Metabolic Optimization and Simulation Tool
MOST is distributed for free on the GNU General Public License.
MOST: A software environment for metabolic modeling and strain design.
MOST is a standalone software package that can be used to create constraint-based models of metabolism, load existing models, export models, and run analyses on these models to predict the production of desired compounds by microbes under genetic manipulations.
MOST implements GDBB (Genetic Design through Branch and Bound) in an intuitive user-friendly interface with Excel-like editing functionality, as well as implementing FBA (Flux Balance Analysis). GDBB is currently the fastest algorithm for finding gene knockouts predicted by FBA to increase production of desired products, but GDBB has only been available on a command line interface which is difficult to use for those without programming knowledge.
MOST requires a Mixed Integer Linear Program solver (MILP) to run FBA and GDBB. MOST offers a choice of solvers, either Gurobi solver which is free for academic use, or GLPK (GNU Linear Programming Kit), a free solver.
MOST loads SBML files and CSV files, and also saves files in these formats. MOST can correct the syntax of a model, if necessary, so that it conforms to SBML specifications, when saving a model in SBML format.
MOST includes standard spreadsheet editing functions, such as Copy and Paste, and also includes functions that are more specialized for model building and editing, such as a Reaction Editor that can be used to construct reaction equations from an existing table of metabolites.
MOST provides menu items to highlight participating reactions and to highlight unused metabolites or delete all unused metabolites.
MOST provides error checking and helps the user to fix errors.
MOST implements undo and redo, so if an entry is mistakenly changed, reverting to the old value is simple.
MOST 2.0 implements Visualization of models if metabolites in the model are identified with KEGG ids or ChEBI ids.