Reconstruction of Genome-Scale Metabolic Model for Hansenula polymorpha Using RAVEN
Book chapter, 2022
Genome-scale metabolic models (GEMs) provide a useful framework for modeling the metabolism of microorganisms. While the applications of GEMs are wide and far reaching, the reconstruction and continuous curation of such models can be perceived as a tedious and time-consuming task. Using RAVEN, a MATLAB-based toolbox designed to facilitate the reconstruction analysis of metabolic networks, this protocol practically demonstrates how researchers can create their own GEMs using a homology-based approach. To provide a complete example, a draft GEM for the industrially relevant yeast Hansenula polymorpha is reconstructed.
Constraint-based model
Metabolism
Genome-scale model
Author
Francisco Zorrilla
Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology
Eduard Kerkhoven
Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology
Methods in Molecular Biology
10643745 (ISSN) 1940-6029 (eISSN)
Vol. 2513 271-290Subject Categories
Bioinformatics (Computational Biology)
Embedded Systems
Computer Systems
DOI
10.1007/978-1-0716-2399-2_16
PubMed
35781211