Modeling BASICS

[NatalieDreux]

Notes that will come in handy when trying to use MATLAB, Colab, etc. when pertaining to FBAs and GEMs

[NatalieDreux]

If you're working with the COBRA (Constraint-Based Reconstruction and Analysis) Toolbox in MATLAB, you can use the following steps to load a BiGG model:

Install the COBRA Toolbox:

Download and install the COBRA Toolbox, which is designed for constraint-based modeling and analysis in systems biology.

• You can find the COBRA Toolbox on the GitHub repository: https://github.com/opencobra/cobratoolbox Download BiGG Model:
• Visit the BiGG Models website (http://bigg.ucsd.edu/) and download the model you are interested in. BiGG Models are often available in SBML format.

  Load BiGG Model with COBRA Toolbox:

Use the 'importModel' function from the COBRA Toolbox to load the BiGG model. matlab

% Load the BiGG model in SBML format using the importModel function

model = importModel('path/to/your/BiGG_model.xml');

Explore and Analyze the Model:

Once the model is loaded, you can use various functions from the COBRA Toolbox to analyze and manipulate the model. For example: matlab

% Display basic information about the model

printModel(model);

% Perform flux balance analysis (FBA)

solution = optimizeCbModel(model);

 #These are just basic examples, and you can explore more advanced analyses provided by the COBRA Toolbox based on your specific needs.

Ensure that your BiGG model is compatible with the version of the COBRA Toolbox you are using. If there are any issues, you may need to check the documentation of both the COBRA Toolbox and the BiGG model to ensure proper compatibility and usage.

[NatalieDreux]

The FBA notebook is becoming too difficult to fully grasp without a better background in the nomenclature of modeling, the understanding of the outputs (how to move forward with solution of the FBA).

Therefore I am taking the time to read the following papers in order to try and get my brain back on track and less paralyzed with the daunting task of making myself understand:

chrome-extension://bomfdkbfpdhijjbeoicnfhjbdhncfhig/view.html?mp=0IXND1Cr "What is a flux balance analysis" chrome-extension://bomfdkbfpdhijjbeoicnfhjbdhncfhig/view.html?mp=8QIrUJMn "Flux analysis ... missing constraints" chrome-extension://bomfdkbfpdhijjbeoicnfhjbdhncfhig/view.html?mp=fRmgFlQD "Reconstruction of biochemical networks in microorganisms" chrome-extension://bomfdkbfpdhijjbeoicnfhjbdhncfhig/view.html?mp=3XwqeaMK "The gorwing .. E. coli"