genome-scale-metabolic-model-isochrysis

This repository contains data about the Genome-scale metabolic model of the Isochysis specie. The following repository will help the user to generate the complete genome-scale metabolic model from scratch guiding the user through all the steps starting from the data retrieval, data curation, and importing to the analysis of the model in the COBRA Toolbox. using the following protocol and code users will be able to create their genome-scale metabolic model of Isochrysis sp. The code works in the MATLAB environment using the Constraint-based reconstruction and analysis (COBRA) Toolbox for generating the entire genome-scale metabolic model using the pre-organized reaction files in the COBRA format. The repository will help the user to understand the protocol for reaction curation and reconstruction of the entire model. The model can later be used for the analysis using the optFlux software to perform Flux Balance Analysis (FBA) by the constraint based approach. After data preparation of data file, the MATLAB software was downloaded from the official website https://in.mathworks.com/matlab/download, register and create an account. After creating an account, open Matlab and log in with your account. After starting MATLAB, select applications and search for the COnstraint Based Reconstruction and Analysis (COBRA) Toolbox, install and add to the path. Now the software is ready to be used. The Constraint-based Reconstruction and Analysis (COBRA) Toolbox is a software package in MATLAB for analyzing metabolic models. The COBRA Toolbox may be downloaded in the MATLAB environment and added to the current path in MATLAB to start working upon. COBRA Toolbox is highly used in metabolic engineering for modeling, designing, analyzing, and visualizing the metabolic model in the MATLAB environment. Initialization of the toolbox is necessary to access its various functions, including the loading of a metabolic network reconstruction which represents the biological system's metabolism. After loading the COBRA Toolbox and adding it to the current path we initialize the COBRA Toolbox using the command ‘initCobraToolbox(false)’, this command is set the true or false depending upon whether the COBRA Toolbox needs to be updated or not, by default it is false. We can now model and manipulate the network and perform optimization analysis by defining the objective function, which is a mathematical representation of the optimization goal. To simulate the metabolic network's behavior under different conditions and predict the effects of perturbations, simulation constraints are varied to represent the biological or experimental constraints that affect the overall network's behavior. After initializing and setting up the COBRA Toolbox in the MATLAB environment, the prepared model reconstruction including unique reaction identifiers, and reaction equations along with mentioned compartments of each metabolite, reaction-associated gene(s), and compartment of the complete reaction are imported in the MATLAB. The reactions are imported as their unique reaction identifiers and genes are imported as grule numbers along with the list of compartments. The reactions and genes are then combined in cell arrays named ReactionIdentifiers and gRuleList respectively. Cell arrays naming ReactionFormulas and ReactionNames are also added to add the formulas and names of the reactions respectively. After adding all the data in the cell arrays, we now apply the createModel command to combine all the reactions and genes in the metabolic reconstruction. Then model is refined and evaluated by first adding the exchange reactions in the model,then evaluated for the presence of duplicates and blocked reactions and bounds of the ATPM reaction were varied and objective reaction determined and set as objective. mostly this reaction is the biomass reaction. After the model is designed and evaluated, now the model needs to be optimized in the COBRA Toolbox to yield the flux value associated with the model and objective reaction generation. After designing, optimizing, and finalizing the genome-scale metabolic model of the Isochrysis specie, the model which was then in COBRA format is converted to Systems Biology markup language (SBML) format. After converting the file to SBML format, the model can be exported and used for visualization and downstream analysis purposes in the optflux software.