Workflows

Chemical structure extractor - img2structure (1)

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Extracts images of chemical structures from PDFs and converts them to usable structure data using the OSRA binaries.An in-progress (incomplete) workflow.This workflow makes use of the External Tool node to access the OSRA structure recognition binaries.So you must have a functioning installation of OSRA and it's dependencies. This may require advanced compiler knowledge on your platform, and may not be a trivial task.OSRA 1.4 is free for both the source & binary distribution. OSRA 2.0...

Created: 2013-05-14 | Last updated: 2013-05-14

Credits: sauberns

Attributions: Chemical term extractor - text2structure

Chemical term extractor - text2structure (1)

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This workflow demonstrates how to extract biological and chemical terms (text!) from a PDF file using the KNIME text processing nodes and attempts to convert the chemistry terms to structures.Requirements:KNIME 2.7.4KNIME Labs nodes - Text ProcessingCommunity Nodes - RDKit (to view structures)See http://tech.knime.org/communityStart by selecting the folder containing the PDF documents. Alternatively, you can use a folder with Word docs.

Created: 2013-04-22 | Last updated: 2013-04-22

Credits: sauberns

Attributions: Chemical structure extractor - img2structure

13C NMR spectra prediction (2)

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This workflow can be used to predict the 13C NMR spectra of a molecule. The generation of the structure of the molecule is done using the IUPAC to Structure node that uses OPSIN to convert the name of the molecule to a structure. Alternativelly, one can read the structure from a file. The spectra prediction is based on the NMRShiftDB implementation and the data used is also from NMRShiftDB. The atom topological environments were represented as Atom Signatures and used to calculate the checmia...

Created: 2012-07-26 | Last updated: 2012-08-10

Credits: Ldpf

CHEMOPREVENTION WORKFLOW2 WITH DATA (1)

 CHEMOPREVENTION WORKFLOW WITH DATA

Created: 2012-05-19 | Last updated: 2012-05-19

Credits: Kleo Achilleos

CHEMOPREVENTION WORKFLOW1 (1)

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 CHEMOPREVENSION WORKFLOW NO DATA INCLUDED

Created: 2012-05-19 | Last updated: 2016-04-30

Credits: Kleo Achilleos

RDKit-bioisosteres (1)

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Implementation of a simple bioisostere replacement workflow using the RDKit (2.0.0) nodes in KNIME (2.5.1). Includes short list of classical bioisostere replacements (not exhaustive), selectable by the functional group to be transformed. We added this control to the workflow as our own internal list of bioisostere replacements generated huge libraries for each structure fed into the workflow. The bioisostere replacement list is stored in a tab separated text file, so can be replaced...

Created: 2012-01-18 | Last updated: 2012-01-18

Credits: sauberns

Attributions: RDKit-pains

The NOTCH2 workflow (1)

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Analysis of the exome sequencing data for the following article: Nat Genet. 2011 Mar 6;43(4):306-8. Truncating mutations in the last exon of NOTCH2 cause a rare skeletal disorder with osteoporosis. Isidor B, Lindenbaum P, Pichon O, Bézieau S, Dina C, Jacquemont S, Martin-Coignard D, Thauvin-Robinet C, Le Merrer M, Mandel JL, David A, Faivre L, Cormier-Daire V, Redon R, Le Caignec C. using knime4bio

Created: 2011-09-06 | Last updated: 2011-09-06

Credits: Pierre Lindenbaum

NGS sample workflow with data (1)

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 Sample workflow for NGS data analysis This worklfow relies on community contributions that can be installed through the following update site: http://tech.knime.org/update/community-contributions/nightly specifically the  KNIME NGS tools and the KNIME R Scripting extensions.    

Created: 2011-06-24 | Last updated: 2011-06-24

Credits: Baj

Bash example from the NGS community contri... (1)

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  BASH Simple workflow that executes "ls" on the command line in the directory "/".

Created: 2011-06-07

Credits: Baj

Workflow for Selenzyme v 1.0 (2)

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No description

Created: 2017-08-18 | Last updated: 2017-09-08

Credits: Pablo Carbonell