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Licence: by-nc-sa
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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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Pack KNIME workflows and associated data from Koch et. al...


Created: 2017-06-29 17:26:00 | Last updated: 2017-12-19 10:19:21

The pack provides the KNIME workflows and associated data from:Koch M, Duigou T, Carbonell P, Faulon JL. Molecular structures enumeration and virtual screening in the chemical space with RetroPath2.0. Journal of Cheminformatics, 9:64, 2017. https://doi.org/10.1186/s13321-017-0252-9Please browse the linked packs below.

4 items in this pack

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Pack Pack #4 - Metabolome completion and metabolomics


Created: 2017-06-30 16:36:44 | Last updated: 2017-12-19 10:22:42

This pack provides part of the supporting material for:Koch M, Duigou T, Carbonell P, Faulon JL. Molecular structures enumeration and virtual screening in the chemical space with RetroPath2.0. Journal of Cheminformatics, 9:64, 2017. https://doi.org/10.1186/s13321-017-0252-9The pack contains (i) the RetroPath2.0-Mods-metabolomics workflow as well as (ii) all the associated data for the metabolome completion use case (see the main text for details, section 2.4 Metabolome completion and metabolo...

2 items in this pack

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Pack Pack #3 - Search for molecules maximizing biological...


Created: 2017-06-30 16:33:44 | Last updated: 2017-12-19 10:22:03

This pack provides part of the supporting material for:Koch M, Duigou T, Carbonell P, Faulon JL. Molecular structures enumeration and virtual screening in the chemical space with RetroPath2.0. Journal of Cheminformatics, 9:64, 2017. https://doi.org/10.1186/s13321-017-0252-9The pack contains (i) the RetroPath2.0-Mods-iQSAR workflow for the search of molecules of interest, (ii) the QSAR-model-aminoglycosides workflow that build a QSAR model for predicting the antibacterial activity, and (iii) t...

3 items in this pack

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Pack Pack #2 - Isomer enumeration (isomer transformation ...


Created: 2017-06-30 16:31:31 | Last updated: 2017-12-19 10:21:41

This pack provides part of the supporting material for:Koch M, Duigou T, Carbonell P, Faulon JL. Molecular structures enumeration and virtual screening in the chemical space with RetroPath2.0. Journal of Cheminformatics, 9:64, 2017. https://doi.org/10.1186/s13321-017-0252-9The pack contains (i) the RetroPath2.0-Mods-isomer-transformation worklfow, (ii) data for the enumeration of alkane isomers using the isomer transformation algorithm (see the main text for details, section 2.1 Isomer enumer...

5 items in this pack

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Pack Pack #1 - Isomer enumeration (canonical augmentation...


Created: 2017-06-30 16:29:21 | Last updated: 2017-12-19 10:20:58

This pack provides part of the supporting material for:Koch M, Duigou T, Carbonell P, Faulon JL. Molecular structures enumeration and virtual screening in the chemical space with RetroPath2.0. Journal of Cheminformatics, 9:64, 2017. https://doi.org/10.1186/s13321-017-0252-9The pack contains the (i) RetroPath2.0-Mods-isomer-augmentation worklfow as well as (ii) the associated data for the enumeration of isomers using the canonical augmentation algorithm (see the main text for details, section ...

2 items in this pack

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Blob Community model and infrastructure for service devel...

Created: 2009-08-04 08:46:13

Credits: User Kimmo Karhu

License: Creative Commons Attribution-Noncommercial-Share Alike 3.0 Unported License

Community model and infrastructure for service development

File type: PNG image

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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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Blob Aminoglycosides-Data

Created: 2017-06-30 17:09:48 | Last updated: 2017-07-03 08:19:12

Credits: User Thomas Duigou Network-member BioRetroSynth

Attributions: Workflow RetroPath2.0-Mods-iQSAR

License: Creative Commons Attribution-Noncommercial-Share Alike 3.0 Unported License

Data to be used with the RetroPath2.0-Mods-iQSAR and QSAR-model-aminoglycosides workflows for the "search for molecules maximizing biological activities" use case:- Source and Rules input.- Pre-generated Results.- Training set for building the QSAR of the antibacterial activity.

File type: application/x-zip-compressed

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Workflow QSAR-model-aminoglycosides (2)

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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.Licence: CC BY-NC-SAThis work is licensed under the Creative Commons Attribution-NonCo...

Created: 2017-06-30 | Last updated: 2017-12-19

Credits: User Thomas Duigou Network-member BioRetroSynth

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