Download User Manual for INCA - VU e

1. Introduction
INCA is a MATLAB-based software package for isotopomer network modeling
and metabolic flux analysis (MFA). The software can simulate both steady-state
and transient isotope labeling experiments using the elementary metabolite unit
(EMU) method [1,2]. 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., uncertainties), 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 text 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.
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