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Licence: by-nc-sa

Workflow RetroPath2.0 - a retrosynthesis workflow w... (3)

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The RetroPath2.0 KNIME 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 effecti...

Created: 2017-05-24 | Last updated: 2017-10-26

Credits: User Baudoin Delépine Network-member BioRetroSynth

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Workflow Detrprok (4)

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In the case study of stranded and prokaryotic RNAseq data, the Det'Rprok workflow detects candidates of 3 kinds of non coding RNA: 5'UTRs, antisense RNAs, and small RNAs.Inputs: i) an mapping file (bam format) containing one valid alignment by read, ii) a feature file (gff format) annotating the genomic sequences used for the mapping. Dependencies (from the Galaxy toolshed): "s_mart", "detrprok_scripts"

Created: 2013-05-20 | Last updated: 2015-11-03

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Workflow RetroPath2.0-Mods-isomer-transformation-queue (1)

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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: 2017-10-12

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 RetroPath2.0-Mods-metabolomics (1)

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Set of workflows for the "Metabolome completion and metabolomics" use case:1) Produces a list of molecules using a user defined set of rules (RetroPath2.0 workflow).2) Takes as input the products generated by RetroPath2.0 and prepare the files to be read by OpenMS nodes.3) The last workflow finally searches for each produced compound the corresponding peak in some MS spectra.See [1] for details. How to useSee instructions embedded in the workflow.Usage specificationsThe workflo...

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

Credits: User Thomas Duigou Network-member BioRetroSynth

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

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Workflow QSAR-model-aminoglycosides (1)

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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.LicenceThis work is licensed under the Creative Commons Attribution-NonCommercial-Shar...

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

Credits: User Thomas Duigou Network-member BioRetroSynth

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Workflow RetroPath2.0-Mods-iQSAR (1)

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The workflow allows one to search chemical structures in the chemical space optimizing biological activites. See [1] for details. How to useSee instructions embedded in the workflow.Usage specificationsThe workflow is compatible starting from version 3.3.2 of Knime Analytics Platform.LicenceThis work is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/4.0/...

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

Credits: User Thomas Duigou Network-member BioRetroSynth

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

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Workflow QSAR-model-Tg-prediction (1)

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The workflow (i) build a QSAR model for Tg prediction with LOO cross-validation and (ii) predict the Tg for enumerated isomers. See [1] for details. Tg values were compiled from Brown et al, JCIM, 2006. How to useSee instructions embedded in the workflow.Usage specificationsThe workflow is compatible starting from version 3.3.2 of Knime Analytics Platform.LicenceThis work is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. To view a copy...

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

Credits: User Thomas Duigou Network-member BioRetroSynth

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Workflow RetroPath2.0-Mods-isomer-transformation (1)

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The workflow allows one to enumerate isomers of chemical structure(s) using the isomer transformation algorithm. See [1] for details. How to useSee instructions embedded in the workflow.Usage specificationsThe workflow is compatible starting from version 3.3.2 of Knime Analytics Platform.LicenceThis work is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/...

Created: 2017-06-30

Credits: User Thomas Duigou Network-member BioRetroSynth

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

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Workflow RetroPath2.0-Mods-isomer-augmentation (1)

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The workflow allows one to enumerate isomers using the isomer augmentation algorithm. See [1] for details. How to useSee instructions embedded in the workflow.Usage specificationsThe workflow is compatible starting from version 3.3.2 of Knime Analytics Platform.LicenceThis work is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/4.0/. [1] M. Koch, T. ...

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

Credits: User Thomas Duigou Network-member BioRetroSynth

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

Workflow recommenderSystem (1)

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Complementary workflow for the modelBuild. It can read the trained model parameters in order to classify samples in another dataset.

Created: 2017-01-20 | Last updated: 2017-01-20

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