Workflow Type: Galaxy
Open
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 |
|
Maximal Pathway Length | Maximal Pathway Length | n/a |
|
Target InChI | Target InChI | n/a |
|
Top Ranking Pathways | Top Ranking Pathways | n/a |
|
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 |
|
_anonymous_output_6 | _anonymous_output_6 | n/a |
|
_anonymous_output_7 | _anonymous_output_7 | n/a |
|
_anonymous_output_8 | _anonymous_output_8 | n/a |
|
_anonymous_output_9 | _anonymous_output_9 | n/a |
|
_anonymous_output_10 | _anonymous_output_10 | n/a |
|
_anonymous_output_11 | _anonymous_output_11 | n/a |
|
_anonymous_output_12 | _anonymous_output_12 | n/a |
|
_anonymous_output_13 | _anonymous_output_13 | n/a |
|
_anonymous_output_14 | _anonymous_output_14 | n/a |
|
_anonymous_output_15 | _anonymous_output_15 | n/a |
|
_anonymous_output_16 | _anonymous_output_16 | n/a |
|
_anonymous_output_17 | _anonymous_output_17 | n/a |
|
Version History
Version 1 (earliest) Created 29th May 2020 at 12:19 by Melchior du Lac
Added/updated 1 files
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master
44ecc1c
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Views: 4373 Downloads: 308 Runs: 0
Created: 29th May 2020 at 12:19
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