Pathway Analysis
Version 1

Workflow Type: Galaxy

Annotation: Evaluating and ranking a set of pathways based on multiple metrics. Given a set of pathways generated by RetroPath2.0, this workflow informs the user as to the theoretically best performing ones based on the four criteria (target product flux, thermodynamic feasibility, pathway length, and enzyme availability).

SEEK ID: https://workflowhub.eu/workflows/2005?version=1

Inputs

ID	Name	Description	Type
Biomass reaction ID	#main/Biomass reaction ID	n/a	string
Cell compartment ID	#main/Cell compartment ID	n/a	string
Chassis where to produce target from	#main/Chassis where to produce target from	n/a	File
Heterologous pathways	#main/Heterologous pathways	n/a	array containing File

Steps

ID	Name	Description
4	Flux Balance Analysis	toolshed.g2.bx.psu.edu/repos/tduigou/rptools_rpfba/rptools_rpfba/6.5.0+galaxy0
5	Thermo	toolshed.g2.bx.psu.edu/repos/tduigou/rptools_rpthermo/rptools_rpthermo/6.5.0
6	Score Pathway	toolshed.g2.bx.psu.edu/repos/tduigou/rptools_rpscore/rptools_rpscore/6.5.0+galaxy0
7	Rank Pathways	toolshed.g2.bx.psu.edu/repos/tduigou/rptools_rpranker/rptools_rpranker/6.5.0+galaxy0

Outputs

ID	Name	Description	Type
Fully Scored Pathways	#main/Fully Scored Pathways	n/a	File
Pathways with FBA + thermo scores	#main/Pathways with FBA + thermo scores	n/a	File
Pathways with FBA score	#main/Pathways with FBA score	n/a	File
Ranked Pathways IDs	#main/Ranked Pathways IDs	n/a	File

Version History

Version 1 (earliest) Created 24th Oct 2025 at 13:31 by ramiz khaled

Initial commit

Frozen Version-1 67d9557

Creators and Submitter

Creators

Not specified

Additional credit

BioRetroSynth

Submitter

ramiz khaled

License

MIT License (MIT)

Activity

Views: 67 Downloads: 13 Runs: 0

Created: 24th Oct 2025 at 13:31

Pathway Analysis Version 1