Projects: CoolWine
Institutions: Norwegian University of Science and Technology
Expertise: Systems Biology
Tools: network theory, FBA, R, Python, Statistics
PhD candidate working on the CoolWine project
Biochemist currently keeping busy as: Research Data Manager (Vrije Universiteit Amsterdam), Software Engineer (Heidelberg University) and member of the SBML Development Team (Caltech).
Construction and manual curated Genome Scale Metabolitic model of M. hyopneumoniae. Dynamic flux balance analysis was performed for glucose uptake
Submitter: Niels Zondervan
Biological problem addressed: Model Analysis Type
Snapshots: No snapshots
Investigation: Modelling of M. pneumoniae metabolism
Study: Genome-scale, constraint-based metabolic modeli...
Organisms: No organisms
Models: Genome Scale Metabolic model of M. hyopneumoniae
SOPs: SOP for generating a Genome Scale Metabolic mod...
Data files: No Data files
The multi-compartmental metabolic network of Arabidopsis thaliana was reconstructed and optimized in order to explain growth stoichiometry of the plant both in light and in dark conditions. Balances and turnover of energy (ATP/ADP) and redox (NAD(P)H/NAD(P)) metabolites as well as proton in different compartments were estimated. The model showed that in light conditions, the plastid ATP balance depended on the relationship between fluxes through photorespiration and photosynthesis including both
...
Submitter: Maksim Zakhartsev
Biological problem addressed: Metabolic Network
Snapshots: No snapshots
Investigation: Metabolic analysis of effects of sucrose transl...
Study: Analysis of central carbon and energy metabolis...
Organisms: Arabidopsis thaliana
Models: ZucAt: multi-compartment metabolic model of gro...
SOPs: No SOPs
Data files: ZucAt: FBA constraints for dark conditions, ZucAt: FBA constraints for light conditions, ZucAt: FBA solution of the model under dark gro..., ZucAt: FBA solution of the model under light gr..., ZucAt: FBA solution of the model under light gr..., ZucAt: FBA solution of the model under light gr..., ZucAt: FBA solution of the model under light gr..., ZucAt: FBA solution of the model under light gr..., ZucAt: The compound database, ZucAt: The gene database, ZucAt: The stoichiometric matrix of the model, ZucAt: The transformers database, ZucAt: the model documentation
Genome scale metabolic model of Sulfolobus solfataricus
specific scenario: modelling of L-fucose degradation pathways
Investigation: L-fucose degradation in Sulfolobus solfataricus P2
Study: Comparison of S. solfataricus grown on l-fucose...
Organisms: Sulfolobus solfataricus
Models: Metabolic model of Sulfolobus solfataricus
SOPs: No SOPs
Data files: No Data files
FBA result of flux distribution in butanol producing e.coli strain, which designed using RobOKoD.
Creator: Natalie Stanford
Submitter: Natalie Stanford
Creator: Niels Zondervan
Submitter: Niels Zondervan
Model type: Metabolic network
Model format: SBML
Environment: JWS Online
Organism: Not specified
Investigations: Modelling of M. pneumoniae metabolism
Studies: Genome-scale, constraint-based metabolic modeli...
Modelling analyses: Construction of a Genome Scale Metabolitic mode...
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
Organism: Sulfolobus solfataricus
Investigations: L-fucose degradation in Sulfolobus solfataricus P2
Studies: Comparison of S. solfataricus grown on l-fucose...
Modelling analyses: Metabolic model of Sulfolobus solfataricus