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GTN: Molecular networking with matchms & cytoscape #3

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hechth opened this issue Jul 2, 2022 · 2 comments
Open
6 tasks

GTN: Molecular networking with matchms & cytoscape #3

hechth opened this issue Jul 2, 2022 · 2 comments
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documentation Improvements or additions to documentation

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@hechth
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hechth commented Jul 2, 2022 •
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This galaxy training should describe how - after obtaining (annotated) spectra in msp format - we can use matchms for molecular networking and similarity computation as well as filtering of our msp libraries.

  • Get started with GitPod and GTN training
  • Assemble preliminary workflow
  • Section on molecular networking
  • Section on spectral matching & MSP data
  • Section on networking tool -> future
  • Section on cytoscape in Galaxy
hechth pushed a commit that referenced this issue Jul 20, 2022
@fpsom
Merge pull request #3 from galaxyproject/git-tutorial
fbfed21 
Tutorial updates for 3507
@hechth hechth changed the title Molecular networking with matchms & cytoscape GTN: Molecular networking with matchms & cytoscape Jul 26, 2022
@maximskorik maximskorik moved this from Todo to In Progress in Molecular Networking in Galaxy Oct 31, 2022
hechth pushed a commit that referenced this issue Nov 1, 2022
@nomadscientist
Monocle3edits (#3)
cf6122f 
* edits to intro text

* editing get data section

* edits up to line 192

* changing column name

* up to monocle3 workflow
@maximskorik
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maximskorik commented Nov 7, 2022 •
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@hechth, any suggestions on the toy dataset to use in the training? Some public datasets from GNPS could be a good fit.

@hechth
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hechth commented Nov 7, 2022

@maximskorik Some clustered spectra from GNPS which are used for networking? Yes, sure.

Maybe even one used in some of the publications for FMN or IIMN?

hechth pushed a commit that referenced this issue Nov 18, 2023
@hexhowells
Merge pull request #3 from nomadscientist/editing_morgan_tutorial
6be757a 
Editing Morgan tutorial - in progress
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documentation Improvements or additions to documentation
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Molecular Networking in Galaxy
Status: In Progress
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@hechth @maximskorik