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Group: BioRetroSynth

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Created at: Wednesday 24 May 2017 12:13:13 (UTC)

Unique name: BioRetroSynth

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  1. 4465?size=48x48
    Pablo Carbonell shared KNIME Workflow for RetroRules and Selenzyme
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    KNIME Workflow for RetroRules and Selenzyme This worflow provides an examples of retrieving the RetroRules reaction rules for some given reaction and selecting enzyme sequences using the Selenzyme tool. 1. Input to the workflow: Chemical reactions expressed using public database identifiers. 2. Each …
    Thursday 26 July 2018 13:02:53 (UTC)
  2. 4465?size=48x48
    Pablo Carbonell shared KNIME Workflow for RetroRules and Retropath2.0
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    KNIME Workflow for RetroRules and RetroPath2.0 This worflow provides an examples of retrieving the RetroRules reaction rules for some given reaction identifiers. 1. Input to the workflow: Chemical reactions expressed using public database identifiers. 2. Each reaction queries RetroRules and outputs t …
    Thursday 26 July 2018 13:02:03 (UTC)
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    Thomas Duigou shared RetroPath2.0-Mods-isomer-transformation-queue
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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 s …
    Thursday 12 October 2017 13:23:02 (UTC)
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    Baudoin Delépine joined the BioRetroSynth group
    Friday 29 September 2017 12:44:10 (UTC)
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    Thomas Duigou shared RetroPath2.0-Mods-metabolomics
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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 finall …
    Friday 30 June 2017 17:15:13 (UTC)
  6. Avatar
    Thomas Duigou shared Aminoglycosides-Data
    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.
    Friday 30 June 2017 17:09:48 (UTC)
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    Thomas Duigou shared QSAR-model-aminoglycosides
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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 use See instructions embedded in the …
    Friday 30 June 2017 17:05:59 (UTC)
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    Thomas Duigou shared RetroPath2.0-Mods-iQSAR
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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 use See instructions embedded in the workflow. Usage specifications The workflow is compatible starting from version 3.3.2 of Knime Analytics Platform. Licen …
    Friday 30 June 2017 17:03:35 (UTC)
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    Thomas Duigou shared Monomers-Data
    Data to be used with the RetroPath2.0-Mods-isomer-augmentation and QSAR-model-Tg-prediction workflows for the monomer enumeration use case: - Source and Rules input. - Pre-generated Results. - Training set for building the QSAR of the glass transition temperature.
    Friday 30 June 2017 17:01:25 (UTC)
  10. Avatar
    Thomas Duigou shared Alkane-Enumeration-Data
    Data to be used with the RetroPath2.0-Mods-isomer-transformation workflow for the alkane enumeration use case: - Source and Rules input. - Pre-generated Results.
    Friday 30 June 2017 16:57:42 (UTC)
  11. Avatar
    Thomas Duigou shared QSAR-model-Tg-prediction
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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 use See instructions embedded in the workflow. Usage specifications The workflow is …
    Friday 30 June 2017 16:55:10 (UTC)
  12. Avatar
    Thomas Duigou shared RetroPath2.0-Mods-isomer-transformation
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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 use See instructions embedded in the workflow. Usage specifications The workflow is compatible starting from version 3.3.2 of Knime Analytics Platform. L …
    Friday 30 June 2017 16:52:39 (UTC)

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Avatar Fr Thomas Duigou

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This group has been credited 17 times

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Blob Monomers-Data

Created: 2017-06-30 17:01:24 | Last updated: 2017-10-12 13:47:22

Credits: User Thomas Duigou Network-member BioRetroSynth

Attributions: Workflow RetroPath2.0-Mods-isomer-transformation

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

Data to be used with the RetroPath2.0-Mods-isomer-augmentation and QSAR-model-Tg-prediction workflows for the monomer enumeration use case:- Source and Rules input.- Pre-generated Results.- Training set for building the QSAR of the glass transition temperature.

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Blob Alkane-Enumeration-Data

Created: 2017-06-30 16:57:41 | Last updated: 2017-10-12 13:45:28

Credits: User Thomas Duigou Network-member BioRetroSynth

Attributions: Workflow RetroPath2.0-Mods-isomer-transformation

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

Data to be used with the RetroPath2.0-Mods-isomer-transformation workflow for the alkane enumeration use case:- Source and Rules input.- Pre-generated Results.

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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.

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Blob Isomer-augmentation-Data

Created: 2017-06-30 16:49:46 | Last updated: 2017-06-30 17:12:54

Credits: User Thomas Duigou Network-member BioRetroSynth

Attributions: Workflow RetroPath2.0-Mods-isomer-augmentation

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

Data to be used with the RetroPath2.0-Mods-isomer-augmentation workflow:- Source and Rules input.- Pre-generated Results.

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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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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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Workflow

KNIME
Uploader
Avatar Fr Thomas Duigou

Workflow RetroPath2.0 - a retrosynthesis workflow w... (15)

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The RetroPath2.0 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 effectively l...

Created: 2017-05-24 | Last updated: 2022-02-24

Credits: User Thomas Duigou User Baudoin Delépine Network-member BioRetroSynth

Workflow

KNIME
Uploader
Avatar Fr Thomas Duigou

Workflow RetroPath2.0-Mods-metabolomics (2)

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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: 2018-11-14

Credits: User Thomas Duigou Network-member BioRetroSynth

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

Workflow

KNIME
Uploader
Avatar Fr Thomas Duigou

Workflow RetroPath2.0-Mods-isomer-transformation-queue (2)

Thumb
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

Workflow

KNIME
Uploader
Avatar Fr Thomas Duigou

Workflow RetroPath2.0-Mods-iQSAR (2)

Thumb
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.Licence: CC BY-NC-SAThis 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/...

Created: 2017-06-30 | 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

KNIME
Uploader
Avatar Fr Thomas Duigou

Workflow QSAR-model-aminoglycosides (2)

Thumb
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

Workflow

KNIME
Uploader
Avatar Fr Thomas Duigou

Workflow RetroPath2.0-Mods-isomer-transformation (2)

Thumb
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.Licence: CC BY-NC-SAThis 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/licen...

Created: 2017-06-30 | 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

KNIME
Uploader
Avatar Fr Thomas Duigou

Workflow QSAR-model-Tg-prediction (2)

Thumb
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.Licence: CC BY-NC-SAThis work is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. T...

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

Credits: User Thomas Duigou Network-member BioRetroSynth

Workflow

KNIME
Uploader
Avatar Fr Thomas Duigou

Workflow RetroPath2.0-Mods-isomer-augmentation (2)

Thumb
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.Licence: CC BY-NC-SAThis 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/.Koch M, D...

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

Credits: User Thomas Duigou Network-member BioRetroSynth

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


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