Authors
Daniel Hyduke, Jan Schellenberger, Richard Que, Ronan Fleming, Ines Thiele, Jeffery Orth, Adam Feist, Daniel Zielinski, Aarash Bordbar, Nathan Lewis, Sorena Rahmanian, Joseph Kang, and Bernhard Palsson
Summary
Over the past decade, a growing community of researchers has emerged around the use of COnstraint-Based Reconstruction and Analysis (COBRA) methods to simulate, analyze and predict a variety of metabolic phenotypes using genome-scale models. The COBRA Toolbox, a MATLAB package for implementing COBRA methods, was presented earlier. Here we present a significant update of this in silico ToolBox. Version 2.0 of the COBRA Toolbox expands the scope of computations by including in silico analysis methods developed since its original release. New functions include: (1) network gap filling, (2) 13C analysis, (3) metabolic engineering, (4) omics-guided analysis, and (5) visualization. As with the first version, the COBRA Toolbox reads and writes Systems Biology Markup Language formatted models. In version 2.0, we improved performance, usability, and the level of documentation. A suite of test scripts can now be used to learn the core functionality of the Toolbox and validate results. This Toolbox lowers the barrier of entry to use powerful COBRA methods.Further details
The protocol was published on Protocol Exchange on 11 May 2011. To see the entire protocol, click on the source link.Advertisement
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