The RAVEN Toolbox and Its Use for Generating a Genome-scale Metabolic Model for Penicillium chrysogenum
Figure 1
The software allows for reconstruction of GEMs based on template models or on the KEGG database. The resulting models can be exported to a number of formats, or they can be used for various types of simulations. The RAVEN Toolbox has a strong focus on quality control. Visualization of simulation result and/or integration of other types of data can be performed by overlaying information on pre-drawn metabolic maps. The software also implements the INIT algorithm, which is a powerful approach for reconstruction of tissue-specific models [59]. HMM: Hidden Markov model, LP: Linear programming, QP: Quadratic programming, MILP: Mixed-integer linear programming.