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 271-290

Subject Categories

Bioinformatics (Computational Biology)

Embedded Systems

Computer Systems

DOI

10.1007/978-1-0716-2399-2_16

PubMed

35781211

More information

Latest update

7/12/2024