Workflows

Search filter terms
Filter by type
Filter by tag
Filter by user
Filter by licence
Filter by group
Results per page:
Sort by:
Showing 70 results. Use the filters on the left and the search box below to refine the results.
Type: KNIME
Uploader

Workflow Chemical structure extractor - img2structure (1)

Thumb
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: User sauberns

Attributions: Workflow Chemical term extractor - text2structure

Uploader

Workflow Chemical term extractor - text2structure (1)

Thumb
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: User sauberns

Attributions: Workflow Chemical structure extractor - img2structure

Uploader

Workflow 13C NMR spectra prediction (2)

Thumb
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: User Ldpf

Workflow CHEMOPREVENTION WORKFLOW2 WITH DATA (1)

Thumb
 CHEMOPREVENTION WORKFLOW WITH DATA

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

Credits: User Kleo Achilleos

Workflow CHEMOPREVENTION WORKFLOW1 (1)

Thumb
 CHEMOPREVENSION WORKFLOW NO DATA INCLUDED

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

Credits: User Kleo Achilleos

Uploader

Workflow RDKit-bioisosteres (1)

Thumb
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: User sauberns

Attributions: Workflow RDKit-pains

Workflow The NOTCH2 workflow (1)

Thumb
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: User Pierre Lindenbaum

Uploader
Avatar Baj

Workflow NGS sample workflow with data (1)

Thumb
 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: User Baj

Uploader
Avatar Baj

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

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

Created: 2011-06-07

Credits: User Baj

Workflow Workflow for Selenzyme v 1.0 (2)

Thumb
No description

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

Credits: User Pablo Carbonell

Results per page:
Sort by: