Pathway Ranker
Version 1

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.

Inputs

ID Name Description Type
GEM SBML GEM SBML n/a
  • File
Maximal Pathway Length Maximal Pathway Length n/a
  • int
Target InChI Target InChI n/a
  • string
Top Ranking Pathways Top Ranking Pathways n/a
  • int

Steps

ID Name Description
1 RetroRules retrorules
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
_anonymous_output_2 _anonymous_output_2 n/a
  • File
_anonymous_output_6 _anonymous_output_6 n/a
  • File
_anonymous_output_7 _anonymous_output_7 n/a
  • File
_anonymous_output_8 _anonymous_output_8 n/a
  • File
_anonymous_output_9 _anonymous_output_9 n/a
  • File
_anonymous_output_10 _anonymous_output_10 n/a
  • File
_anonymous_output_11 _anonymous_output_11 n/a
  • File
_anonymous_output_12 _anonymous_output_12 n/a
  • File
_anonymous_output_13 _anonymous_output_13 n/a
  • File
_anonymous_output_14 _anonymous_output_14 n/a
  • File
_anonymous_output_15 _anonymous_output_15 n/a
  • File
_anonymous_output_16 _anonymous_output_16 n/a
  • File
_anonymous_output_17 _anonymous_output_17 n/a
  • File

Version History

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

Added/updated 1 files


Open master 44ecc1c
help Creators and Submitter
Creator
Submitter
License
Activity

Views: 3363   Downloads: 189

Created: 29th May 2020 at 12:19

help Attributions

None

Total size: 14.3 KB
Powered by
(v.1.15.0)
Copyright © 2008 - 2024 The University of Manchester and HITS gGmbH