Pathway Ranker
Version 1

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.

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
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Views: 196   Downloads: 6

Created: 29th May 2020 at 12:19

Last used: 14th Aug 2020 at 01:55

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