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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Created: 29th May 2020 at 12:19
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https://orcid.org/0000-0002-9984-4689