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

Created: 2017-05-24 12:50:16      Last updated: 2022-02-24 15:12:01

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 link a source to a subset of sink compounds. This sub-network is considered as a scope and is output in dedicated files (see below).

The workflow handles both monomolecular (1 substrate) and bimolecular (2 substrates) reactions.

Getting started
See instructions in RetroPath2.0_tutorial file.

Usage specifications
RetroPath2.0 workflow is compatible up to version 3.6.2 of the KNIME Analytics Platform.

Limitations as of 2019/10/07
Scope is only relevant for retrosynthetic usage (target/source to chassis/sink).

Release: r20191007

How to cite
Delépine B, Duigou T, Carbonell P, Faulon JL. RetroPath2.0: A retrosynthesis workflow for metabolic engineers. Metabolic Engineering (2018). DOI: https://doi.org/10.1016/j.ymben.2017.12.002

Please report bugs to thomas.duigou@inra.fr

Worfklow Licence: GNU General Public License v3.0
T Duigou, B Delépine, JL Faulon, 2017-2019. This work is licensed under the GNU General Public License v3.0. To view a copy of the license please visit https://www.gnu.org/licenses/gpl-3.0.html.
 

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GNU General Public License (GPL) 3.0

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Version History

In chronological order:

  1. RetroPath2.0 - a retrosynthesis workflow with tutorial and example data

    Created by Baudoin Delépine on Wednesday 24 May 2017 12:50:15 (UTC)

  2. RetroPath2.0 - a retrosynthesis workflow with tutorial and example data

    Created by Baudoin Delépine on Thursday 28 September 2017 09:23:13 (UTC)

    Last edited by Thomas Duigou on Thursday 28 September 2017 09:27:13 (UTC)

    Revision comment:

    Bug fix: Open Babel nodes lead to errors (only on Mac OS) since the last KNIME update (v3.4.1). Replacing the Open Babel nodes by RDKit nodes.

  3. RetroPath2.0 - a retrosynthesis workflow with tutorial and example data

    Created by Baudoin Delépine on Thursday 26 October 2017 17:18:29 (UTC)

    Last edited by Thomas Duigou on Thursday 26 October 2017 17:19:14 (UTC)

    Revision comment:

    Bug fix: Cannot generate InChIKey in some case. Now using SMILES as starting point for generating the InChIKey.

  4. RetroPath2.0 - a retrosynthesis workflow with tutorial and example data

    Created by Baudoin Delépine on Monday 18 December 2017 13:47:34 (UTC)

    Last edited by Thomas Duigou on Monday 18 December 2017 13:48:03 (UTC)

    Revision comment:

    Citation update: "How to cite" section that now points out to the Metabolic Engineering paper.

  5. RetroPath2.0 - a retrosynthesis workflow with tutorial and example data

    Created by Baudoin Delépine on Friday 16 February 2018 10:35:04 (UTC)

    Last edited by Thomas Duigou on Friday 16 February 2018 10:37:51 (UTC)

    Revision comment:

    Feature update: Scope Viewer generate crosslinks to Selenzyme

  6. RetroPath2.0 - a retrosynthesis workflow with tutorial and example data

    Created by Baudoin Delépine on Monday 30 July 2018 09:52:22 (UTC)

    Last edited by Thomas Duigou on Monday 30 July 2018 09:52:49 (UTC)

    Revision comment:

    Bug fix: SVG generation is now based of Marvin node, due to bug in RDKit node in KNIME v3.6.0

  7. RetroPath2.0 - a retrosynthesis workflow with tutorial and example data

    Created by Baudoin Delépine on Wednesday 19 September 2018 16:33:46 (UTC)

    Last edited by Thomas Duigou on Wednesday 19 September 2018 16:34:05 (UTC)

    Revision comment:

    Bug fix: reset input/output settings not reseted by default

  8. RetroPath2.0 - a retrosynthesis workflow with tutorial and example data

    Created by Thomas Duigou on Thursday 11 October 2018 15:25:59 (UTC)

    Last edited by Thomas Duigou on Wednesday 02 October 2019 11:57:54 (UTC)

    Revision comment:

    - Bug fix: multiple EC number annotation correctly displayed in Scope Viewer
    - Updated installation procedure

  9. RetroPath2.0 - a retrosynthesis workflow with tutorial and example data

    Created by Thomas Duigou on Tuesday 08 October 2019 15:57:59 (UTC)

    Last edited by Thomas Duigou on Friday 03 January 2020 10:33:20 (UTC)

    Revision comment:

    - Scope viewer update. For details see https://github.com/brsynth/scope-viewer
    - License update, we're now under GPL v3
     

  10. RetroPath2.0 - a retrosynthesis workflow with tutorial and example data

    Created by Thomas Duigou on Thursday 28 January 2021 15:33:38 (UTC)

    Last edited by Thomas Duigou on Thursday 28 January 2021 15:34:04 (UTC)

    Revision comment:

    - Update scope-viewer to release 20190926 (compatible with RetroPath RL)
    - Feat: SVG generation is now based of RDKit renderer, Marvin extension is now longer needed
    - Feat: add FAQ about RetroPath2.0 and rp2paths

  11. RetroPath2.0 - a retrosynthesis workflow with tutorial and example data

    Created by Thomas Duigou on Tuesday 21 December 2021 16:56:04 (UTC)

    Last edited by Thomas Duigou on Thursday 23 December 2021 10:45:56 (UTC)

    Revision comment:

    - Bug fix: output the right number of compounds in reaction SMILES according stoichiometric coefficients
    - Replace some deprecated Joiner nodes
     

  12. RetroPath2.0 - a retrosynthesis workflow with tutorial and example data

    Created by Thomas Duigou on Thursday 23 December 2021 11:07:57 (UTC)

    Last edited by Thomas Duigou on Thursday 23 December 2021 11:08:18 (UTC)

    Revision comment:

    - New uploaded zip file for release r20211221

  13. RetroPath2.0 - a retrosynthesis workflow with tutorial and example data

    Created by Thomas Duigou on Thursday 30 December 2021 14:59:42 (UTC)

    Last edited by Thomas Duigou on Thursday 30 December 2021 15:00:50 (UTC)

    Revision comment:

    - New uploaded zip file for release r20211221 (again)

  14. RetroPath2.0 - a retrosynthesis workflow with tutorial and example data

    Created by Thomas Duigou on Tuesday 04 January 2022 13:30:52 (UTC)

    Last edited by Thomas Duigou on Tuesday 04 January 2022 13:31:11 (UTC)

    Revision comment:

    - Compatibility improvment: worklow exported using KNIME 4.3.0

  15. RetroPath2.0 - a retrosynthesis workflow with tutorial and example data

    Created by Thomas Duigou on Thursday 24 February 2022 15:11:46 (UTC)

    Last edited by Thomas Duigou on Thursday 24 February 2022 15:12:01 (UTC)

    Revision comment:

    - fix: solve issue due to coeff column missing when no results are found



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