Models
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PGK yeast Fig1a
Creator: Jacky Snoep
Submitter: Jacky Snoep
Model type: Ordinary differential equations (ODE)
Model format: Mathematica
Environment: Mathematica
DownloadPGK yeast with/without recycling
Creator: Jacky Snoep
Submitter: Jacky Snoep
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
Metabolic model of Sulfolobus solfataricus P2 in the SBML (sbml) and metano (txt, sce, fba) format. Scenarios are specific for growth on D-glucose or caseinhydrolysate as sole carbon source.
Creator: Helge Stark
Submitter: Helge Stark
Model type: Metabolic network
Model format: SBML
Environment: Not specified
Creator: Robert Muetzelfeldt
Submitter: Robert Muetzelfeldt
Model type: Ordinary differential equations (ODE)
Model format: Not specified
Environment: Not specified
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Not specified
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Not specified
Metabolic model of Sulfolobus solfataricus P2 in the SBML (xml) and metano (txt, sce, fba) format. Scenarios are specific for growth on D-glucose or L-fucose as sole carbon source. Different theoretical routes of L-fucose degradation were modeled (E. coli-like, Xanthomonas-like and lactaldehyde-forming). Highest overall agreement between the model and experimental data was observed for the lactaldehyde-forming route.
Creators: Jacqueline Wolf, Helge Stark, Dietmar Schomburg
Submitter: Jacqueline Wolf
Model type: Metabolic network
Model format: SBML
Environment: Not specified
Creator: Matthias König
Submitter: Matthias König
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Not specified
The model presents a multi-compartmental (mesophyll, phloem and root) metabolic model of growing Arabidopsis thaliana. The flux balance analysis (FBA) of the model quantifies: sugar metabolism, central carbon and nitrogen metabolism, energy and redox metabolism, proton turnover, sucrose translocation from mesophyll to root and biomass growth under both dark- and light-growth conditions with corresponding growth either on starch (in darkness) or on CO2 (under light). The FBA predicts that ...
Creators: Maksim Zakhartsev, Olga Krebs, Irina Medvedeva, Ilya Akberdin, Yuriy Orlov
Submitter: Maksim Zakhartsev
Model type: Metabolic network
Model format: SBML
Environment: Not specified
E.coli Core model, with additional reactions added to generate the beta-oxadation cycle. This is the basic model used in RobOKoD: microbial strain design for (over)production of target compounds (http://fairdomhub.org/publications/236).
Creator: Natalie Stanford
Submitter: Natalie Stanford
Model type: Metabolic network
Model format: SBML
Environment: Matlab
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
SBML description of L. lactis glycolysis. Same as the uploaded Copasi file
Creator: Mark Musters
Submitter: Mark Musters
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Not specified
Creator: Jacky Snoep
Submitter: Jacky Snoep
Model type: Not specified
Model format: Not specified
Environment: Not specified
Creator: Jacky Snoep
Submitter: Jacky Snoep
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
Creator: Jacky Snoep
Submitter: Jacky Snoep
Model type: Not specified
Model format: SBML
Environment: JWS Online
Creator: Jacky Snoep
Submitter: Jacky Snoep
Model type: Not specified
Model format: SBML
Environment: JWS Online
Creator: Malgorzata Adamczyk
Submitter: Malgorzata Adamczyk
Model type: Not specified
Model format: SBML
Environment: Not specified
Preliminary metabolic network of S. pyogenes including primary metabolism, polysaccharide metabolism, purine and pyrimidine biosoynthesis, teichoic acid biosynthesis, fatty acid and phospholipid bioynthesis, amino acid metabolism, vitamins and cofactors. The model still needs to be validated.
Creator: Jennifer Levering
Submitter: Jennifer Levering
Model type: Metabolic network
Model format: SBML
Environment: Not specified
Creator: Nadine Veith
Submitter: Nadine Veith
Model type: Partial differential equations (PDE)
Model format: SBML
Environment: Not specified
Batch and chemostat model of L lactis. Scope of the model is to provide a mechanistic explanation of the switch between mixed acid and homolactic fermentation.
Creator: domenico bellomo
Submitter: domenico bellomo
Model type: Partial differential equations (PDE)
Model format: Matlab package
Environment: Matlab
The principles of Stealthy Engineering (Adamczyk et al.: Biotechnology Journal 2012; 7(7):877-83) are illustrated in this model by emulating a cross engineering intervention between L. lactis and S. cerevisiae.
The case study consists of replacing the native glucose uptake system of L. lactis with that native to the yeast S. cerevisiae. A modified version of Hoefnagel et al.’s model of L. lacrtis’ central metabolism was used as starting point. The total functional replacement of the PTS with the ...
Creators: Malgorzata Adamczyk, Hans V. Westerhoff, Ettore Murabito
Submitter: Ettore Murabito
Model type: Ordinary differential equations (ODE)
Model format: Copasi
Environment: Copasi
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Not specified
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Model type: Ordinary differential equations (ODE)
Model format: Mathematica
Environment: Not specified
