The Cobra Toolbox utilizes the MATLAB platform so that people can perform "Constraint-based Reconstruction and Analysis." Our team took advantage of this toolbox to perform flux balance analysis on our organism Methanococcus maripaludis.
Besides the use of MatLab for our metabolic modeling, another software was particularly helpful for this project. The RNA Fold webserver of the University of Vienna was utilized to visualize mRNA secondary structures. This consideration of intramolecular hydrogen bonding was incorporated into the project so that the effect of secondary structure on translational efficiency could also be examined as a factor.