 2014-05-27 | Last updated: 2014-11-25

Credits: User Emiliano Cuadrado User Joseline Ratnam User Daniela Digles Network-member Open PHACTS

Workflow Use Case C, Worflow 2 (1)

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Workflow used to obtain data for the research paper ‘The application of the Open Pharmacological Concepts Triple Store (Open PHACTS) to support Drug Discovery Research’, currently submitted to PLOS ONE.  Requirements:- Knime v2.9- Open PHACTS Knime nodes version 1.0.0 (DON'T use any later version!): https://github.com/openphacts/OPS-KnimeInstallation:- Download "org.openphacts.utils.json_1.0.0.zip" and unzip it in the plugins folder of your KNIME installation- D...

Created: 2014-05-26 | Last updated: 2014-11-25

Credits: User Emiliano Cuadrado User Joseline Ratnam User Daniela Digles Network-member Open PHACTS

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