MFA Suite™

MFA Suite™ consists of two applications: Extracellular Timecourse Analysis (ETA) and Isotopomer Network Compartmental Analysis (INCA). 

MFA Suite™ ETA is used to estimate specific rates (i.e., on a per-cell basis) of nutrient uptake and product excretion in cultured cells. The user provides the program with measurements of the target analyte concentrations in extracellular medium that has been exposed to cells for varying lengths of time. The user must also provide measurements of cell number or concentration over time. Based on these inputs, the program will perform regression analysis to estimate the specific growth rate of the cells and the specific uptake and excretion rates of the target analytes. The program also calculates statistical metrics of goodness-of-fit and standard errors of the estimated parameters. The ETA application is available for license free of charge as downloadable MATLAB P-code.

MFA Suite™ INCA is a MATLAB-based software package for isotopomer network modeling and metabolic flux analysis. The software can simulate both steady-state and transient isotope labeling experiments using the elementary metabolite unit (EMU) method. It can also estimate pathway fluxes based on extracellular flux measurements, pool size measurements, and/or mass isotopomer measurements supplied to the program. The software can perform a variety of statistical tests to determine goodness-of-fit, to compute parameter confidence intervals (i.e., uncertainty), and to assess model identifiability. It can also perform constraint-based analysis of metabolic networks (e.g., flux balance analysis, flux coupling analysis, etc.) and optimize the design of isotope labeling experiments using computational search algorithms. The software provides a framework for comprehensive analysis of metabolic networks using mass balances and isotopomer balances. The generation of balance equations and their computational solution is completely automated and can be performed on networks of arbitrary complexity. The graphical user interface (GUI) allows the user to input reaction information and experimental data in a simple format, while offering a variety of powerful analysis tools to design and interpret isotope labeling experiments. All INCA data objects can be loaded and manipulated from the MATLAB command line, and the driver routines can be called directly from the command line or invoked within custom MATLAB scripts. INCA also offers built-in parallelization capabilities for running certain functions within a distributed computing environment. The INCA application is available for licensing free of charge to academic users and for an annual end user license fee for non-academic customers.