This repository contains the genome-scale metabolic model (GEM) of Microchloropsis gaditana, named iMgadit23.
Clémence Dupont-Thibert1,2, Sónia Carneiro3, Bruno Pereira3, Rafael Carreira3, Paulo Vilaça3, Giovanni Finazzi1, Séverine Collin2, Eric Maréchal1, Elodie Billey2, Gilles Curien1, Maxime Durot2, Juliette Jouhet1
1 - Université Grenoble Alpes, CNRS, CEA, INRAE, Interdisciplinary Research Institute of Grenoble, IRIG-Laboratoire de Physiologie Cellulaire et Végétale, 17 Avenue des Martyrs, 38000 Grenoble, France
2 - TotalEnergies, OneTech, Centre de Recherche de Solaize CRES, Chemin du Canal, 69360 Solaize, France
3 - SilicoLife Lda. Rua do Canastreiro, 15 4715-387 Braga, Portugal
Utilisation: experimental data reconstruction; multi-omics integrative analysis; in silico strain design; model template
Field: metabolic-network reconstruction
Type of model: reconstruction; curated
Model publication: https://doi.org/10.1101/2023.12.06.570374
Omic source: genomics; lipidomics
Taxonomic name: Microchloropsis gaditana (formerly Nannochloropsis gaditana)
Taxonomy ID: taxonomy:72520
Genome ID: insdc.gca:GCA_000569095.1
Metabolic system: general metabolism
Strain: B-31
Biomass Objective Functions: iMgadit23 contains two independent BOFs, representing respectively biomass composition of WT526 and MgACSBG#31 strains
Condition: photo-autotrophy, photon uptake upper bound constrained to -23 mmol.gDW-1.h-1
| Taxonomy | Version | Reactions | Metabolites | Genes |
|---|---|---|---|---|
| Microchloropsis gaditana | 1.0.0 | 2330 | 1977 | 889 |
If you want to use the model, any software that accepts SBML Level 3 Version 1 formatted model files will work. We recommend the following as they are well-maintained and used by most researchers in the constraint-based metabolic modeling community:
- MATLAB
- Python
The model and its 2D-Pathway Map are also provided in JSON format compatible with Escher and Escher-FBA.