Pathway Ranker
Version 1

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Run on usegalaxy.eu

Workflow Type: Galaxy

Stable

The workflow runs the RetroSynthesis algorithm to generate a collection of heterologous pathways in a host organism of choice, converts them to SBML files, performs analysis on the pathways to then rank the theoretical best performing ones.

SEEK ID: https://workflowhub.eu/workflows/25?version=1

Steps

ID	Name	Description
0	Target InChI
1	RetroRules	retrorules
2	GEM SBML
3	Maximal Pathway Length
4	Top Ranking Pathways
5	Make Source	makeSource
6	Sink from SBML	rpExtractSink
7	RetroPath2.0	retropath2
8	RP2paths	rp2paths
9	Pathways to SBML	rpReader
10	Complete Reactions	rpCofactors
11	Thermodynamics	rpThermo
12	FBA	rpFBA
13	Rank Pathways	rpGlobalScore
14	Pathway Visualiser	rpVisualiser
15	Report	rpReport

Outputs

ID	Name	Description	Type
output	output	n/a	tar
sourceFile	sourceFile	n/a	csv
output	output	n/a	csv
scope_csv	scope_csv	n/a	csv
rp2paths_pathways	rp2paths_pathways	n/a	csv
rp2paths_compounds	rp2paths_compounds	n/a	tsv
output	output	n/a	tar
output	output	n/a	tar
output	output	n/a	tar
output	output	n/a	tar
output	output	n/a	tar
output	output	n/a	html
output	output	n/a	csv

Creators and Submitter

Creator

Melchior du Lac

Submitter

Melchior du Lac

License

MIT License

Activity

Views: 682 Downloads: 41

Created: 29th May 2020 at 12:19

Last used: 17th Sep 2021 at 05:08

Version History

Version 1 Created 29th May 2020 at 12:19 by Melchior du Lac

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Pathway Ranker Version 1