Workflows

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

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

Credits: Pablo Carbonell

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: Thomas Duigou BioRetroSynth

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

MSA Gaps Trimming Workflow (1)

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The workflow for prefix and suffix gaps trimming of MSA result in the Phylip format.Input: MSA result in the Phylip format.Output: Trimmed prefix and suffix of the MSA result.

Created: 2016-02-28

Credits: Kasikrit Damkliang

MSA Similarity Score Estimation (1)

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The workflow for MSA Similarity Score Estimation 

Created: 2016-02-28

Credits: Kasikrit Damkliang

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: Insilicoconsulting

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: Insilicoconsulting

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: Insilicoconsulting

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: Insilicoconsulting

Chemical2URIs (1)

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This workflow will map a chemical name or identifier to uniform resource identifiers (URIs). First the ChemSpider web service is used to map the chemical name to a ChemSpider identifier, then the ChemSpider identifier is mapped to URIs via the Open PHACTS platform.

Created: 2015-08-18

Credits: Kristina Hettne Eelke van der Horst BioSemantics

Access OpenDAP (1)

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Created: 2015-06-09

Credits: Siddeswara Guru