Dataset Open Access
Galaxy Training Data for "Evaluating and ranking a set of pathways based on multiple metrics"
BAZI KABBAJ Kenza;
DUIGOU Thomas;
HERISSON Joan;
GRICOURT Guillaume
This dataset provides the inputs needed for the Galaxy Pathway Analysis workflow training tutorial (https://galaxy-synbiocad.org). This workflow asseses the performance of predicted pathways by computing 4 criteria (target product flux, thermodynamic feasibility, pathway length, and enzyme availability). A score inform the user about the best candidate pathways to produce a compound of interest. The generated output is a collection of scored and ranked heterologous pathways. The content of the dataset is as follows: - A set of pathways provided in the SBML format (Systems Biology Markup Language) to be ranked, modeling heterologous pathways such as those outputted by the RetroSynthesis workflow (https://galaxy-synbiocad.org). - The GEM (Genome-scale metabolic models) which is a formalized representation of the metabolism of the host organism (the model is E. coli iML1515), provided in the SBML format.
Files
(11.6 MB)
| Name | Size | |
|---|---|---|
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rp_001_0001.xml
md5:acbda45f651314c27ff0d0b5a270bf2d |
24.7 kB | Download |
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rp_001_0006.xml
md5:4bfa0bdff297d42b275395ef0cd0f379 |
24.7 kB | Download |
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rp_001_0011.xml
md5:430e824fcb0084362bd77bf020f86ab5 |
24.7 kB | Download |
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rp_002_0001.xml
md5:2ed23edf2e0f2eb02e5a3ccb82ac16b5 |
24.7 kB | Download |
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rp_002_0006.xml
md5:7c6f2b06fd07ee9764cefdeb73ea852f |
24.7 kB | Download |
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rp_002_0011.xml
md5:1ae3aa93853897ad39fa2499452dbcf2 |
24.7 kB | Download |
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rp_003_0001.xml
md5:013f510e5dc13f79b85c51fcad1a7293 |
26.6 kB | Download |
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rp_003_0116.xml
md5:23cfe40681c6394a45a51eb0a62bcff6 |
26.6 kB | Download |
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rp_003_0231.xml
md5:80069c18719585ddf346ed93e83f596a |
26.6 kB | Download |
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SBML_Model_iML1515.xml
md5:9bf81d20cab5476700697ded95b716d1 |
11.4 MB | Download |
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views
downloads
| All versions | This version | |
|---|---|---|
| Views | 66 | 66 |
| Downloads | 350 | 350 |
| Data volume | 441.6 MB | 441.6 MB |
| Unique views | 39 | 39 |
| Unique downloads | 24 | 24 |
Indexed in
- Publication date:
- June 9, 2022
- DOI:
-
- Keyword(s):
- pathway analysis
- Communities:
- License (for files):
- Creative Commons Attribution 4.0 International